Re: [gmx-users] error while running pdb2gmx

[Mark Abraham]

Probably the default behaviour of pdb2gmx for termini is not appropriate
for your input. Use pdb2gmx -ter and choose wisely

Mark
On Nov 13, 2013 12:03 PM, "hasthi"  wrote:

> Hello GROMACS users,
>   I have phosphorylated Serine residue in my
> protein (140 residues) of interest, now when I run pdb2gmx I get this
> following error
>
> Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms
> while sorting atoms.
>
> I checked aminoacid.rtp, there is no separate entry for OXT there.When I
> did the simulation for the same protein prior phosphorylation I did not get
> this error. What is the reason for this and how should I rectify this
> error?
>
> Please help me with this regard
>
>
> Regards,
> Hasthi
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Re: [gmx-users] error while running pdb2gmx

[Justin Lemkul]

On 11/13/13 6:02 AM, hasthi wrote:

Hello GROMACS users,
   I have phosphorylated Serine residue in my
protein (140 residues) of interest, now when I run pdb2gmx I get this
following error

Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms
while sorting atoms.

I checked aminoacid.rtp, there is no separate entry for OXT there.When I
did the simulation for the same protein prior phosphorylation I did not get
this error. What is the reason for this and how should I rectify this error?

Please help me with this regard



Presumably you have modified the force field to include the phosphorylated 
residue, correct?   Have you followed every one of the steps shown at 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue?


If you need further help, we will need more information, which will include (at 
minimum):


1. Snippet of the PDB file containing the problematic residue
2. Your exact pdb2gmx command
3. The screen output of pdb2gmx (all of it, not just the error message)

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] error while running pdb2gmx

[hasthi]

Hello GROMACS users,
  I have phosphorylated Serine residue in my
protein (140 residues) of interest, now when I run pdb2gmx I get this
following error

Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms
while sorting atoms.

I checked aminoacid.rtp, there is no separate entry for OXT there.When I
did the simulation for the same protein prior phosphorylation I did not get
this error. What is the reason for this and how should I rectify this error?

Please help me with this regard


Regards,
Hasthi
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Re: [gmx-users] Error in Umbrella sampling command

[Justin Lemkul]

On 11/7/13 6:27 AM, Arunima Shilpi wrote:

Dear Sir
Presently I am working with the example file as given in the umbrella
sampling tutorial.

While running the following command

grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr

I got the following error. How to debug this error.


Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#

NOTE 1 [file npt_umbrella.mdp]:
   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
   nstcomm to nstcalcenergy


NOTE 2 [file npt_umbrella.mdp]:
   leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1


WARNING 1 [file npt_umbrella.mdp]:
   You are generating velocities so I am assuming you are equilibrating a
   system. You are using Parrinello-Rahman pressure coupling, but this can
   be unstable for equilibration. If your system crashes, try equilibrating
   first with Berendsen pressure coupling. If you are not equilibrating the
   system, you can probably ignore this warning.


ERROR 1 [file npt_umbrella.mdp]:
   Generating velocities is inconsistent with attempting to continue a
   previous run. Choose only one of gen-vel = yes and continuation = yes.



Either the run is starting for the first time (gen_vel = yes and continuation = 
no) or it is a continuation (gen_vel = no and continuation = yes).  In this 
case, set continuation = no since it is the first run.


-Justin


Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_D'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_E'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Velocities were taken from a Maxwell distribution at 300 K

There were 2 notes

There was 1 warning

---
Program grompp_mpi_d, VERSION 4.6.3
Source code file:
/opt/apps/GROMACS/GROMACS-SOURCE/gromacs-4.6.3/src/kernel/gromp

p.c, line: 1593

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I request you to kindly help me to debug the error

Regards

Arunima



--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Error in Umbrella sampling command

[Arunima Shilpi]

Dear Sir
Presently I am working with the example file as given in the umbrella
sampling tutorial.

While running the following command

grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr

I got the following error. How to debug this error.


Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#

NOTE 1 [file npt_umbrella.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy


NOTE 2 [file npt_umbrella.mdp]:
  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1


WARNING 1 [file npt_umbrella.mdp]:
  You are generating velocities so I am assuming you are equilibrating a
  system. You are using Parrinello-Rahman pressure coupling, but this can
  be unstable for equilibration. If your system crashes, try equilibrating
  first with Berendsen pressure coupling. If you are not equilibrating the
  system, you can probably ignore this warning.


ERROR 1 [file npt_umbrella.mdp]:
  Generating velocities is inconsistent with attempting to continue a
  previous run. Choose only one of gen-vel = yes and continuation = yes.

Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_D'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_E'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Velocities were taken from a Maxwell distribution at 300 K

There were 2 notes

There was 1 warning

---
Program grompp_mpi_d, VERSION 4.6.3
Source code file:
/opt/apps/GROMACS/GROMACS-SOURCE/gromacs-4.6.3/src/kernel/gromp

p.c, line: 1593

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I request you to kindly help me to debug the error

Regards

Arunima
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Re: [gmx-users] error in umbralla sampling step 6

[Justin Lemkul]

On 10/27/13 11:23 AM, sunyeping wrote:



Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
--
发件人：Justin Lemkul 
发送时间：2013年10月27日(星期日) 20:27
收件人：gromacs 
主　题：Re: 答复: [gmx-users] error in umbralla sampling step 6


Please keep the discussion on the list.

On 10/27/13 5:09 AM, sunyeping wrote:

Dear professor Lemkul,

For warning 1:
I use the npt_umbrella.mdp file you provided in step 6 in the umbralla sampling
tutorial. You told us to start by running a brief NPT equilibration in each
window using this mdp file. If Parrinello-Rahman pressure coupling should be
used, why did you put it in the mdp file?



I know the tutorial system is robust enough that it won't matter.  That is not
necessarily true for whatever other system you come up with.  Be careful when
extrapolating something that works in a tutorial with something that is
untested.  The general logic is the same (you need to equilibrate for a little
while first), but you have to think a bit about the proper settings.  There is
also no guarantee that the length of time I set in the tutorial simulation
processes (equilibration, SMD, and umbrella sampling) will necessarily be
sufficient for whatever you're doing.


For warning 2:
I check the gro files using vmd but I cann't find any molecule broken? How can I
find the brroken molecule?


The only way to find them is to look.  I have no special advice for this.


I add -pbc whole option to the  trjconv as following:

trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep -pbc whole

then It seems that the problemis solved. Is that a correct wayyou mean to solve 
the problem?



Then clearly something was broken across PBC, which means there is no real 
problem.

-Justin



In case that something was broken across PBC, why there is no real problem? Do 
you mean molecule breaking will not affect the simulation result?



We use the term "broken" very loosely.  The molecule is still intact from a 
topological standpoint.  It is only "broken" in the way that we see it.  The 
dynamics of a given molecule are the same if the molecule is "intact" in the 
"center" of the box (also a misnomer in a periodic system) or "broken" and a 
boundary.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] error in umbralla sampling step 6

[sunyeping]

Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
--
发件人：Justin Lemkul 
发送时间：2013年10月27日(星期日) 20:27
收件人：gromacs 
主　题：Re: 答复: [gmx-users] error in umbralla sampling step 6


Please keep the discussion on the list.

On 10/27/13 5:09 AM, sunyeping wrote:
> Dear professor Lemkul,
>
> For warning 1:
> I use the npt_umbrella.mdp file you provided in step 6 in the umbralla 
> sampling
> tutorial. You told us to start by running a brief NPT equilibration in each
> window using this mdp file. If Parrinello-Rahman pressure coupling should be
> used, why did you put it in the mdp file?
>

I know the tutorial system is robust enough that it won't matter.  That is not 
necessarily true for whatever other system you come up with.  Be careful when 
extrapolating something that works in a tutorial with something that is 
untested.  The general logic is the same (you need to equilibrate for a little 
while first), but you have to think a bit about the proper settings.  There is 
also no guarantee that the length of time I set in the tutorial simulation 
processes (equilibration, SMD, and umbrella sampling) will necessarily be 
sufficient for whatever you're doing.

> For warning 2:
> I check the gro files using vmd but I cann't find any molecule broken? How 
> can I
> find the brroken molecule?

The only way to find them is to look.  I have no special advice for this.

> I add -pbc whole option to the  trjconv as following:
>
> trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep -pbc whole
>
> then It seems that the problemis solved. Is that a correct wayyou mean to 
> solve the problem?
>

Then clearly something was broken across PBC, which means there is no real 
problem.

-JustinIn case that something was broken across PBC, why there is no real 
problem? Do you mean molecule breaking will not affect the simulation result?

-- 
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: 答复: [gmx-users] error in umbralla sampling step 6

[Justin Lemkul]

Please keep the discussion on the list.

On 10/27/13 5:09 AM, sunyeping wrote:

Dear professor Lemkul,

For warning 1:
I use the npt_umbrella.mdp file you provided in step 6 in the umbralla sampling
tutorial. You told us to start by running a brief NPT equilibration in each
window using this mdp file. If Parrinello-Rahman pressure coupling should be
used, why did you put it in the mdp file?



I know the tutorial system is robust enough that it won't matter.  That is not 
necessarily true for whatever other system you come up with.  Be careful when 
extrapolating something that works in a tutorial with something that is 
untested.  The general logic is the same (you need to equilibrate for a little 
while first), but you have to think a bit about the proper settings.  There is 
also no guarantee that the length of time I set in the tutorial simulation 
processes (equilibration, SMD, and umbrella sampling) will necessarily be 
sufficient for whatever you're doing.



For warning 2:
I check the gro files using vmd but I cann't find any molecule broken? How can I
find the brroken molecule?


The only way to find them is to look.  I have no special advice for this.


I add -pbc whole option to the  trjconv as following:

trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep -pbc whole

then It seems that the problemis solved. Is that a correct wayyou mean to solve 
the problem?



Then clearly something was broken across PBC, which means there is no real 
problem.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] error in umbralla sampling step 6

[Justin Lemkul]

On 10/26/13 10:45 AM, sunyeping wrote:

Dear gromacs user,
I am doing umbralla sampling on a protein-ligand system following the gromacs 
umbralla sampling turial. It seems that the first five steps go well, and I 
select 23 gro files as the starting configurations of adjacent umbrella 
sampling windows. However when I use grompp to generate tpr files for these 
individual configurations as following:
grompp -f npt_umbrella.mdp -c conf86.gro -p topol.top -n index.ndx -o 
npt86.tprI get the following notes, warning and error information:NOTE 1 [file 
npt_umbrella.mdp]:
   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
   nstcomm to nstcalcenergy
NOTE 2 [file npt_umbrella.mdp]:
   leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1



The notes are harmless.


WARNING 1 [file npt_umbrella.mdp]:
   You are generating velocities so I am assuming you are equilibrating a
   system. You are using Parrinello-Rahman pressure coupling, but this can
   be unstable for equilibration. If your system crashes, try equilibrating
   first with Berendsen pressure coupling. If you are not equilibrating the
   system, you can probably ignore this warning.


You should not use Nose-Hoover for your initial equilibration.  Heed what grompp 
says.



...Largest charge group radii for Van der Waals: 16.306, 16.297 nm
Largest charge group radii for Coulomb:   16.306, 16.297 nm

WARNING 2 [file npt_umbrella.mdp]:
   The sum of the two largest charge group radii (32.603355) is larger than
   rlist (1.40)
Fatal error:
Too many warnings (2), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
Discussion
  aout warring 2 on the mail-list points out that the error that cause
warning 2 will impact the results and lead to artifacts. I cann't
understand why the warning occurs here, because it didn't appear when I
use grompp in the my previous steps.  Could you explain why it occur in this 
step? Will it really affect umbralla sampling? Can I use the -maxwarn option to 
ignore it?


Given the size of the cited charge group radii, you probably have a molecule 
broken across PBC, which is not a real issue.  trjconv -pbc mol or -pbc whole 
would confirm.  If trjconv processing causes the error to go away, that's all it 
was.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] error in umbralla sampling step 6

[sunyeping]

Dear gromacs user,
I am doing umbralla sampling on a protein-ligand system following the gromacs 
umbralla sampling turial. It seems that the first five steps go well, and I 
select 23 gro files as the starting configurations of adjacent umbrella 
sampling windows. However when I use grompp to generate tpr files for these 
individual configurations as following: 
grompp -f npt_umbrella.mdp -c conf86.gro -p topol.top -n index.ndx -o 
npt86.tprI get the following notes, warning and error information:NOTE 1 [file 
npt_umbrella.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy
NOTE 2 [file npt_umbrella.mdp]:
  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

WARNING 1 [file npt_umbrella.mdp]:
  You are generating velocities so I am assuming you are equilibrating a
  system. You are using Parrinello-Rahman pressure coupling, but this can
  be unstable for equilibration. If your system crashes, try equilibrating
  first with Berendsen pressure coupling. If you are not equilibrating the
  system, you can probably ignore this warning.
...Largest charge group radii for Van der Waals: 16.306, 16.297 nm
Largest charge group radii for Coulomb:   16.306, 16.297 nm

WARNING 2 [file npt_umbrella.mdp]:
  The sum of the two largest charge group radii (32.603355) is larger than
  rlist (1.40)
Fatal error:
Too many warnings (2), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
Discussion
 aout warring 2 on the mail-list points out that the error that cause 
warning 2 will impact the results and lead to artifacts. I cann't 
understand why the warning occurs here, because it didn't appear when I 
use grompp in the my previous steps.  Could you explain why it occur in this 
step? Will it really affect umbralla sampling? Can I use the -maxwarn option to 
ignore it?
Best Regards,Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences

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Re: [gmx-users] Error while simulating Protein in SDS/Water

[Mark Abraham]

Look at the numbers, count the number of atoms you expect in each
moleculetype, and work out what the mismatch is.

Mark

On Wed, Sep 18, 2013 at 2:58 PM, naresh_sssihl  wrote:
> Dear GMX users,
>
> I am trying to simulate a protein in SDS/Water box.
>
> 1. No problems with pdb2gmx - .gro file and .top files were generated.
> /pdb2gmx -f protein.pdb -o protein_pro.gro -water spce/
> selected ff 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>
> 2. Created a Cubic box using editconf
>   /editconf -f protein_pro.gro -o protein_newbox.gro -c -d 1.0 -bt cubic/
>
> 3. Then solvated the system using genbox
>   genbox -cp protein_newbox.gro -cs spc216.gro -ci sds.gro -nmol 215 -o
> protein_solv.gro -p topol.top
>
> 4. After this step I looked at the topol.top file and I found that it was
> not fully updated and so I manually updated by adding no. of SDS molecules
> under [ molecules ] section at the very end. Also I added #include sds.itp
> whereever it was required.
> In fact I followed the discussion between Justin, Mark and Anna Marabotti at
> the following link:
> http://lists.gromacs.org/pipermail/gmx-users/2009-June/042704.html  and did
> everything that was suggested.
>
> 5. When I use grompp after the step 4
> grompp -f minim.mdp -c protein_solv.gro -p topol.top -o protein.tpr
>
> This is where I am getting a Fatal Error saying that the number of
> Co-ordinates in protein_solv.gro do not match with the number of
> co-ordinates in topol.top.
>
> Could you please help regarding this... Please give me your valuable
> suggestions.
>
> With Thanks and Best Regards
>
> Naresh
>
>
>
>
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/Error-while-simulating-Protein-in-SDS-Water-tp5011282.html
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[gmx-users] Error while simulating Protein in SDS/Water

[naresh_sssihl]

Dear GMX users,

I am trying to simulate a protein in SDS/Water box. 

1. No problems with pdb2gmx - .gro file and .top files were generated.
/pdb2gmx -f protein.pdb -o protein_pro.gro -water spce/
selected ff 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)

2. Created a Cubic box using editconf
  /editconf -f protein_pro.gro -o protein_newbox.gro -c -d 1.0 -bt cubic/

3. Then solvated the system using genbox
  genbox -cp protein_newbox.gro -cs spc216.gro -ci sds.gro -nmol 215 -o
protein_solv.gro -p topol.top

4. After this step I looked at the topol.top file and I found that it was
not fully updated and so I manually updated by adding no. of SDS molecules
under [ molecules ] section at the very end. Also I added #include sds.itp
whereever it was required.
In fact I followed the discussion between Justin, Mark and Anna Marabotti at
the following link:
http://lists.gromacs.org/pipermail/gmx-users/2009-June/042704.html  and did
everything that was suggested. 

5. When I use grompp after the step 4
grompp -f minim.mdp -c protein_solv.gro -p topol.top -o protein.tpr

This is where I am getting a Fatal Error saying that the number of
Co-ordinates in protein_solv.gro do not match with the number of
co-ordinates in topol.top.

Could you please help regarding this... Please give me your valuable
suggestions.

With Thanks and Best Regards

Naresh




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Re: [gmx-users] Error in Installing gromacs4.6.3 with mpi

[Qin Qiao]

On Wed, Sep 11, 2013 at 3:08 PM, Mark Abraham wrote:

> No idea if it's causing your problem, but you need all the Ds in
> -DBUILD_SHARED_LIBS=no
>
> Mark
>
> On Wed, Sep 11, 2013 at 6:15 AM, Qin Qiao  wrote:
> > Dear all,
> >
> > I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster
> > and got the following error in step 'make':
> >
> > "/usr/bin/ld:
> > /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation
> > R_X86_64_32 against `.bss' can not be used when making a shared object;
> > recompile with -fPIC
> > /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a: could not read symbols: Bad
> > value
> > "
> >
> > I was using command
> > "cmake ../  -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/.../gromacs-4.6.3/
> > -DGMX_BUILD_OWN_FFTW=ON -BUILD_SHARED_LIBS='no'
>

Thanks, Mark! I get to know -D is a must for cmake to define variables.

Best

Qin

> "

> > and I thought the mvapich is compiled with --enable-shared...
> >
> > Could you give me some advice if possible? Thanks in advance.
> >
> > Best
> >
> > Qin
> > --
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Re: [gmx-users] ERROR while compiling gromacs4.6.1

[Mark Abraham]

If the version of gcc is unsuitable, you can write the path to it in
gold leaf and it still won't help :-) Check gcc --version for the
exercise, and then find out how to install 4.7.x or 4.8.x.

Mark

On Wed, Sep 11, 2013 at 5:09 AM, Golshan Hejazi
 wrote:
>
>
> Hello,
>
> i am trying to compile gromacs-4.6.1 on a linux machine. I used already the 
> following compile script and it worked
>
> export CCDIR=/usr/bin/gcc
> export MPICCDIR=/usr/mpi/gcc/openmpi-1.4.1/bin
> export CXX=mpicxx
> export CC=mpicc
>
> cd /home/fbafti/CODE
>
> tar -xvf gromacs-4.6.1.tar.gz
> cd mv gromacs-4.6.1 gromacs-4.6.1-plumed/
> cd build-gromacs-4.6.1-plumed/
>
> /home/fbafti/CODE/cmake-2.8.11.2-Linux-i386/bin/cmake   
> /home/fbafti/CODE/gromacs-4.6.1-plumed \
> -DFFTWF_LIBRARY=/home/fbafti/CODE/fftw-3.3.3/lib/libfftw3f.so \
> -DFFTW3F_INCLUDE_DIR=/home/fbafti/CODE/fftw-3.3.3/include  \
> -DFFTW3F_LIBRARIES=/home/fbafti/CODE/fftw-3.3.3/lib/libfftw3f.a \
> -DCMAKE_INSTALL_PREFIX=/home/fbafti/CODE/build-gromacs-4.6.1-plumed \
> -DGMX_X11=OFF \
> -DCMAKE_CXX_COMPILER=/usr/mpi/gcc/openmpi-1.4.1/bin/mpicxx \
> -DCMAKE_C_COMPILER=/usr/mpi/gcc/openmpi-1.4.1/bin/mpicc \
> -DGMX_MPI=ON \
> -DGMX_PREFER_STATIC_LIBS=ON
>
>
> However I am trying it now on another machine with the same linux platform 
> and I get the following error:
>
> CMake Warning at CMakeLists.txt:727 (message):
>   No C SSE4.1 flag found.  Consider a newer compiler, or use SSE2 for
>   slightly lower performance
>
>
> -- Looking for smmintrin.h
> -- Looking for smmintrin.h - not found
> CMake Error at CMakeLists.txt:750 (message):
>   Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support.
>
>
> -- Configuring incomplete, errors occurred!
>
> I thought if the gcc path is already defined ... it shouldn't complain !
> Can you help me figure out what causes the error?
>
> Many thanks
> G.
> --
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Re: [gmx-users] Error in Installing gromacs4.6.3 with mpi

[Mark Abraham]

No idea if it's causing your problem, but you need all the Ds in
-DBUILD_SHARED_LIBS=no

Mark

On Wed, Sep 11, 2013 at 6:15 AM, Qin Qiao  wrote:
> Dear all,
>
> I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster
> and got the following error in step 'make':
>
> "/usr/bin/ld:
> /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation
> R_X86_64_32 against `.bss' can not be used when making a shared object;
> recompile with -fPIC
> /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a: could not read symbols: Bad
> value
> "
>
> I was using command
> "cmake ../  -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/.../gromacs-4.6.3/
> -DGMX_BUILD_OWN_FFTW=ON -BUILD_SHARED_LIBS='no'
> "
> and I thought the mvapich is compiled with --enable-shared...
>
> Could you give me some advice if possible? Thanks in advance.
>
> Best
>
> Qin
> --
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[gmx-users] Error in Installing gromacs4.6.3 with mpi

[Qin Qiao]

Dear all,

I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster
and got the following error in step 'make':

"/usr/bin/ld:
/usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation
R_X86_64_32 against `.bss' can not be used when making a shared object;
recompile with -fPIC
/usr/local/mvapich2-1.9a-gcc/lib/libmpich.a: could not read symbols: Bad
value
"

I was using command
"cmake ../  -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/.../gromacs-4.6.3/
-DGMX_BUILD_OWN_FFTW=ON -BUILD_SHARED_LIBS='no'
"
and I thought the mvapich is compiled with --enable-shared...

Could you give me some advice if possible? Thanks in advance.

Best

Qin
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[gmx-users] ERROR while compiling gromacs4.6.1

[Golshan Hejazi]

Hello,

i am trying to compile gromacs-4.6.1 on a linux machine. I used already the 
following compile script and it worked

export CCDIR=/usr/bin/gcc
export MPICCDIR=/usr/mpi/gcc/openmpi-1.4.1/bin
export CXX=mpicxx
export CC=mpicc

cd /home/fbafti/CODE

tar -xvf gromacs-4.6.1.tar.gz
cd mv gromacs-4.6.1 gromacs-4.6.1-plumed/
cd build-gromacs-4.6.1-plumed/

/home/fbafti/CODE/cmake-2.8.11.2-Linux-i386/bin/cmake   
/home/fbafti/CODE/gromacs-4.6.1-plumed \
-DFFTWF_LIBRARY=/home/fbafti/CODE/fftw-3.3.3/lib/libfftw3f.so \
-DFFTW3F_INCLUDE_DIR=/home/fbafti/CODE/fftw-3.3.3/include  \
-DFFTW3F_LIBRARIES=/home/fbafti/CODE/fftw-3.3.3/lib/libfftw3f.a \
-DCMAKE_INSTALL_PREFIX=/home/fbafti/CODE/build-gromacs-4.6.1-plumed \
-DGMX_X11=OFF \
-DCMAKE_CXX_COMPILER=/usr/mpi/gcc/openmpi-1.4.1/bin/mpicxx \
-DCMAKE_C_COMPILER=/usr/mpi/gcc/openmpi-1.4.1/bin/mpicc \
-DGMX_MPI=ON \
-DGMX_PREFER_STATIC_LIBS=ON


However I am trying it now on another machine with the same linux platform and 
I get the following error:

CMake Warning at CMakeLists.txt:727 (message):
  No C SSE4.1 flag found.  Consider a newer compiler, or use SSE2 for
  slightly lower performance


-- Looking for smmintrin.h
-- Looking for smmintrin.h - not found
CMake Error at CMakeLists.txt:750 (message):
  Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support.


-- Configuring incomplete, errors occurred!

I thought if the gcc path is already defined ... it shouldn't complain !
Can you help me figure out what causes the error?

Many thanks
G.
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[gmx-users] Error bar for free energy

[afsaneh maleki]

Hi Dear Gromacs users,

I would like to calculate the standard deviation (as the error bar) for
dV/dlambda.xvg file. I used g_analyze command as the following:



g_analyze   -ffree0.9.xvg  -av  average_0.9

I got:

set   average*standard  deviation**std. dev.  /
sqrt(n-1)*…

SS1 6.053822e+01   3.062230e+01  1.936724e-02
  …

Is the amount of in third (standard deviation) or fourth column (std. dev.  /
sqrt(n-1) ) better than to use as the error bar?

I want to draw dG/d lambda via lambda and show error bar for free energy
differences.



Thanks in advance

Afsaneh
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Re: [gmx-users] ERROR : GROMACS finsihed with error 74

[Tsjerk Wassenaar]

Hi Sri,

I guess that this simulation was run through the WeNMR GMX portal? It's not
really a Gromacs question. Problems with that portal should be directed to
the adminstrator, who will send it to me anyway, so I'll respond here :)

The error means 1. that I should put time in writing more clear error
messages and 2. that mdrun finished with a non-zero exit value in step 7:
NpT equilibration. The actual error can be found in the log file for that
step in the archive 07-NPT-*.log If you can send me that log file
(off-list), then I can have a closer look.

Best,

Tsjerk




On Thu, Aug 29, 2013 at 8:15 AM, sri2201 wrote:

> Dear Gromacs ,
>
> I running the md simulation for protein complex (44 kd ) with
> amber99sb-ildn
> force filed . iam getting error as follows , looks like it is syntax error
> .
>
> Input file: gmx-495644.pdb Base name: gmx-495644 Source directory:
> /scratch/home/enmr028/home_cream_840250368/CREAM840250368 GROMACS mdrun
> will
> run for a maximum of hours. (voms proxy lifetime 0 sec.) Starting MD
> protocol for
> /scratch/home/enmr028/home_cream_840250368/CREAM840250368/gmx-495644.pdb
> Using amber force field amber99sb-ildn with tip3p water model Using PME for
> treatment of long range coulomb interactions Not using virtual sites
> Simulations will be performed in a rhombic dodecahedron unit cell 750
> #---= THIS IS WHERE WE START =-- #---STEP 1A: GENERATE STRUCTURE AND
> TOPOLOGY FOR INPUT PDB FILE Wed Aug 28 17:54:19 BST 2013:
> /mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/pdb2gmx -v -f
> /scratch/home/enmr028/home_cream_840250368/CREAM840250368/gmx-495644.pdb -o
> gmx-495644.gro -p gmx-495644.top -ignh -ff amber99sb-ildn -water tip3p -i
> gmx-495644-posre.itp -posrefc 999 Removing duplicate moleculetype
> definition
> in gmx-495644_Protein_chain_D.itp #---STEP 1B: ADD LIGANDS SPECIFIED ON
> COMMAND LINE #---STEP 2: SET PERIODIC BOUNDARY CONDITIONS Wed Aug 28
> 17:54:21 BST 2013:
> /mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/editconf -f
> gmx-495644.gro -o gmx-495644-pbc.gro -bt dodecahedron -d 1.125 -c #---STEP
> 3: RUN EM IN VACUUM Wed Aug 28 17:54:21 BST 2013:
> /mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -f
> em-vac.mdp -po em-vac-out.mdp -c gmx-495644-pbc.gro -p gmx-495644.top -o
> gmx-495644-EMv.tpr -maxwarn 1 Wed Aug 28 17:54:21 BST 2013:
> /mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/mdrun -nice 0
> -deffnm gmx-495644-EMv -c gmx-495644-EMv.gro -cpi gmx-495644-EMv.cpt -nt 1
> -maxh 12000 Wed Aug 28 17:54:29 BST 2013: FINISHED MDRUN EMVACUUM #---STEP
> 4: SOLVATION AND ADDING IONS Wed Aug 28 17:54:29 BST 2013:
> /mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/genbox -cp
> gmx-495644-EMv.gro -cs -o gmx-495644-sol-b4ions.gro Solvent added: 25839
> molecules Wed Aug 28 17:54:30 BST 2013:
> /mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -v -f
> empty.mdp -c gmx-495644-sol-b4ions.gro -p gmx-495644-sol-b4ions.top -o
> gmx-495644-sol-b4ions.tpr -po defaults.mdp -maxwarn 1 Net charge of system:
> 6 Replacing 142 solvent molecules with 68 NA (1) and 74 CL (-1) ions. Wed
> Aug 28 17:54:33 BST 2013:
> /mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/genion -s
> gmx-495644-sol-b4ions.tpr -o gmx-495644-sol.gro -g genion.log -n sol.ndx
> -pq
> 1 -nn 74 -np 68 -pname NA -nname CL -nq -1 -rmin 0.5 -random #---STEP 5:
> ENERGY MINIMIZATION IN SOLVENT (NVT) Wed Aug 28 17:54:38 BST 2013:
> /mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -f
> em-sol.mdp -po em-sol-out.mdp -c gmx-495644-sol.gro -p gmx-495644-sol.top
> -o
> gmx-495644-EMs.tpr -maxwarn 1 Wed Aug 28 17:54:39 BST 2013:
> /mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/mdrun -nice 0
> -deffnm gmx-495644-EMs -c gmx-495644-EMs.gro -cpi gmx-495644-EMs.cpt -nt 1
> -maxh 12000 Wed Aug 28 17:56:49 BST 2013: FINISHED MDRUN EMSOLVENT #---STEP
> 6: POSITION RESTRAINT MD, NVT -- CYCLE THROUGH PRFC AND TEMP/TAU_T Solute
> Solvent Equilibration (NVT/PR): Temperatures: 300.0 Coupling times: 0.1
> Position restraint Fcs: 200 200 200 NVT Equilibration at 300.0 Kelvin
> (tau_t=0.1) with Position restraint force 200 Wed Aug 28 17:56:54 BST 2013:
> /mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -f
> pr-200-nvt-300.0-0.1.mdp -po pr-200-nvt-300.0-0.1-out.mdp -c
> gmx-495644-EMs.gro -p gmx-495644-sol.top -n gmx-495644-sol.ndx -o
> gmx-495644-PR-200-NVT-300.0-0.1.tpr -maxwarn 1 -r gmx-495644-EMs.gro Wed
> Aug
> 28 17:56:55 BST 2013:
> /mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/mdrun -nice 0
> -deffnm gmx-495644-PR-200-NVT-300.0-0.1 -c
> gmx-495644-PR-200-NVT-300.0-0.1.gro -cpi
> gmx-495644-PR-200-NVT-300.0-0.1.cpt
> -nt 1 -maxh 12000 Thu Aug 29 03:04:27 BST 2013: FINISHED MDRUN NVT-PR 200
> NVT Equilibration at 300.0 Kelvin (tau_t=0.1) with Position restraint force
> 200 Output found (gmx-495644-PR-200-NVT-300.0-0.1.gro). Skipping step
> NVT-PR
> #---STEP 7: UNRESTRAINED MD 20 ps NPT -- CYCLE THROUGH PRESSURE

[gmx-users] ERROR : GROMACS finsihed with error 74

[sri2201]

Dear Gromacs , 

I running the md simulation for protein complex (44 kd ) with amber99sb-ildn
force filed . iam getting error as follows , looks like it is syntax error .

Input file: gmx-495644.pdb Base name: gmx-495644 Source directory:
/scratch/home/enmr028/home_cream_840250368/CREAM840250368 GROMACS mdrun will
run for a maximum of hours. (voms proxy lifetime 0 sec.) Starting MD
protocol for
/scratch/home/enmr028/home_cream_840250368/CREAM840250368/gmx-495644.pdb
Using amber force field amber99sb-ildn with tip3p water model Using PME for
treatment of long range coulomb interactions Not using virtual sites
Simulations will be performed in a rhombic dodecahedron unit cell 750
#---= THIS IS WHERE WE START =-- #---STEP 1A: GENERATE STRUCTURE AND
TOPOLOGY FOR INPUT PDB FILE Wed Aug 28 17:54:19 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/pdb2gmx -v -f
/scratch/home/enmr028/home_cream_840250368/CREAM840250368/gmx-495644.pdb -o
gmx-495644.gro -p gmx-495644.top -ignh -ff amber99sb-ildn -water tip3p -i
gmx-495644-posre.itp -posrefc 999 Removing duplicate moleculetype definition
in gmx-495644_Protein_chain_D.itp #---STEP 1B: ADD LIGANDS SPECIFIED ON
COMMAND LINE #---STEP 2: SET PERIODIC BOUNDARY CONDITIONS Wed Aug 28
17:54:21 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/editconf -f
gmx-495644.gro -o gmx-495644-pbc.gro -bt dodecahedron -d 1.125 -c #---STEP
3: RUN EM IN VACUUM Wed Aug 28 17:54:21 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -f
em-vac.mdp -po em-vac-out.mdp -c gmx-495644-pbc.gro -p gmx-495644.top -o
gmx-495644-EMv.tpr -maxwarn 1 Wed Aug 28 17:54:21 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/mdrun -nice 0
-deffnm gmx-495644-EMv -c gmx-495644-EMv.gro -cpi gmx-495644-EMv.cpt -nt 1
-maxh 12000 Wed Aug 28 17:54:29 BST 2013: FINISHED MDRUN EMVACUUM #---STEP
4: SOLVATION AND ADDING IONS Wed Aug 28 17:54:29 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/genbox -cp
gmx-495644-EMv.gro -cs -o gmx-495644-sol-b4ions.gro Solvent added: 25839
molecules Wed Aug 28 17:54:30 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -v -f
empty.mdp -c gmx-495644-sol-b4ions.gro -p gmx-495644-sol-b4ions.top -o
gmx-495644-sol-b4ions.tpr -po defaults.mdp -maxwarn 1 Net charge of system:
6 Replacing 142 solvent molecules with 68 NA (1) and 74 CL (-1) ions. Wed
Aug 28 17:54:33 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/genion -s
gmx-495644-sol-b4ions.tpr -o gmx-495644-sol.gro -g genion.log -n sol.ndx -pq
1 -nn 74 -np 68 -pname NA -nname CL -nq -1 -rmin 0.5 -random #---STEP 5:
ENERGY MINIMIZATION IN SOLVENT (NVT) Wed Aug 28 17:54:38 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -f
em-sol.mdp -po em-sol-out.mdp -c gmx-495644-sol.gro -p gmx-495644-sol.top -o
gmx-495644-EMs.tpr -maxwarn 1 Wed Aug 28 17:54:39 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/mdrun -nice 0
-deffnm gmx-495644-EMs -c gmx-495644-EMs.gro -cpi gmx-495644-EMs.cpt -nt 1
-maxh 12000 Wed Aug 28 17:56:49 BST 2013: FINISHED MDRUN EMSOLVENT #---STEP
6: POSITION RESTRAINT MD, NVT -- CYCLE THROUGH PRFC AND TEMP/TAU_T Solute
Solvent Equilibration (NVT/PR): Temperatures: 300.0 Coupling times: 0.1
Position restraint Fcs: 200 200 200 NVT Equilibration at 300.0 Kelvin
(tau_t=0.1) with Position restraint force 200 Wed Aug 28 17:56:54 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -f
pr-200-nvt-300.0-0.1.mdp -po pr-200-nvt-300.0-0.1-out.mdp -c
gmx-495644-EMs.gro -p gmx-495644-sol.top -n gmx-495644-sol.ndx -o
gmx-495644-PR-200-NVT-300.0-0.1.tpr -maxwarn 1 -r gmx-495644-EMs.gro Wed Aug
28 17:56:55 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/mdrun -nice 0
-deffnm gmx-495644-PR-200-NVT-300.0-0.1 -c
gmx-495644-PR-200-NVT-300.0-0.1.gro -cpi gmx-495644-PR-200-NVT-300.0-0.1.cpt
-nt 1 -maxh 12000 Thu Aug 29 03:04:27 BST 2013: FINISHED MDRUN NVT-PR 200
NVT Equilibration at 300.0 Kelvin (tau_t=0.1) with Position restraint force
200 Output found (gmx-495644-PR-200-NVT-300.0-0.1.gro). Skipping step NVT-PR
#---STEP 7: UNRESTRAINED MD 20 ps NPT -- CYCLE THROUGH PRESSURE/TAU_P
Equilibration (NpT): Pressures: 1.01325 Coupling times: 0.5 NpT
Equilibration at 1.01325 bar (tau_p=0.5) Thu Aug 29 03:05:00 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/grompp -f
npt-1.01325-0.5.mdp -po npt-1.01325-0.5-out.mdp -c
gmx-495644-PR-200-NVT-300.0-0.1.gro -p gmx-495644-sol.top -n
gmx-495644-sol.ndx -o gmx-495644-NPT-1.01325-0.5.tpr -maxwarn 1 -r
gmx-495644-EMs.gro Thu Aug 29 03:05:01 BST 2013:
/mt/experiment-software//enmr/BCBR/gromacs/4.5.3-rtc/bin/mdrun -nice 0
-deffnm gmx-495644-NPT-1.01325-0.5 -c gmx-495644-NPT-1.01325-0.5.gro -cpi
gmx-495644-NPT-1.01325-0.5.cpt -nt 1 -maxh 12000 Thu Aug 29 06:04:39 2013 

MDS ERROR : GROMACS finsihed with error 74,

Please suggest me to aviod this bug or my input errors .

Thanking you in

Re: [gmx-users] error with g_dist

[Justin Lemkul]

On 8/26/13 4:05 PM, chinnu657 wrote:

Hello all, I am trying to find the distance between 2 centres of mass using
g_dist.

I use the command:  g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n
index.ndx

but i get the error:
Fatal error:
Molecule in topology has atom numbers below and above natoms (1707).
You are probably trying to use a trajectory which does not match the first
1707 atoms of the run input file.
You can make a matching run input file with tpbconv.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I tried using tpbconv like suggested. But that did not help. I really need
help on this as my submission deadline is getting closer and this is the
last simulation I need..



The most likely explanation is that you did not save groups correctly using 
xtc-grps in the .mdp file.  In the absence of a description of what you're 
trying to measure, the contents of the index groups, and the gmxcheck output on 
the .xtc file, there's little anyone can do to help.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] error with g_dist

[chinnu657]

Hello all, I am trying to find the distance between 2 centres of mass using
g_dist.

I use the command:  g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n
index.ndx

but i get the error:
Fatal error:
Molecule in topology has atom numbers below and above natoms (1707).
You are probably trying to use a trajectory which does not match the first
1707 atoms of the run input file.
You can make a matching run input file with tpbconv.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
 
I tried using tpbconv like suggested. But that did not help. I really need
help on this as my submission deadline is getting closer and this is the
last simulation I need..

Thank you so much in advance

Chinnu




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Re: [gmx-users] Error while using genion

[Justin Lemkul]

Please do not reply to the entire digest.  It gets hopelessly confusing.

On 6/24/13 10:51 AM, Raji Viswanathan wrote:

I am using Red Hat Enterprise Linux 5.5
Raji


Something about your shell environment is probably hosed.  Do other commands 
that prompt for interactive input work, or just genion?  Does the following work?


echo 13 | genion -s ion.tpr -o fws-b4em.gro -neutral -conc 0.15 -p fws.top -g 
ion.log


-Justin




Message: 2
Date: Thu, 20 Jun 2013 17:57:28 +
From: Raji Viswanathan 
Subject: [gmx-users] Error while using genion
To: "gmx-users@gromacs.org" 
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin
peptide.  I was going through the steps in the tutorial but got stuck with the
genion command.  When I am prompted to select a group, I get the error that it
is not found.  I tried many different ways of specifying this but still get
the same error.  I would appreciate your help.  I am enclosing the output
below:

   GROtesk MACabre and Sinister

 :-)  VERSION 4.5.5  (-:

 Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
   Aldert van Buuren, P?r Bjelkmar, Rudi van Drunen, Anton Feenstra,
 Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
 Michael Shirts, Alfons Sijbers, Peter Tieleman,

Berk Hess, David van der Spoel, and Erik Lindahl.

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2010, The GROMACS development team at
 Uppsala University & The Royal Institute of Technology, Sweden.
 check out http://www.gromacs.org for more information.

  This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 2
  of the License, or (at your option) any later version.

 :-)  genion  (-:

Option Filename  Type Description

   -sion.tpr  InputRun input file: tpr tpb tpa
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
   -n  index.ndx  Input, Opt.  Index file
   -o   fws-b4em.gro  Output   Structure file: gro g96 pdb etc.
   -gion.log  Output   Log file
-potpot.pdb  Output, Opt. Protein data bank file
   -pfws.top  In/Out, Opt! Topology file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint19  Set the nicelevel
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-np  int0   Number of positive ions
-pname   string NA  Name of the positive ion
-pq  int1   Charge of the positive ion
-nn  int0   Number of negative ions
-nname   string CL  Name of the negative ion
-nq  int-1  Charge of the negative ion
-rminreal   0.6 Minimum distance between ions
-[no]random  bool   yes Use random placement of ions instead of based on
 potential. The rmin option should still work
-seedint1993Seed for random number generator
-scale   real   0.001   Scaling factor for the potential for -pot
-concreal   0.15Specify salt concentration (mol/liter). This will
 add sufficient ions to reach up to the specified
 concentration as computed from the volume of the
 cell in the input .tpr file. Overrides the -np
 and -nn options.
-[no]neutral bool   yes This option will add enough ions to neutralize
 the system. In combination with the concentration
 option a neutral system at a given salt
 concentration will be generated.

Reading file ion.tpr, VERSION 4.5.5 (single precision)
Using a coulomb cut-off of 1 nm
Will try to add 12 NA ions and 14 CL ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 12666 elements
Group 1 (Protein) has   495 elements
Group 2 (  Protein-H) has   257 elements
Group 3 (C-alpha) has35 elements
Group 4 (   Backbone) has   105 elements
Group 5 (  MainChain) has   141 elements
Group 6 (   MainChain+Cb) has   171 elements
Group 7 (MainChain+H) has   176 elements
Group 8 (  SideChain) has   319 elements
Group 9 (SideChain-H) has   116 elements

Re: [gmx-users] Error while using genion

[Justin Lemkul]

On 6/20/13 1:57 PM, Raji Viswanathan wrote:

I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin 
peptide.  I was going through the steps in the tutorial but got stuck with the 
genion command.  When I am prompted to select a group, I get the error that it 
is not found.  I tried many different ways of specifying this but still get the 
same error.  I would appreciate your help.  I am enclosing the output below:

   GROtesk MACabre and Sinister

 :-)  VERSION 4.5.5  (-:

 Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
   Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
 Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
 Michael Shirts, Alfons Sijbers, Peter Tieleman,

Berk Hess, David van der Spoel, and Erik Lindahl.

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2010, The GROMACS development team at
 Uppsala University & The Royal Institute of Technology, Sweden.
 check out http://www.gromacs.org for more information.

  This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 2
  of the License, or (at your option) any later version.

 :-)  genion  (-:

Option Filename  Type Description

   -sion.tpr  InputRun input file: tpr tpb tpa
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
   -n  index.ndx  Input, Opt.  Index file
   -o   fws-b4em.gro  Output   Structure file: gro g96 pdb etc.
   -gion.log  Output   Log file
-potpot.pdb  Output, Opt. Protein data bank file
   -pfws.top  In/Out, Opt! Topology file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint19  Set the nicelevel
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-np  int0   Number of positive ions
-pname   string NA  Name of the positive ion
-pq  int1   Charge of the positive ion
-nn  int0   Number of negative ions
-nname   string CL  Name of the negative ion
-nq  int-1  Charge of the negative ion
-rminreal   0.6 Minimum distance between ions
-[no]random  bool   yes Use random placement of ions instead of based on
 potential. The rmin option should still work
-seedint1993Seed for random number generator
-scale   real   0.001   Scaling factor for the potential for -pot
-concreal   0.15Specify salt concentration (mol/liter). This will
 add sufficient ions to reach up to the specified
 concentration as computed from the volume of the
 cell in the input .tpr file. Overrides the -np
 and -nn options.
-[no]neutral bool   yes This option will add enough ions to neutralize
 the system. In combination with the concentration
 option a neutral system at a given salt
 concentration will be generated.

Reading file ion.tpr, VERSION 4.5.5 (single precision)
Using a coulomb cut-off of 1 nm
Will try to add 12 NA ions and 14 CL ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 12666 elements
Group 1 (Protein) has   495 elements
Group 2 (  Protein-H) has   257 elements
Group 3 (C-alpha) has35 elements
Group 4 (   Backbone) has   105 elements
Group 5 (  MainChain) has   141 elements
Group 6 (   MainChain+Cb) has   171 elements
Group 7 (MainChain+H) has   176 elements
Group 8 (  SideChain) has   319 elements
Group 9 (SideChain-H) has   116 elements
Group10 (Prot-Masses) has   495 elements
Group11 (non-Protein) has 12171 elements
Group12 (  Water) has 12171 elements
Group13 (SOL) has 12171 elements
Group14 (  non-Water) has   495 elements
Select a group:   13
bash: 13: command not found

[9]+  Stopped genion -s ion.tpr -o fws-b4em.gro -neutral -conc 
0.15 -p fws.top -g ion.log



Your shell is interpreting your selection as a command rather than an input file 
stream.  What OS are you running?


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
De

[gmx-users] Error while using genion

[Raji Viswanathan]

I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin 
peptide.  I was going through the steps in the tutorial but got stuck with the 
genion command.  When I am prompted to select a group, I get the error that it 
is not found.  I tried many different ways of specifying this but still get the 
same error.  I would appreciate your help.  I am enclosing the output below:

  GROtesk MACabre and Sinister

:-)  VERSION 4.5.5  (-:

Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
  Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

:-)  genion  (-:

Option Filename  Type Description

  -sion.tpr  InputRun input file: tpr tpb tpa
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
  -n  index.ndx  Input, Opt.  Index file
  -o   fws-b4em.gro  Output   Structure file: gro g96 pdb etc.
  -gion.log  Output   Log file
-potpot.pdb  Output, Opt. Protein data bank file
  -pfws.top  In/Out, Opt! Topology file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint19  Set the nicelevel
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-np  int0   Number of positive ions
-pname   string NA  Name of the positive ion
-pq  int1   Charge of the positive ion
-nn  int0   Number of negative ions
-nname   string CL  Name of the negative ion
-nq  int-1  Charge of the negative ion
-rminreal   0.6 Minimum distance between ions
-[no]random  bool   yes Use random placement of ions instead of based on
potential. The rmin option should still work
-seedint1993Seed for random number generator
-scale   real   0.001   Scaling factor for the potential for -pot
-concreal   0.15Specify salt concentration (mol/liter). This will
add sufficient ions to reach up to the specified
concentration as computed from the volume of the
cell in the input .tpr file. Overrides the -np
and -nn options.
-[no]neutral bool   yes This option will add enough ions to neutralize
the system. In combination with the concentration
option a neutral system at a given salt
concentration will be generated.

Reading file ion.tpr, VERSION 4.5.5 (single precision)
Using a coulomb cut-off of 1 nm
Will try to add 12 NA ions and 14 CL ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 12666 elements
Group 1 (Protein) has   495 elements
Group 2 (  Protein-H) has   257 elements
Group 3 (C-alpha) has35 elements
Group 4 (   Backbone) has   105 elements
Group 5 (  MainChain) has   141 elements
Group 6 (   MainChain+Cb) has   171 elements
Group 7 (MainChain+H) has   176 elements
Group 8 (  SideChain) has   319 elements
Group 9 (SideChain-H) has   116 elements
Group10 (Prot-Masses) has   495 elements
Group11 (non-Protein) has 12171 elements
Group12 (  Water) has 12171 elements
Group13 (SOL) has 12171 elements
Group14 (  non-Water) has   495 elements
Select a group:   13
bash: 13: command not found

[9]+  Stopped genion -s ion.tpr -o fws-b4em.gro -neutral -conc 
0.15 -p fws.top -g ion.log
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Re: [gmx-users] Error in grompp minimization

[Souilem Safa]

Dear Justin,
thank you for your reply.
Yes, you are right , I have corrected it already and now it works well.
Cheers,
Safa


On 11 June 2013 09:53, Justin Lemkul  wrote:

>
>
> On 6/10/13 8:51 PM, Souilem Safa wrote:
>
>> Dear gromacs users,
>>
>> I'm trying to simulate a single molecule in cyclohexane.
>> I made a box of my molecule using editconf command and next I solvate with
>> cyclohexane using genbox command :
>> genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro
>>
>> I did next a position restraint in the topolgy file and I tried to
>> minimize, i got this fatal error:
>> Fatal error:
>> No such moleculetype CHX
>>
>> What could be the origin of this error.
>>
>
> You probably forgot to #include the topology that introduces CHX as a
> valid [moleculetype].
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
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Re: [gmx-users] Error in grompp minimization

[Justin Lemkul]

On 6/10/13 8:51 PM, Souilem Safa wrote:

Dear gromacs users,

I'm trying to simulate a single molecule in cyclohexane.
I made a box of my molecule using editconf command and next I solvate with
cyclohexane using genbox command :
genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro

I did next a position restraint in the topolgy file and I tried to
minimize, i got this fatal error:
Fatal error:
No such moleculetype CHX

What could be the origin of this error.


You probably forgot to #include the topology that introduces CHX as a valid 
[moleculetype].


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Error in grompp minimization

[Souilem Safa]

Dear gromacs users,

I'm trying to simulate a single molecule in cyclohexane.
I made a box of my molecule using editconf command and next I solvate with
cyclohexane using genbox command :
genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro

I did next a position restraint in the topolgy file and I tried to
minimize, i got this fatal error:
Fatal error:
No such moleculetype CHX

What could be the origin of this error.
Thanks :)
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Re: [gmx-users] error in running g_dist

[Mark Abraham]

Use gmxcheck to find out what's in the files. Think about how you used
xtcgroups. Consider using tpbconv to make a matching subset from your .tpr.

Mark


On Wed, May 22, 2013 at 11:53 AM, Arunima Shilpi wrote:

> Respected sir
>
> I want to calculate the distance between protein and ligand after I  have
> run the production step. I used the following command..
>
> g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx
>
> Groups I selected was
> Group 1 (protein)
> Group 13 (ligand)
>
> It says the following error
>
> Molecule in topology has atom numbers below and above natoms (11793).
> You are probably trying to use a trajectory which does not match the first
> 11793 atoms of the run input file.
>
> how to debug the error...
>
> --
>
> Thanking You with Regards.
>
> Arunima Shilpi
>
> Ph. D Research Scholar(Cancer & Epigenetics)
> Department of Life Science
> National Institute of Technology
> Rourkela
> Odisha
> --
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[gmx-users] error in running g_dist

[Arunima Shilpi]

Respected sir

I want to calculate the distance between protein and ligand after I  have
run the production step. I used the following command..

g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx

Groups I selected was
Group 1 (protein)
Group 13 (ligand)

It says the following error

Molecule in topology has atom numbers below and above natoms (11793).
You are probably trying to use a trajectory which does not match the first
11793 atoms of the run input file.

how to debug the error...

-- 

Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha
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Re: [gmx-users] error after grompp

[Abhishek Acharya]

Hello,

> Hi all,
>
> I need to do simulation which same as protein-ligand tutorial by Justin.
> The different is i'm using my protein and the ligand was zinc.
> I already follow everything in that tutorial and suddenly when i want
> to heat my protein by using the nvt.mdp there was an error state like
> below :
>
> Fatal error:
> Atom 410 in multiple T-Coupling groups (1 and 2)

This means that atom no. 410 is defined in both the coupling groups which
you have defined in the temperature coupling segment of your mdp file.
Looking at your file it seems to me that the Zn atom is the culprit. In
case the parameters for the Zn are being directly taken from the force
field ions.itp file, then i think gromacs treats this as an ion and would
automatically assigns to Water_and _ions group.
>
> Actually I do not understand what the error said even when i'm Google
> it to forum there was no one
> facing like mine..Here i put together my topology and the nvt.mdp.
> Hope you can give me some idea that i cant see.
>
> Another question,why is in the nvt.mdp at the temperature coupling
> there were twice of 300 of tcoupl and also the tau_t : 01. 01. Can u
> explain it why?
this has been explained quite clearly in the gromacs manual. In essence,
defining different coupling groups allows control over the temperature of
the Groups especially protein and water which otherwise have been seen to
differ in the temperature attained by a large degree.
>

Cheers

Abhishek Acharya
Structural and Computational Biology Lab
IIt Kanpur
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[gmx-users] error after grompp

[Nur Syafiqah Abdul Ghani]

Hi all,

I need to do simulation which same as protein-ligand tutorial by Justin.
The different is i'm using my protein and the ligand was zinc.
I already follow everything in that tutorial and suddenly when i want
to heat my protein by using the nvt.mdp there was an error state like
below :

Fatal error:
Atom 410 in multiple T-Coupling groups (1 and 2)

Actually I do not understand what the error said even when i'm Google
it to forum there was no one
facing like mine..Here i put together my topology and the nvt.mdp.
Hope you can give me some idea that i cant see.

Another question,why is in the nvt.mdp at the temperature coupling
there were twice of 300 of tcoupl and also the tau_t : 01. 01. Can u
explain it why?

topology :

; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"

; Include chain topologies
#include "metal_Protein_chain_A.itp"

; Include position restraint for protein
#ifdef POSRES
#include "posre_Protein_chain_A.itp"
#endif

; Include ion chain topologies
#include "metal_Ion_chain_A2.itp"

; Include position restraint for metal
#ifdef POSRES_ION
#include "posre_Ion_chain_A2.itp"
#endif

; Include water topology
#include "gromos53a6.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "gromos53a6.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
Ion_chain_A21
SOL 8780
NA   1


nvt.mdp :

title   = Protein-ligand complex NVT equilibration
cpp = /usr/bin/cpp
include = -I/usr/share/gromacs/top
define  = -DPOSRES  ; position restrain the protein and ligand
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
energygrps  = Protein ZN
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 10 fs
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_ZN Water_and_ions; two coupling groups - more accurate
tau_t   = 0.1 0.1 ; time constant, in ps
ref_t   = 300 300 ; reference temperature, one
for each group, in K
; Pressure coupling
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed






Thanks for your help in advance,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my
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Re: [gmx-users] error in running distances.pl

[Justin Lemkul]

On 5/8/13 8:16 AM, Arunima Shilpi wrote:

Hello Sir

While running command for perl distances.pl.. system gets hanged...while
processing  particular group file...

I will be thankful to you if you can guide me in debugging the error



If you created groups.txt in accordance with what the tutorial says and your 
index file contains the necessary groups (again, explained in the tutorial), 
there should be no problem.


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] error in running distances.pl

[Arunima Shilpi]

Hello Sir

While running command for perl distances.pl.. system gets hanged...while
processing  particular group file...

I will be thankful to you if you can guide me in debugging the error
-- 

Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha
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[gmx-users] error in running perl distance.pl

[Arunima Shilpi]

Hello sir

While runnimg command for "perl distance.pl" in umbrella sampling it gives
the following  error

"Use of uninitialized value $distance in concatenation (.) or string at
distance.pl line 30.
readline() on closed filehandle IN at distance.pl line 16."

Can you guide me in rectifying the error


-- 

Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha
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Re: [gmx-users] Error after trjconf processing

[James Starlight]

The problem was solved by adding -pbc mol -ur compact flags to the trjconv.
So the problems were indeed in pbc conditions


James

2013/5/3 Mark Abraham 

> On Fri, May 3, 2013 at 3:17 PM, James Starlight  >wrote:
>
> > Mark,
> >
> >
> > but if I run npt equilibration onto minimized structure (without
> > velocities)  without definition of the new velocities in the npt.mdp file
> >
> > gen_vel = No
> >
> > I noticed that in npt.gro file velocities present. Have it been assigned
> > inspite on
> > gen_vel = No in mdp?
>
>
> I can't answer - I don't know from your description and filename what was
> in
> 1) the coordinte file you input to the EM grompp,
> 2) the .gro file you got out of EM mdrun (which presumably went into the
> NPT grompp),
> 3) the .tpr file you got out of NPT grompp, and
> 4) the .gro file you got out of NPT mdrun (which will always have
> velocities regardless of the foregoing)
>
> Please respect your reader's time and describe your observations carefully
> :-)
>
> I think there should never be velocities in 2. Velocities in 3 should
> follow what the .mdp file said (but if 2 wrote velocities, then it is
> conceivable that those are still the velocities in 3 iff gen_vel=no, but
> you would have to inspect the values with gmxdump to see what was
> happening).
>
> Mark
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Re: [gmx-users] Error after trjconf processing

[Mark Abraham]

On Fri, May 3, 2013 at 3:17 PM, James Starlight wrote:

> Mark,
>
>
> but if I run npt equilibration onto minimized structure (without
> velocities)  without definition of the new velocities in the npt.mdp file
>
> gen_vel = No
>
> I noticed that in npt.gro file velocities present. Have it been assigned
> inspite on
> gen_vel = No in mdp?


I can't answer - I don't know from your description and filename what was in
1) the coordinte file you input to the EM grompp,
2) the .gro file you got out of EM mdrun (which presumably went into the
NPT grompp),
3) the .tpr file you got out of NPT grompp, and
4) the .gro file you got out of NPT mdrun (which will always have
velocities regardless of the foregoing)

Please respect your reader's time and describe your observations carefully
:-)

I think there should never be velocities in 2. Velocities in 3 should
follow what the .mdp file said (but if 2 wrote velocities, then it is
conceivable that those are still the velocities in 3 iff gen_vel=no, but
you would have to inspect the values with gmxdump to see what was
happening).

Mark
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Re: [gmx-users] Error after trjconf processing

[James Starlight]

Mark,


but if I run npt equilibration onto minimized structure (without
velocities)  without definition of the new velocities in the npt.mdp file

gen_vel = No

I noticed that in npt.gro file velocities present. Have it been assigned
inspite on
gen_vel = No in mdp?


James

2013/5/3 Mark Abraham 

> EM has no velocities, by definition. Does the EM mdrun write a .gro file
> with velocities? If so, that's a bug.
>
>
> On Fri, May 3, 2013 at 2:51 PM, James Starlight  >wrote:
>
> > I've noticed that the minimized conformers no longer has the velocities
> in
> > gro file (and npt rus without warnings in that case) in comparison to the
> > not-minimized structures ( where velocities were present and gromp sent
> > warnings). All pbc options lare the same for all conformers and box
> vectors
> > correctly defined in boundary regions.
> >
> > But after npt equilibration of the minimized structures ( velocities
> again
> > present in the gro file) my system have crushed at the beginning of the
> > production run. So the problem in the velocities set which wre taken from
> > the initial pulling run (the same for each conformers).
>
>
> Huh? After EM there should be no velocities, and you should instruct the
> grompp before your equilibration to generate new ones regardless.
>
>
> > Should I re-assign
> > velocities for each conformer (addition nvt run) to fix it ?
> >
>
> There seems to be no purpose to trying to start a new simulation from some
> configuration, doing EM on it, and then trying to equilibrate starting with
> the pre-EM velocities (even if it is possible, which I do not think it
> should be). The energy distributions are guaranteed to be mutually
> inconsistent.
>
> Mark
>
>
> >
> > James
> >
> > 2013/5/3 Mark Abraham 
> >
> > > On Fri, May 3, 2013 at 11:15 AM, James Starlight <
> jmsstarli...@gmail.com
> > > >wrote:
> > >
> > > > Mark,
> > > >
> > > > thanks for suggestions
> > > >
> > > > as I've told previously I've removed pbc via trjconv witout -pbc mol
> > and
> > > > -pbc
> > > > nojump flags
> > >
> > >
> > > I didn't see anything like that in this thread...
> > >
> > >
> > > > (the same way I found in Justin's umbrella tutorial where
> > > > conformers were extracted from pulling trajectory). Might it be
> source
> > of
> > > > the some artifacts with pbc ?
> > > >
> > >
> > > Don't know. Look at your files and see what's there :-)
> > >
> > >
> > > > so if I understood correctly subsequent minimization (with maxwarn 1
> > > flag)
> > > > restored original pbc (based on box vectors defined in gro file )
> > because
> > > > in next production MD there were no warnings
> > > >
> > >
> > > The PBC was always there. The question is likely whether the code
> assumes
> > > molecules have coordinates that do not straddle the current box, or
> not.
> > > mdrun goes to the expense of ensuring that it does it correctly, but
> > there
> > > are countless other points where the code may or may not still be doing
> > > something that was correct at some point in the last 15 years under
> > certain
> > > assumptions, but may not be correct now or under new conditions...
> > >
> > > Mark
> > >
> > > 2013/5/3 Mark Abraham 
> > > >
> > > > > Trajectory frames written by mdrun are not post-processed to guess
> > how
> > > > you
> > > > > would like PBC to be treated for whatever purpose you have next. So
> > if
> > > a
> > > > > molecule straddles a periodic boundary given the current center
> > > position,
> > > > > that's what it looks like. If there are things you want to do, then
> > > > there's
> > > > > the instructions at
> > > > >
> > > > >
> > > >
> > >
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> > > > > .
> > > > >
> > > > > In turn, it seems grompp applies a whole collection of basic
> checks,
> > > and
> > > > it
> > > > > seems that one of them might not be sufficiently PBC-aware. Such
> > checks
> > > > > appropriate for a normal grompp workflow, where this is the first
> > point
> > > > the
> > > > > GROMACS machinery gets to see what you intend to do and is the
> point
> > > > where
> > > > > it can help you ensure sanity. It seems there's room for a small
> > > > > improvement, too.
> > > > >
> > > > > If the subsequent MD works, then you need have no concern, but if
> you
> > > > want
> > > > > to post-process your trjconv frames so that the molecules are
> whole,
> > > you
> > > > > will suppress this warning the "correct" way.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Fri, May 3, 2013 at 8:18 AM, James Starlight <
> > > jmsstarli...@gmail.com
> > > > > >wrote:
> > > > >
> > > > > > Dear Gromacs users!
> > > > > >
> > > > > > I have performed long md run. From the production trajectory by
> > means
> > > > of
> > > > > >
> > > > > > trjconv -f md_.trr -s cam.tpr  -dt 10 -e 300 -sep -o ./pdbs/.pdb
>  #
> > > > > extract
> > > > > > conformers from first 300 ps each 10ps steps
> > > > > >
> > > > > >
> > > > > > I've extracted 10 conformers in t

Re: [gmx-users] Error after trjconf processing

[Mark Abraham]

EM has no velocities, by definition. Does the EM mdrun write a .gro file
with velocities? If so, that's a bug.


On Fri, May 3, 2013 at 2:51 PM, James Starlight wrote:

> I've noticed that the minimized conformers no longer has the velocities in
> gro file (and npt rus without warnings in that case) in comparison to the
> not-minimized structures ( where velocities were present and gromp sent
> warnings). All pbc options lare the same for all conformers and box vectors
> correctly defined in boundary regions.
>
> But after npt equilibration of the minimized structures ( velocities again
> present in the gro file) my system have crushed at the beginning of the
> production run. So the problem in the velocities set which wre taken from
> the initial pulling run (the same for each conformers).


Huh? After EM there should be no velocities, and you should instruct the
grompp before your equilibration to generate new ones regardless.


> Should I re-assign
> velocities for each conformer (addition nvt run) to fix it ?
>

There seems to be no purpose to trying to start a new simulation from some
configuration, doing EM on it, and then trying to equilibrate starting with
the pre-EM velocities (even if it is possible, which I do not think it
should be). The energy distributions are guaranteed to be mutually
inconsistent.

Mark


>
> James
>
> 2013/5/3 Mark Abraham 
>
> > On Fri, May 3, 2013 at 11:15 AM, James Starlight  > >wrote:
> >
> > > Mark,
> > >
> > > thanks for suggestions
> > >
> > > as I've told previously I've removed pbc via trjconv witout -pbc mol
> and
> > > -pbc
> > > nojump flags
> >
> >
> > I didn't see anything like that in this thread...
> >
> >
> > > (the same way I found in Justin's umbrella tutorial where
> > > conformers were extracted from pulling trajectory). Might it be source
> of
> > > the some artifacts with pbc ?
> > >
> >
> > Don't know. Look at your files and see what's there :-)
> >
> >
> > > so if I understood correctly subsequent minimization (with maxwarn 1
> > flag)
> > > restored original pbc (based on box vectors defined in gro file )
> because
> > > in next production MD there were no warnings
> > >
> >
> > The PBC was always there. The question is likely whether the code assumes
> > molecules have coordinates that do not straddle the current box, or not.
> > mdrun goes to the expense of ensuring that it does it correctly, but
> there
> > are countless other points where the code may or may not still be doing
> > something that was correct at some point in the last 15 years under
> certain
> > assumptions, but may not be correct now or under new conditions...
> >
> > Mark
> >
> > 2013/5/3 Mark Abraham 
> > >
> > > > Trajectory frames written by mdrun are not post-processed to guess
> how
> > > you
> > > > would like PBC to be treated for whatever purpose you have next. So
> if
> > a
> > > > molecule straddles a periodic boundary given the current center
> > position,
> > > > that's what it looks like. If there are things you want to do, then
> > > there's
> > > > the instructions at
> > > >
> > > >
> > >
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> > > > .
> > > >
> > > > In turn, it seems grompp applies a whole collection of basic checks,
> > and
> > > it
> > > > seems that one of them might not be sufficiently PBC-aware. Such
> checks
> > > > appropriate for a normal grompp workflow, where this is the first
> point
> > > the
> > > > GROMACS machinery gets to see what you intend to do and is the point
> > > where
> > > > it can help you ensure sanity. It seems there's room for a small
> > > > improvement, too.
> > > >
> > > > If the subsequent MD works, then you need have no concern, but if you
> > > want
> > > > to post-process your trjconv frames so that the molecules are whole,
> > you
> > > > will suppress this warning the "correct" way.
> > > >
> > > > Mark
> > > >
> > > > On Fri, May 3, 2013 at 8:18 AM, James Starlight <
> > jmsstarli...@gmail.com
> > > > >wrote:
> > > >
> > > > > Dear Gromacs users!
> > > > >
> > > > > I have performed long md run. From the production trajectory by
> means
> > > of
> > > > >
> > > > > trjconv -f md_.trr -s cam.tpr  -dt 10 -e 300 -sep -o ./pdbs/.pdb  #
> > > > extract
> > > > > conformers from first 300 ps each 10ps steps
> > > > >
> > > > >
> > > > > I've extracted 10 conformers in the desired time step
> > > > >
> > > > > Than when I perform MD on each conformer I obtain error (when I
> > loaded
> > > in
> > > > > grompp  conformer from the initial run I have no such error)
> > > > >
> > > > > Number of degrees of freedom in T-Coupling group rest is 130551.00
> > > > > Largest charge group radii for Van der Waals: 8.895, 7.586 nm
> > > > > Largest charge group radii for Coulomb:   8.895, 8.474 nm
> > > > >
> > > > > WARNING 1 [file ./mdps/minim.mdp]:
> > > > >   The sum of the two largest charge group radii (17.368397) is
> larger
> > > > than
> > > > >   rlist (1.00)
> > > > >
> > > >

Re: [gmx-users] Error after trjconf processing

[James Starlight]

I've noticed that the minimized conformers no longer has the velocities in
gro file (and npt rus without warnings in that case) in comparison to the
not-minimized structures ( where velocities were present and gromp sent
warnings). All pbc options lare the same for all conformers and box vectors
correctly defined in boundary regions.

But after npt equilibration of the minimized structures ( velocities again
present in the gro file) my system have crushed at the beginning of the
production run. So the problem in the velocities set which wre taken from
the initial pulling run (the same for each conformers). Should I re-assign
velocities for each conformer (addition nvt run) to fix it ?

James

2013/5/3 Mark Abraham 

> On Fri, May 3, 2013 at 11:15 AM, James Starlight  >wrote:
>
> > Mark,
> >
> > thanks for suggestions
> >
> > as I've told previously I've removed pbc via trjconv witout -pbc mol and
> > -pbc
> > nojump flags
>
>
> I didn't see anything like that in this thread...
>
>
> > (the same way I found in Justin's umbrella tutorial where
> > conformers were extracted from pulling trajectory). Might it be source of
> > the some artifacts with pbc ?
> >
>
> Don't know. Look at your files and see what's there :-)
>
>
> > so if I understood correctly subsequent minimization (with maxwarn 1
> flag)
> > restored original pbc (based on box vectors defined in gro file ) because
> > in next production MD there were no warnings
> >
>
> The PBC was always there. The question is likely whether the code assumes
> molecules have coordinates that do not straddle the current box, or not.
> mdrun goes to the expense of ensuring that it does it correctly, but there
> are countless other points where the code may or may not still be doing
> something that was correct at some point in the last 15 years under certain
> assumptions, but may not be correct now or under new conditions...
>
> Mark
>
> 2013/5/3 Mark Abraham 
> >
> > > Trajectory frames written by mdrun are not post-processed to guess how
> > you
> > > would like PBC to be treated for whatever purpose you have next. So if
> a
> > > molecule straddles a periodic boundary given the current center
> position,
> > > that's what it looks like. If there are things you want to do, then
> > there's
> > > the instructions at
> > >
> > >
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> > > .
> > >
> > > In turn, it seems grompp applies a whole collection of basic checks,
> and
> > it
> > > seems that one of them might not be sufficiently PBC-aware. Such checks
> > > appropriate for a normal grompp workflow, where this is the first point
> > the
> > > GROMACS machinery gets to see what you intend to do and is the point
> > where
> > > it can help you ensure sanity. It seems there's room for a small
> > > improvement, too.
> > >
> > > If the subsequent MD works, then you need have no concern, but if you
> > want
> > > to post-process your trjconv frames so that the molecules are whole,
> you
> > > will suppress this warning the "correct" way.
> > >
> > > Mark
> > >
> > > On Fri, May 3, 2013 at 8:18 AM, James Starlight <
> jmsstarli...@gmail.com
> > > >wrote:
> > >
> > > > Dear Gromacs users!
> > > >
> > > > I have performed long md run. From the production trajectory by means
> > of
> > > >
> > > > trjconv -f md_.trr -s cam.tpr  -dt 10 -e 300 -sep -o ./pdbs/.pdb  #
> > > extract
> > > > conformers from first 300 ps each 10ps steps
> > > >
> > > >
> > > > I've extracted 10 conformers in the desired time step
> > > >
> > > > Than when I perform MD on each conformer I obtain error (when I
> loaded
> > in
> > > > grompp  conformer from the initial run I have no such error)
> > > >
> > > > Number of degrees of freedom in T-Coupling group rest is 130551.00
> > > > Largest charge group radii for Van der Waals: 8.895, 7.586 nm
> > > > Largest charge group radii for Coulomb:   8.895, 8.474 nm
> > > >
> > > > WARNING 1 [file ./mdps/minim.mdp]:
> > > >   The sum of the two largest charge group radii (17.368397) is larger
> > > than
> > > >   rlist (1.00)
> > > >
> > > >
> > > > Finally after minimization of each conformer with the same R_list
> (with
> > > > maxwarn 1 flag) and starting new MD on the minimizing conformer I
> have
> > no
> > > > such error:
> > > > Largest charge group radii for Van der Waals: 0.241, 0.237 nm
> > > > Largest charge group radii for Coulomb:   0.241, 0.237 nm
> > > >
> > > > Why this error have occurred (with no minimized conformers) and how
> it
> > > > could be fixed correctly ?
> > > >
> > > > James
> > > > --
> > > > gmx-users mailing listgmx-users@gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > > * Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > > * Can't post? Read htt

Re: [gmx-users] Error after trjconf processing

[Mark Abraham]

On Fri, May 3, 2013 at 11:15 AM, James Starlight wrote:

> Mark,
>
> thanks for suggestions
>
> as I've told previously I've removed pbc via trjconv witout -pbc mol and
> -pbc
> nojump flags


I didn't see anything like that in this thread...


> (the same way I found in Justin's umbrella tutorial where
> conformers were extracted from pulling trajectory). Might it be source of
> the some artifacts with pbc ?
>

Don't know. Look at your files and see what's there :-)


> so if I understood correctly subsequent minimization (with maxwarn 1 flag)
> restored original pbc (based on box vectors defined in gro file ) because
> in next production MD there were no warnings
>

The PBC was always there. The question is likely whether the code assumes
molecules have coordinates that do not straddle the current box, or not.
mdrun goes to the expense of ensuring that it does it correctly, but there
are countless other points where the code may or may not still be doing
something that was correct at some point in the last 15 years under certain
assumptions, but may not be correct now or under new conditions...

Mark

2013/5/3 Mark Abraham 
>
> > Trajectory frames written by mdrun are not post-processed to guess how
> you
> > would like PBC to be treated for whatever purpose you have next. So if a
> > molecule straddles a periodic boundary given the current center position,
> > that's what it looks like. If there are things you want to do, then
> there's
> > the instructions at
> >
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> > .
> >
> > In turn, it seems grompp applies a whole collection of basic checks, and
> it
> > seems that one of them might not be sufficiently PBC-aware. Such checks
> > appropriate for a normal grompp workflow, where this is the first point
> the
> > GROMACS machinery gets to see what you intend to do and is the point
> where
> > it can help you ensure sanity. It seems there's room for a small
> > improvement, too.
> >
> > If the subsequent MD works, then you need have no concern, but if you
> want
> > to post-process your trjconv frames so that the molecules are whole, you
> > will suppress this warning the "correct" way.
> >
> > Mark
> >
> > On Fri, May 3, 2013 at 8:18 AM, James Starlight  > >wrote:
> >
> > > Dear Gromacs users!
> > >
> > > I have performed long md run. From the production trajectory by means
> of
> > >
> > > trjconv -f md_.trr -s cam.tpr  -dt 10 -e 300 -sep -o ./pdbs/.pdb  #
> > extract
> > > conformers from first 300 ps each 10ps steps
> > >
> > >
> > > I've extracted 10 conformers in the desired time step
> > >
> > > Than when I perform MD on each conformer I obtain error (when I loaded
> in
> > > grompp  conformer from the initial run I have no such error)
> > >
> > > Number of degrees of freedom in T-Coupling group rest is 130551.00
> > > Largest charge group radii for Van der Waals: 8.895, 7.586 nm
> > > Largest charge group radii for Coulomb:   8.895, 8.474 nm
> > >
> > > WARNING 1 [file ./mdps/minim.mdp]:
> > >   The sum of the two largest charge group radii (17.368397) is larger
> > than
> > >   rlist (1.00)
> > >
> > >
> > > Finally after minimization of each conformer with the same R_list (with
> > > maxwarn 1 flag) and starting new MD on the minimizing conformer I have
> no
> > > such error:
> > > Largest charge group radii for Van der Waals: 0.241, 0.237 nm
> > > Largest charge group radii for Coulomb:   0.241, 0.237 nm
> > >
> > > Why this error have occurred (with no minimized conformers) and how it
> > > could be fixed correctly ?
> > >
> > > James
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
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>
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http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please se

Re: [gmx-users] Error after trjconf processing

[James Starlight]

Mark,

thanks for suggestions

as I've told previously I've removed pbc via trjconv witout -pbc mol and -pbc
nojump flags (the same way I found in Justin's umbrella tutorial where
conformers were extracted from pulling trajectory). Might it be source of
the some artifacts with pbc ?

so if I understood correctly subsequent minimization (with maxwarn 1 flag)
restored original pbc (based on box vectors defined in gro file ) because
in next production MD there were no warnings

2013/5/3 Mark Abraham 

> Trajectory frames written by mdrun are not post-processed to guess how you
> would like PBC to be treated for whatever purpose you have next. So if a
> molecule straddles a periodic boundary given the current center position,
> that's what it looks like. If there are things you want to do, then there's
> the instructions at
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> .
>
> In turn, it seems grompp applies a whole collection of basic checks, and it
> seems that one of them might not be sufficiently PBC-aware. Such checks
> appropriate for a normal grompp workflow, where this is the first point the
> GROMACS machinery gets to see what you intend to do and is the point where
> it can help you ensure sanity. It seems there's room for a small
> improvement, too.
>
> If the subsequent MD works, then you need have no concern, but if you want
> to post-process your trjconv frames so that the molecules are whole, you
> will suppress this warning the "correct" way.
>
> Mark
>
> On Fri, May 3, 2013 at 8:18 AM, James Starlight  >wrote:
>
> > Dear Gromacs users!
> >
> > I have performed long md run. From the production trajectory by means of
> >
> > trjconv -f md_.trr -s cam.tpr  -dt 10 -e 300 -sep -o ./pdbs/.pdb  #
> extract
> > conformers from first 300 ps each 10ps steps
> >
> >
> > I've extracted 10 conformers in the desired time step
> >
> > Than when I perform MD on each conformer I obtain error (when I loaded in
> > grompp  conformer from the initial run I have no such error)
> >
> > Number of degrees of freedom in T-Coupling group rest is 130551.00
> > Largest charge group radii for Van der Waals: 8.895, 7.586 nm
> > Largest charge group radii for Coulomb:   8.895, 8.474 nm
> >
> > WARNING 1 [file ./mdps/minim.mdp]:
> >   The sum of the two largest charge group radii (17.368397) is larger
> than
> >   rlist (1.00)
> >
> >
> > Finally after minimization of each conformer with the same R_list (with
> > maxwarn 1 flag) and starting new MD on the minimizing conformer I have no
> > such error:
> > Largest charge group radii for Van der Waals: 0.241, 0.237 nm
> > Largest charge group radii for Coulomb:   0.241, 0.237 nm
> >
> > Why this error have occurred (with no minimized conformers) and how it
> > could be fixed correctly ?
> >
> > James
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Error after trjconf processing

[Mark Abraham]

Trajectory frames written by mdrun are not post-processed to guess how you
would like PBC to be treated for whatever purpose you have next. So if a
molecule straddles a periodic boundary given the current center position,
that's what it looks like. If there are things you want to do, then there's
the instructions at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
.

In turn, it seems grompp applies a whole collection of basic checks, and it
seems that one of them might not be sufficiently PBC-aware. Such checks
appropriate for a normal grompp workflow, where this is the first point the
GROMACS machinery gets to see what you intend to do and is the point where
it can help you ensure sanity. It seems there's room for a small
improvement, too.

If the subsequent MD works, then you need have no concern, but if you want
to post-process your trjconv frames so that the molecules are whole, you
will suppress this warning the "correct" way.

Mark

On Fri, May 3, 2013 at 8:18 AM, James Starlight wrote:

> Dear Gromacs users!
>
> I have performed long md run. From the production trajectory by means of
>
> trjconv -f md_.trr -s cam.tpr  -dt 10 -e 300 -sep -o ./pdbs/.pdb  # extract
> conformers from first 300 ps each 10ps steps
>
>
> I've extracted 10 conformers in the desired time step
>
> Than when I perform MD on each conformer I obtain error (when I loaded in
> grompp  conformer from the initial run I have no such error)
>
> Number of degrees of freedom in T-Coupling group rest is 130551.00
> Largest charge group radii for Van der Waals: 8.895, 7.586 nm
> Largest charge group radii for Coulomb:   8.895, 8.474 nm
>
> WARNING 1 [file ./mdps/minim.mdp]:
>   The sum of the two largest charge group radii (17.368397) is larger than
>   rlist (1.00)
>
>
> Finally after minimization of each conformer with the same R_list (with
> maxwarn 1 flag) and starting new MD on the minimizing conformer I have no
> such error:
> Largest charge group radii for Van der Waals: 0.241, 0.237 nm
> Largest charge group radii for Coulomb:   0.241, 0.237 nm
>
> Why this error have occurred (with no minimized conformers) and how it
> could be fixed correctly ?
>
> James
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
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* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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[gmx-users] Error after trjconf processing

[James Starlight]

Dear Gromacs users!

I have performed long md run. From the production trajectory by means of

trjconv -f md_.trr -s cam.tpr  -dt 10 -e 300 -sep -o ./pdbs/.pdb  # extract
conformers from first 300 ps each 10ps steps


I've extracted 10 conformers in the desired time step

Than when I perform MD on each conformer I obtain error (when I loaded in
grompp  conformer from the initial run I have no such error)

Number of degrees of freedom in T-Coupling group rest is 130551.00
Largest charge group radii for Van der Waals: 8.895, 7.586 nm
Largest charge group radii for Coulomb:   8.895, 8.474 nm

WARNING 1 [file ./mdps/minim.mdp]:
  The sum of the two largest charge group radii (17.368397) is larger than
  rlist (1.00)


Finally after minimization of each conformer with the same R_list (with
maxwarn 1 flag) and starting new MD on the minimizing conformer I have no
such error:
Largest charge group radii for Van der Waals: 0.241, 0.237 nm
Largest charge group radii for Coulomb:   0.241, 0.237 nm

Why this error have occurred (with no minimized conformers) and how it
could be fixed correctly ?

James
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Error in pdb2gmx

[Justin Lemkul]

On 4/30/13 6:10 AM, Nikunj Maheshwari wrote:

Thanks Justin. I know that using -ignh will solve the problem. But I was
just curious because I got the same error message ("Fatal error: Atom HD1
in residue HIS 65 was not found in rtp entry HISE with 17 atoms while
sorting atoms. ") when I used OPLS, this time it was His 65.

So I used -his option in pdb2gmx and got the following options to choose

Which HISTIDINE type do you want for residue 65
0. H on ND1 only (HISD)   #Works. total charge= -17.000
1. H on NE2 only (HISE)   # Error
2. H on ND1 and NE2 (HISH)#Works. total charge= -16.000
3. Coupled to Heme (HIS1)   #Works. total charge= -17.000

So shall I go ahead with any of the option except 1, or use -ignh?



In this case, pdb2gmx is detecting that you should have epsilon-protonated 
histidine at His65, but the proton is at the delta position, so there is a 
conflict.  HISD and HISH work because they both should have a proton on ND1.


-Justin


On Tue, Apr 30, 2013 at 3:33 PM, Justin Lemkul  wrote:




On 4/30/13 2:59 AM, Nikunj Maheshwari wrote:


Dear all,

I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
output.gro)

I used 13. GROMOS 53a6 force field

"Fatal error:
Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms
while
sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input."

So I used -glu option in pdb2gmx (pdb2gmx -f 123.pdb -o output.gro -glu)

I get the following options.

Which GLUTAMIC ACID type do you want for residue 1
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUH)

Both options give the same error as before.

The same error occurs for HB1 as well.

Will I have to edit the pdb or rtp file? Or any other suggestions?



Read the error message again; it tells you what to do.

Consider what you're doing - you're supplying a united-atom force field
with an all-atom structure.  The chosen parameter set doesn't have explicit
hydrogens on nonpolar groups.  Hence pdb2gmx complains that you're giving
it atoms it doesn't understand.  Use of -ignh solves this issue, which is
precisely what the error message is telling you.

-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin

==**==
--
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 posting!
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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Error in pdb2gmx

[Nikunj Maheshwari]

Thanks Justin. I know that using -ignh will solve the problem. But I was
just curious because I got the same error message ("Fatal error: Atom HD1
in residue HIS 65 was not found in rtp entry HISE with 17 atoms while
sorting atoms. ") when I used OPLS, this time it was His 65.

So I used -his option in pdb2gmx and got the following options to choose

Which HISTIDINE type do you want for residue 65
0. H on ND1 only (HISD)   #Works. total charge= -17.000
1. H on NE2 only (HISE)   # Error
2. H on ND1 and NE2 (HISH)#Works. total charge= -16.000
3. Coupled to Heme (HIS1)   #Works. total charge= -17.000

So shall I go ahead with any of the option except 1, or use -ignh?

On Tue, Apr 30, 2013 at 3:33 PM, Justin Lemkul  wrote:

>
>
> On 4/30/13 2:59 AM, Nikunj Maheshwari wrote:
>
>> Dear all,
>>
>> I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
>> output.gro)
>>
>> I used 13. GROMOS 53a6 force field
>>
>> "Fatal error:
>> Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms
>> while
>> sorting atoms.
>>
>> For a hydrogen, this can be a different protonation state, or it
>> might have had a different number in the PDB file and was rebuilt
>> (it might for instance have been H3, and we only expected H1 & H2).
>> Note that hydrogens might have been added to the entry for the N-terminus.
>> Remove this hydrogen or choose a different protonation state to solve it.
>> Option -ignh will ignore all hydrogens in the input."
>>
>> So I used -glu option in pdb2gmx (pdb2gmx -f 123.pdb -o output.gro -glu)
>>
>> I get the following options.
>>
>> Which GLUTAMIC ACID type do you want for residue 1
>> 0. Not protonated (charge -1) (GLU)
>> 1. Protonated (charge 0) (GLUH)
>>
>> Both options give the same error as before.
>>
>> The same error occurs for HB1 as well.
>>
>> Will I have to edit the pdb or rtp file? Or any other suggestions?
>>
>>
> Read the error message again; it tells you what to do.
>
> Consider what you're doing - you're supplying a united-atom force field
> with an all-atom structure.  The chosen parameter set doesn't have explicit
> hydrogens on nonpolar groups.  Hence pdb2gmx complains that you're giving
> it atoms it doesn't understand.  Use of -ignh solves this issue, which is
> precisely what the error message is telling you.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] Error in pdb2gmx

[Justin Lemkul]

On 4/30/13 2:59 AM, Nikunj Maheshwari wrote:

Dear all,

I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
output.gro)

I used 13. GROMOS 53a6 force field

"Fatal error:
Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while
sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input."

So I used -glu option in pdb2gmx (pdb2gmx -f 123.pdb -o output.gro -glu)

I get the following options.

Which GLUTAMIC ACID type do you want for residue 1
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUH)

Both options give the same error as before.

The same error occurs for HB1 as well.

Will I have to edit the pdb or rtp file? Or any other suggestions?



Read the error message again; it tells you what to do.

Consider what you're doing - you're supplying a united-atom force field with an 
all-atom structure.  The chosen parameter set doesn't have explicit hydrogens on 
nonpolar groups.  Hence pdb2gmx complains that you're giving it atoms it doesn't 
understand.  Use of -ignh solves this issue, which is precisely what the error 
message is telling you.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Error in pdb2gmx

[Nikunj Maheshwari]

Dear all,

I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
output.gro)

I used 13. GROMOS 53a6 force field

"Fatal error:
Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while
sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input."

So I used -glu option in pdb2gmx (pdb2gmx -f 123.pdb -o output.gro -glu)

I get the following options.

Which GLUTAMIC ACID type do you want for residue 1
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUH)

Both options give the same error as before.

The same error occurs for HB1 as well.

Will I have to edit the pdb or rtp file? Or any other suggestions?

Thanks..
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Re: [gmx-users] Error in make install "no valid ELF RPATH". Cray XE6m

[Szilárd Páll]

Hi,

Your problem will likely be solved by not writing the rpath to the
binaries which can be accomplished by setting -DCMAKE_SKIP_RPATH=OFF.
This will mean that you will have to make sure that the library path
is set for mdrun to work.

If that does not fully solve the problem, you might have to build
static binaries.

Cheers,
--
Szilárd


On Sat, Apr 20, 2013 at 3:04 AM, Daniel Adriano Silva M
 wrote:
> Dear Gromacs users&devs,
>
> I just installed gromacs-4.5.7 in a Cray XE6m, the serial installation
> went fine, however the mpi installation presents a problem. It
> compiles fine, but the "make install" (or make install-mdrun) seems to
> have problems copying the executable files to the installation
> directory.
>
> If I run the executable from the compilation directory (for instance:
> gromacs-4.5.7/build_mpi/src/kernel/mdrun_mpi), everything seems fine.
>
> My command(s):
>
> cmake ../ -DCMAKE_INSTALL_PREFIX=$HOME/PROGRAMS/gromacs-4.5.7-icc-fftw-mpi
> -DBUILD_SHARED_LIBS=OFF
> -DFFTW3F_INCLUDE_DIR=$HOME/PROGRAMS/fftw-3.3.3-icc/include
> -DFFTW3F_LIBRARIES=$HOME/PROGRAMS/fftw-3.3.3-icc/lib/libfftw3f.a
> -DGMX_MPI=ON 
> -DMPI_INCLUDE_PATH="/opt/cray/mpt/5.5.4/gni/mpich2-intel/120/include/"
> -DMPI_LIBRARY="/opt/cray/mpt/5.5.4/gni/mpich2-intel/120/lib/libmpich.a;/opt/cray/mpt/5.5.4/gni/mpich2-intel/120/lib/libmpich_intel.a;/opt/cray/mpt/5.5.4/gni/mpich2-intel/120/lib/libmpl.a;/opt/cray/pmi/3.0.1-1..8917.33.1.gem/lib64/libpmi.a"
>
>
> The ERROR:
>
> CMake Error at src/kernel/cmake_install.cmake:65 (FILE):
>   file RPATH_CHANGE could not write new RPATH:
>
> /u/dadriano/PROGRAMS/gromacs-4.5.7-icc-fftw-mpi/lib
>
>   to the file:
>
> /u/dadriano/PROGRAMS/gromacs-4.5.7-icc-fftw-mpi/bin/mdrun_mpi
>
>   No valid ELF RPATH or RUNPATH entry exists in the file;
> Call Stack (most recent call first):
>   src/cmake_install.cmake:39 (INCLUDE)
>   cmake_install.cmake:40 (INCLUDE)
>
>
> make: *** [install] Error 1
>
>
> Any help will be appreciated,
> Daniel
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[gmx-users] Error in make install "no valid ELF RPATH". Cray XE6m

[Daniel Adriano Silva M]

Dear Gromacs users&devs,

I just installed gromacs-4.5.7 in a Cray XE6m, the serial installation
went fine, however the mpi installation presents a problem. It
compiles fine, but the "make install" (or make install-mdrun) seems to
have problems copying the executable files to the installation
directory.

If I run the executable from the compilation directory (for instance:
gromacs-4.5.7/build_mpi/src/kernel/mdrun_mpi), everything seems fine.

My command(s):

cmake ../ -DCMAKE_INSTALL_PREFIX=$HOME/PROGRAMS/gromacs-4.5.7-icc-fftw-mpi
-DBUILD_SHARED_LIBS=OFF
-DFFTW3F_INCLUDE_DIR=$HOME/PROGRAMS/fftw-3.3.3-icc/include
-DFFTW3F_LIBRARIES=$HOME/PROGRAMS/fftw-3.3.3-icc/lib/libfftw3f.a
-DGMX_MPI=ON 
-DMPI_INCLUDE_PATH="/opt/cray/mpt/5.5.4/gni/mpich2-intel/120/include/"
-DMPI_LIBRARY="/opt/cray/mpt/5.5.4/gni/mpich2-intel/120/lib/libmpich.a;/opt/cray/mpt/5.5.4/gni/mpich2-intel/120/lib/libmpich_intel.a;/opt/cray/mpt/5.5.4/gni/mpich2-intel/120/lib/libmpl.a;/opt/cray/pmi/3.0.1-1..8917.33.1.gem/lib64/libpmi.a"


The ERROR:

CMake Error at src/kernel/cmake_install.cmake:65 (FILE):
  file RPATH_CHANGE could not write new RPATH:

/u/dadriano/PROGRAMS/gromacs-4.5.7-icc-fftw-mpi/lib

  to the file:

/u/dadriano/PROGRAMS/gromacs-4.5.7-icc-fftw-mpi/bin/mdrun_mpi

  No valid ELF RPATH or RUNPATH entry exists in the file;
Call Stack (most recent call first):
  src/cmake_install.cmake:39 (INCLUDE)
  cmake_install.cmake:40 (INCLUDE)


make: *** [install] Error 1


Any help will be appreciated,
Daniel
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Re: [gmx-users] Error in REMD

[Mark Abraham]

This would normally mean you are somehow calling code from one GROMACS
version with code from another. Some kind of dynamic library loading mishap?

Mark

On Fri, Mar 22, 2013 at 10:41 AM, Nikunj Maheshwari <
nixcrazyfor...@gmail.com> wrote:

> Dear all...
>
> We ran REMD simulations for 36 replicas. We got an error which stopped the
> whole simulation.
>
> "
> Reading file md21.tpr, VERSION 4.5.5 (single precision)
> Loaded with Money
>
> Reading file md24.tpr, VERSION 4.5.5 (single precision)
> Loaded with Money
>
>
> ---
> Program mdrun_mpi, VERSION 4.5.5
> Source code file: symtab.c, line: 108
>
> Fatal error:
> symtab get_symtab_handle 1031126655 not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "The World is a Friendly Place" (Magnapop)
>
> Error on node 35, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 35 out of 36
>
> gcq#103: "The World is a Friendly Place" (Magnapop)
>
> MPI: Global rank 35 is aborting with error code -1.
> "
>
> Can someone help us in knowing what the error means and how to it can be
> rectified?
>
> Thanks
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Error in REMD

[Nikunj Maheshwari]

Dear all...

We ran REMD simulations for 36 replicas. We got an error which stopped the
whole simulation.

"
Reading file md21.tpr, VERSION 4.5.5 (single precision)
Loaded with Money

Reading file md24.tpr, VERSION 4.5.5 (single precision)
Loaded with Money


---
Program mdrun_mpi, VERSION 4.5.5
Source code file: symtab.c, line: 108

Fatal error:
symtab get_symtab_handle 1031126655 not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"The World is a Friendly Place" (Magnapop)

Error on node 35, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 35 out of 36

gcq#103: "The World is a Friendly Place" (Magnapop)

MPI: Global rank 35 is aborting with error code -1.
"

Can someone help us in knowing what the error means and how to it can be
rectified?

Thanks
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Re: [gmx-users] Error during grompp run

[Justin Lemkul]

On Wed, Mar 20, 2013 at 2:30 AM, Kshatresh Dutta Dubey
wrote:

> Dear Justin,
>
> I checked for it several times and I am quite sure there is no typo error,
> permission problem and location of posre_Protein.itp file. Even, I run same
> job on different machines from beginning and I found same type of error.
>
>

Without seeing the relevant topology snippet, listing of files in the
working directory (ls -l), and the grompp command invoked, there's no way
for anyone to help you.  This should be a relatively easy fix.  The fact
that it does not work on multiple machines indicates there is indeed a
problem with either the file name or the manner in which it is included in
the topology.  What is posre_Protein.itp?  What it written by pdb2gmx with
a nonstandard name or was it something you created?

-Justin


>   --
> *From:* Justin Lemkul 
> *To:* Kshatresh Dutta Dubey ; Discussion list for
> GROMACS users 
> *Sent:* Tuesday, March 19, 2013 10:48 PM
> *Subject:* Re: [gmx-users] Error during grompp run
>
>
>
> On Tue, Mar 19, 2013 at 10:46 AM, Kshatresh Dutta Dubey <
> kshatr...@ymail.com> wrote:
>
> Dear Users
>
> I am using groamcs 4.4.4 and when I run grompp during equilibration
> process, it closes with error
>  " Fatal error:Topology include file "posre_Protein.itp" not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors";
>
> However, I found Topology include file "posre_Protein.itp" in current
> directory. I am able to successfully run previous grompp
> during minimization, but I am facing this problem during equilibration only.
>
> Please help me to get rid of this issue. I welcome all suggestions.
>
>
> If grompp says it's not there, it's not there.  Check carefully for typos
> in file names or #include statements as well as read permissions on the
> file itself.
>
> -Justin
>
> --
>
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 
> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
>
>
>


-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Error during grompp run

[Justin Lemkul]

On Tue, Mar 19, 2013 at 10:46 AM, Kshatresh Dutta Dubey  wrote:

> Dear Users
>
> I am using groamcs 4.4.4 and when I run grompp during equilibration
> process, it closes with error
>  " Fatal error:Topology include file "posre_Protein.itp" not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors";
>
> However, I found Topology include file "posre_Protein.itp" in current
> directory. I am able to successfully run previous grompp
> during minimization, but I am facing this problem during equilibration only.
>
> Please help me to get rid of this issue. I welcome all suggestions.
>
>
If grompp says it's not there, it's not there.  Check carefully for typos
in file names or #include statements as well as read permissions on the
file itself.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Error during grompp run

[Kshatresh Dutta Dubey]

Dear Users

I am using groamcs 4.4.4 and when I run grompp during equilibration process, it 
closes with error
 " Fatal error:Topology include file "posre_Protein.itp" not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors";

However, I found Topology include file "posre_Protein.itp" in current 
directory. I am able to successfully run previous grompp during minimization, 
but I am facing this problem during equilibration only.

Please help me to get rid of this issue. I welcome all suggestions.

Thanks in advance

Kshatresh Dutta Dubey 
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Re: [gmx-users] Error Quick and Dirty installation

[Mark Abraham]

That means the automatic download of FFTW did not succeed for some reason.
GROMACS is not going to compile an FFTW for you unless it's sure the FFTW
download was complete and the right file. Either do "make clean" and try
again, or follow the other build instructions to prepare a suitable FFTW
for yourself.

Note that you should not use sudo for anything before the "make install"
stage. That's the only time you need to consider allowing code that you
have no idea about to perhaps trash your system.

Mark

On Fri, Mar 15, 2013 at 6:47 PM, Juando11  wrote:

> Hi, I need install gromacs 4.6.1 in Ubuntu 12.10 when I make the quick and
> dirty installation I have this errors:
>
> [  1%] Performing download step (download, verify and extract) for
> 'gmxfftw'
> -- downloading...
>  src='http://www.fftw.org/fftw-3.3.2.tar.gz'
>
>
> dst='/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz'
>  timeout='none'
> CMake Error at gmxfftw-stamp/download-gmxfftw.cmake:6 (file):
>   file DOWNLOAD MD5 mismatch
>
> for file:
>
> [/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz]
>   expected MD5 sum: [6977ee770ed68c85698c7168ffa6e178]
> actual MD5 sum: [d41d8cd98f00b204e9800998ecf8427e]
>
>
>
> make[2]: ***
> [src/contrib/fftw/gmxfftw-prefix/src/gmxfftw-stamp/gmxfftw-download] Error
> 1
> make[1]: *** [src/contrib/fftw/CMakeFiles/gmxfftw.dir/all] Error 2
> make: *** [all] Error 2
> biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ sudo
> apt-get
> install libfftw3-devLeyendo lista de paquetes... Hecho
> Creando árbol de dependencias
> Leyendo la información de estado... Hecho
> libfftw3-dev ya está en su versión más reciente.
> 0 actualizados, 0 se instalarán, 0 para eliminar y 305 no actualizados.
> biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ ./configure
> bash: ./configure: No existe el archivo o el directorio
> biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ sudo make
> [  1%] Performing download step (download, verify and extract) for
> 'gmxfftw'
> -- downloading...
>  src='http://www.fftw.org/fftw-3.3.2.tar.gz'
>
>
> dst='/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz'
>  timeout='none'
> CMake Error at gmxfftw-stamp/download-gmxfftw.cmake:6 (file):
>   file DOWNLOAD MD5 mismatch
>
> for file:
>
> [/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz]
>   expected MD5 sum: [6977ee770ed68c85698c7168ffa6e178]
> actual MD5 sum: [d41d8cd98f00b204e9800998ecf8427e]
>
>
>
> make[2]: ***
> [src/contrib/fftw/gmxfftw-prefix/src/gmxfftw-stamp/gmxfftw-download] Error
> 1
> make[1]: *** [src/contrib/fftw/CMakeFiles/gmxfftw.dir/all] Error 2
> make: *** [all] Error 2
> biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ sudo make
> install
> [  1%] Performing download step (download, verify and extract) for
> 'gmxfftw'
> -- downloading...
>  src='http://www.fftw.org/fftw-3.3.2.tar.gz'
>
>
> dst='/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz'
>  timeout='none'
> CMake Error at gmxfftw-stamp/download-gmxfftw.cmake:6 (file):
>   file DOWNLOAD MD5 mismatch
>
> for file:
>
> [/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz]
>   expected MD5 sum: [6977ee770ed68c85698c7168ffa6e178]
> actual MD5 sum: [d41d8cd98f00b204e9800998ecf8427e]
>
>
>
> make[2]: ***
> [src/contrib/fftw/gmxfftw-prefix/src/gmxfftw-stamp/gmxfftw-download] Error
> 1
> make[1]: *** [src/contrib/fftw/CMakeFiles/gmxfftw.dir/all] Error 2
> make: *** [all] Error 2
>
> Please help me
> Thanks
>
>
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/Error-Quick-and-Dirty-installation-tp5006348.html
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[gmx-users] Error Quick and Dirty installation

[Juando11]

Hi, I need install gromacs 4.6.1 in Ubuntu 12.10 when I make the quick and
dirty installation I have this errors:

[  1%] Performing download step (download, verify and extract) for 'gmxfftw'
-- downloading...
 src='http://www.fftw.org/fftw-3.3.2.tar.gz'

dst='/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz'
 timeout='none'
CMake Error at gmxfftw-stamp/download-gmxfftw.cmake:6 (file):
  file DOWNLOAD MD5 mismatch

for file:
[/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz]
  expected MD5 sum: [6977ee770ed68c85698c7168ffa6e178]
actual MD5 sum: [d41d8cd98f00b204e9800998ecf8427e]



make[2]: ***
[src/contrib/fftw/gmxfftw-prefix/src/gmxfftw-stamp/gmxfftw-download] Error 1
make[1]: *** [src/contrib/fftw/CMakeFiles/gmxfftw.dir/all] Error 2
make: *** [all] Error 2
biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ sudo apt-get
install libfftw3-devLeyendo lista de paquetes... Hecho
Creando árbol de dependencias   
Leyendo la información de estado... Hecho
libfftw3-dev ya está en su versión más reciente.
0 actualizados, 0 se instalarán, 0 para eliminar y 305 no actualizados.
biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ ./configure
bash: ./configure: No existe el archivo o el directorio
biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ sudo make
[  1%] Performing download step (download, verify and extract) for 'gmxfftw'
-- downloading...
 src='http://www.fftw.org/fftw-3.3.2.tar.gz'

dst='/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz'
 timeout='none'
CMake Error at gmxfftw-stamp/download-gmxfftw.cmake:6 (file):
  file DOWNLOAD MD5 mismatch

for file:
[/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz]
  expected MD5 sum: [6977ee770ed68c85698c7168ffa6e178]
actual MD5 sum: [d41d8cd98f00b204e9800998ecf8427e]



make[2]: ***
[src/contrib/fftw/gmxfftw-prefix/src/gmxfftw-stamp/gmxfftw-download] Error 1
make[1]: *** [src/contrib/fftw/CMakeFiles/gmxfftw.dir/all] Error 2
make: *** [all] Error 2
biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ sudo make
install
[  1%] Performing download step (download, verify and extract) for 'gmxfftw'
-- downloading...
 src='http://www.fftw.org/fftw-3.3.2.tar.gz'

dst='/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz'
 timeout='none'
CMake Error at gmxfftw-stamp/download-gmxfftw.cmake:6 (file):
  file DOWNLOAD MD5 mismatch

for file:
[/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz]
  expected MD5 sum: [6977ee770ed68c85698c7168ffa6e178]
actual MD5 sum: [d41d8cd98f00b204e9800998ecf8427e]



make[2]: ***
[src/contrib/fftw/gmxfftw-prefix/src/gmxfftw-stamp/gmxfftw-download] Error 1
make[1]: *** [src/contrib/fftw/CMakeFiles/gmxfftw.dir/all] Error 2
make: *** [all] Error 2

Please help me
Thanks



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Re: [gmx-users] Error: invalid initializer, though GCC version 2006

[Mark Abraham]

2006 is prehistoric, for a compiler. See
http://www.gromacs.org/Documentation/Installation_Instructions#3.2._Compiler

Mark

On Wed, Mar 13, 2013 at 7:24 AM, nikunj  wrote:

> Hi.
> When I use the "make" command, it always stops at 56% and gives this error:
>
> [ 56%] Building C object
>
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_sse2_single.c.o
> In file included from
>
> /home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_sse2_single.c:50:
>
> /home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h:
> In function
> `gmx_mm_load_shift_and_4rvec_broadcast_ps':/home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h:207:
> warning: implicit declaration of function `_mm_castpd_ps'
>
> /home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h:207:
> error: incompatible types in assignment
>
> /home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h:
> In function `gmx_mm_load_1rvec_4ptr_swizzle_ps':
>
> /home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h:248:
> error: incompatible types in assignment
>
> /home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h:249:
> error: incompatible types in assignment
>
> /home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h:250:
> error: incompatible types in assignment
>
> /home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h:251:
> error: incompatible types in assignment
>
> /home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_sse2_single.c:
> In function `nb_kernel_ElecRF_VdwCSTab_GeomW3P1_VF_sse2_single':
>
> /home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_sse2_single.c:109:
> warning: implicit declaration of function `_mm_castsi128_ps'
>
> /home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_sse2_single.c:109:
> error: invalid initializer
>
> /home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_sse2_single.c:
> In function `nb_kernel_ElecRF_VdwCSTab_GeomW3P1_F_sse2_single':
>
> /home/arpit/Desktop/gromacs-4.6/src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_sse2_single.c:684:
> error: invalid initializer
> make[2]: ***
> [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_sse2_single.c.o]
> Error 1
> make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
> make: *** [all] Error 2
>
>
>
> I checked my GCC version. Its 2006.
> Can anybody help ?
>
> Thanks...
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/Error-invalid-initializer-though-GCC-version-2006-tp5006283.html
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[gmx-users] error in gromacs 4.0.7-Source code file: domdec.c, line: 5888

[Hamid Mosaddeghi]

Dear users

I used gromacs for my system include CNT-water-ion-protein (400,000atom), I
used grompp without error.

after used mdrun with 16 node on cluster, I get this error:

Reading file nvt.tpr, VERSION 4.0.7 (single precision)
Loaded with Money


NOTE: Periodic molecules: can not easily determine the required minimum
bonded cut-off, using half the non-bonded cut-off


Will use 15 particle-particle and 1 PME only nodes
This is a guess, check the performance at the end of the log file

---
Program mdrun, VERSION 4.0.7
Source code file: domdec.c, line: 5888

Fatal error:
There is no domain decomposition for 15 nodes that is compatible with the
given box and a minimum cell size of 3.75 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
---

"Good Music Saves your Soul" (Lemmy)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 16

---

my box size is 14*14*18.

I used mdrun -rdd 1 , gromacs run without error is it correct or not?

I get this error in NVT (Em run without error.

Best Regards.

Hamid Mosaddeghi



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Re: [gmx-users] Error when extending simulation

[sebastian]

On 03/05/2013 03:50 PM, Mark Abraham wrote:

... and your GROMACS version!
   


4.6 running on nodes with NVIDIA Keppler K10 and Intel E5 CPU


Mark

On Tue, Mar 5, 2013 at 3:11 PM, Justin Lemkul  wrote:

   


On 3/5/13 4:41 AM, sebastian wrote:

 

On 03/04/2013 09:47 AM, sebastian wrote:

   

Hi Gromacs user,

when I try to extend on of my simulations with

mdrun -deffnm pdz_cis_NVT_disre_equi_3  -cpi
pdz_cis_NVT_disre_equi_3.cpt -append

I get the  following error

Fatal error:
Count mismatch for state entry disre_rm3tav, code count is 0, file count
is 13

and have no idea whats wrong.


 

I tried the same thing for a second simulation and get the same error. It
seems
that this error is connected with restraints. Extending the same
simulation
without any restraints everything is working perfectly fine.

  Any suggestion is very much appreciated
   


 

I would suggest filing a bug report on redmine.gromacs.org.  Please
include all files necessary to reproduce the problem.

-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin

==**==

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Re: [gmx-users] Error when extending simulation

[Mark Abraham]

... and your GROMACS version!

Mark

On Tue, Mar 5, 2013 at 3:11 PM, Justin Lemkul  wrote:

>
>
> On 3/5/13 4:41 AM, sebastian wrote:
>
>> On 03/04/2013 09:47 AM, sebastian wrote:
>>
>>> Hi Gromacs user,
>>>
>>> when I try to extend on of my simulations with
>>>
>>> mdrun -deffnm pdz_cis_NVT_disre_equi_3  -cpi
>>> pdz_cis_NVT_disre_equi_3.cpt -append
>>>
>>> I get the  following error
>>>
>>> Fatal error:
>>> Count mismatch for state entry disre_rm3tav, code count is 0, file count
>>> is 13
>>>
>>> and have no idea whats wrong.
>>>
>>>
>> I tried the same thing for a second simulation and get the same error. It
>> seems
>> that this error is connected with restraints. Extending the same
>> simulation
>> without any restraints everything is working perfectly fine.
>>
>>  Any suggestion is very much appreciated
>>>
>>>
> I would suggest filing a bug report on redmine.gromacs.org.  Please
> include all files necessary to reproduce the problem.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
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Re: [gmx-users] Error when extending simulation

[Justin Lemkul]

On 3/5/13 4:41 AM, sebastian wrote:

On 03/04/2013 09:47 AM, sebastian wrote:

Hi Gromacs user,

when I try to extend on of my simulations with

mdrun -deffnm pdz_cis_NVT_disre_equi_3  -cpi pdz_cis_NVT_disre_equi_3.cpt 
-append

I get the  following error

Fatal error:
Count mismatch for state entry disre_rm3tav, code count is 0, file count is 13

and have no idea whats wrong.



I tried the same thing for a second simulation and get the same error. It seems
that this error is connected with restraints. Extending the same simulation
without any restraints everything is working perfectly fine.


Any suggestion is very much appreciated



I would suggest filing a bug report on redmine.gromacs.org.  Please include all 
files necessary to reproduce the problem.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Error when extending simulation

[sebastian]

On 03/04/2013 09:47 AM, sebastian wrote:

Hi Gromacs user,

when I try to extend on of my simulations with

mdrun -deffnm pdz_cis_NVT_disre_equi_3  -cpi 
pdz_cis_NVT_disre_equi_3.cpt -append


I get the  following error

Fatal error:
Count mismatch for state entry disre_rm3tav, code count is 0, file 
count is 13


and have no idea whats wrong.



I tried the same thing for a second simulation and get the same error. 
It seems that this error is connected with restraints. Extending the 
same simulation without any restraints everything is working perfectly 
fine.



Any suggestion is very much appreciated

Yours

Sebastian


Sebastian again

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[gmx-users] Error when extending simulation

[sebastian]

Hi Gromacs user,

when I try to extend on of my simulations with

mdrun -deffnm pdz_cis_NVT_disre_equi_3  -cpi 
pdz_cis_NVT_disre_equi_3.cpt -append


I get the  following error

Fatal error:
Count mismatch for state entry disre_rm3tav, code count is 0, file count 
is 13


and have no idea whats wrong.

Any suggestion is very much appreciated

Yours

Sebastian
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Re: [gmx-users] error in energy minimzation step

[Justin Lemkul]

On 3/3/13 6:44 AM, az kalsom wrote:

hi ,

while ruuning the COMMAND

g_energy -f em.edr -o potential.xvg

and following the tutorial

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html

  i am getting the following error


Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
---
   1  Bond 2  Angle3  Proper-Dih.  4
Ryckaert-Bell.
   5  LJ-146  Coulomb-14   7  LJ-(SR)  8
Coulomb-(SR)
   9  Coul.-recip.10  Potential   11  Pressure12
Vir-XX
  13  Vir-XY  14  Vir-XZ  15  Vir-YX  16
Vir-YY
  17  Vir-YZ  18  Vir-ZX  19  Vir-ZY  20
Vir-ZZ
  21  Pres-XX 22  Pres-XY 23  Pres-XZ 24
Pres-YX
  25  Pres-YY 26  Pres-YZ 27  Pres-ZX 28
Pres-ZY
  29  Pres-ZZ 30  #Surf*SurfTen   31  Mu-X32
Mu-Y
  33  Mu-Z34  T-rest

10 0
Last energy frame read 1545 time 1952.000

Statistics over 1953 steps [ 0. through 1952. ps ], 1 data sets
All statistics are over 1546 points (frames)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential-2.30149e+06  39000 520034-251635
(kJ/mol)

You may want to use the -driftcorr flag in order to correct
for spurious drift in the graphs. Note that this is not
a substitute for proper equilibration and sampling!
You should select the temperature in order to obtain fluctuation properties.



please help me , what should i change or do to remove error this error



What error?

The average potential energy during EM is also a meaningless quantity, because 
it changes at each step.  A plot of the potential energy will give you an 
indication about convergence, but the average tells you nothing.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] ERROR No default G96Angle types

[Justin Lemkul]

On 3/1/13 3:49 PM, Villarealed wrote:

Dear Gromacs-Users,
I am using Gromos96 43a1 FF extended to include phosphorylated residues.
I have a peptide-capped with 17 aminoacids.
When I tried to add ions to the virtual box
I obtained these error

ERROR 1 [file topol.top, line 566]:
   No default G96Angle types
ERROR 2 [file topol.top, line 801]:
   No default Proper Dih. types

The second error  was resolved by modified the archive "residuetypes.dat".
I only add this line "SEP Protein"
To be honest I don't know how to resolve the ERROR 1.
If someone could help me I will appreciate.
Eduardo


grompp -f ions.mdp -c newbox_solv.gro -p topol.top -o ions.tpr

ERROR 1 [file topol.top, line 566]:
   No default G96Angle types

topol.top

[ angles ]
;  aiajak functc0c1c2
c3
 1 2 3 2

newbox_solc.gro
 1ACE CA1   2.759   1.040   1.830
 1ACE  C2   2.881   1.130   1.839
 1ACE  O3   2.988   1.083   1.878
 2SER  N4   2.872   1.258   1.805

aminoacids.rtp
[ ACE ]
  [ atoms ]
 CA   CH3   0.000 0
  C C   0.380 1
  O O  -0.380 1
  [ bonds ]
  CCA   gb_26
  C O   gb_4
  C+N   gb_9
  [ angles ]
CA C+Nga_18
 O C+Nga_32
  [ impropers ]
 CCA+N Ogi_1



It looks like you are using an old version of Gromacs.  This was a bug that was 
fixed some time ago.  There is a missing angle here:


   CA C Oga_30


ERROR 2 [file topol.top, line 801]:
   No default Proper Dih. types

topol.top
[ dihedrals ]
;  aiajakal functc0c1c2
c3c4c5
72717374 1
H N CACB


There should not be a dihedral assigned here.  It is not specified in the .rtp, 
nor do the Gromos force fields assign dihedrals for H-N-X-X.  The -N-CA- torsion 
is defined by heavy atoms only.  Are you sure the numbering is correct?  The 
numbers listed in topol.top correspond to the [moleculetype] numbering, which is 
not necessarily the same numbering in the coordinate file, if (for example) the 
residue/atom numbering does not start at 1 in the coordinate file.


-Justin


newbox_sol.gro
10SEP  N   71   2.348   2.562   2.883
10SEP  H   72   2.446   2.556   2.863
10SEP CA   73   2.260   2.594   2.768
10SEP CB   74   2.186   2.467   2.720
10SEP OG   75   2.110   2.424   2.827
10SEP  P   76   2.001   2.314   2.797
10SEPO1P   77   2.066   2.200   2.732
10SEPO2P   78   1.949   2.275   2.928
10SEPO3P   79   1.895   2.372   2.710
10SEP  C   80   2.164   2.714   2.789
10SEP  O   81   2.051   2.714   2.741

aminoacids.rtp
[ SEP ]tar -zcvf prog-1-jan-2005.tar.gz /home/jerry/prog
  [ atoms ]
 N N-0.28000 0
 H H 0.28000 0
CA   CH1 0.0 1
CB   CH2 0.0 2
OGOA-0.36000 2
 P P 0.94000 2
   O1POP-0.86000 2
   O2POP-0.86000 2
   O3POP-0.86000 2
 C C   0.380 3
 O O  -0.380 3
  [ bonds ]
 N Hgb_2
 NCAgb_20
CA Cgb_26
 C Ogb_4
 C+Ngb_9
CACBgb_26
CBOGgb_17
OG Pgb_27
 P   O1Pgb_23
 P   O2Pgb_23
 P   O3Pgb_23
  [ angles ]
;  aiajak   gromos type
-C N H ga_31
 H NCA ga_17
-C NCA ga_30
 NCA C ga_12
CA C+N ga_18
CA C O ga_29
 O C+N ga_32
 NCACB ga_12
 CCACB ga_12
CACBOG ga_12
CBOG P ga_25
OG P   O1P ga_13
OG P   O2P ga_13
OG P   O3P ga_13
   O1P P   O2P ga_28
   O1P P   O3P ga_28
   O2P P   O3P ga_28
  [ impropers ]
;  aiajakal   gromos type
 N-CCA H gi_1
 CCA+N O gi_1
CA N CCB gi_2
  [ dihedrals ]
;  aiajakal   gromos type
   -CA-C NCA gd_4
-C NCA C gd_19
 NCA C+N gd_20
 NCACBOG gd_17
CACBOG P gd_14
CBOG P   O1P gd_11





-
Eduardo Villarreal Ramírez
Postdoctoral Research Fellow
Mineralized Tissue Laboratory,
Hospital for Special Surgery.


--
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Sent from the GROMACS Users Forum mailing list archive at Nabble.com.



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

===

[gmx-users] ERROR No default G96Angle types

[Villarealed]

Dear Gromacs-Users,
I am using Gromos96 43a1 FF extended to include phosphorylated residues.
I have a peptide-capped with 17 aminoacids. 
When I tried to add ions to the virtual box
I obtained these error

ERROR 1 [file topol.top, line 566]:
  No default G96Angle types
ERROR 2 [file topol.top, line 801]:
  No default Proper Dih. types

The second error  was resolved by modified the archive "residuetypes.dat". 
I only add this line "SEP Protein"
To be honest I don't know how to resolve the ERROR 1.
If someone could help me I will appreciate.
Eduardo 

 
grompp -f ions.mdp -c newbox_solv.gro -p topol.top -o ions.tpr

ERROR 1 [file topol.top, line 566]:
  No default G96Angle types

topol.top

[ angles ]
;  aiajak functc0c1c2   
c3
1 2 3 2 

newbox_solc.gro
1ACE CA1   2.759   1.040   1.830
1ACE  C2   2.881   1.130   1.839
1ACE  O3   2.988   1.083   1.878
2SER  N4   2.872   1.258   1.805

aminoacids.rtp
[ ACE ]
 [ atoms ]
CA   CH3   0.000 0
 C C   0.380 1
 O O  -0.380 1
 [ bonds ]
 CCA   gb_26
 C O   gb_4
 C+N   gb_9
 [ angles ]
   CA C+Nga_18
O C+Nga_32
 [ impropers ]
CCA+N Ogi_1 

ERROR 2 [file topol.top, line 801]:
  No default Proper Dih. types

topol.top
[ dihedrals ]
;  aiajakal functc0c1c2 
  
c3c4c5
   72717374 1
   H N CACB  
newbox_sol.gro
   10SEP  N   71   2.348   2.562   2.883
   10SEP  H   72   2.446   2.556   2.863
   10SEP CA   73   2.260   2.594   2.768
   10SEP CB   74   2.186   2.467   2.720
   10SEP OG   75   2.110   2.424   2.827
   10SEP  P   76   2.001   2.314   2.797
   10SEPO1P   77   2.066   2.200   2.732
   10SEPO2P   78   1.949   2.275   2.928
   10SEPO3P   79   1.895   2.372   2.710
   10SEP  C   80   2.164   2.714   2.789
   10SEP  O   81   2.051   2.714   2.741

aminoacids.rtp
[ SEP ]tar -zcvf prog-1-jan-2005.tar.gz /home/jerry/prog
 [ atoms ]
N N-0.28000 0
H H 0.28000 0
   CA   CH1 0.0 1
   CB   CH2 0.0 2
   OGOA-0.36000 2
P P 0.94000 2
  O1POP-0.86000 2
  O2POP-0.86000 2
  O3POP-0.86000 2
C C   0.380 3
O O  -0.380 3
 [ bonds ]
N Hgb_2
NCAgb_20   
   CA Cgb_26   
C Ogb_4
C+Ngb_9
   CACBgb_26   
   CBOGgb_17   
   OG Pgb_27
P   O1Pgb_23
P   O2Pgb_23
P   O3Pgb_23
 [ angles ]
;  aiajak   gromos type
   -C N H ga_31   
H NCA ga_17   
   -C NCA ga_30   
NCA C ga_12   
   CA C+N ga_18   
   CA C O ga_29   
O C+N ga_32   
NCACB ga_12   
CCACB ga_12   
   CACBOG ga_12   
   CBOG P ga_25
   OG P   O1P ga_13
   OG P   O2P ga_13
   OG P   O3P ga_13
  O1P P   O2P ga_28
  O1P P   O3P ga_28
  O2P P   O3P ga_28
 [ impropers ]
;  aiajakal   gromos type
N-CCA H gi_1
CCA+N O gi_1
   CA N CCB gi_2
 [ dihedrals ]
;  aiajakal   gromos type
  -CA-C NCA gd_4
   -C NCA C gd_19   
NCA C+N gd_20   
NCACBOG gd_17   
   CACBOG P gd_14   
   CBOG P   O1P gd_11





-
Eduardo Villarreal Ramírez   
Postdoctoral Research Fellow
Mineralized Tissue Laboratory,
Hospital for Special Surgery.


--
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Re: [gmx-users] Error bars - g_wham

[Jochen Hub]

Hi Stephen,

computing errors from umbrella sampling is not trivial at al.

Generally, there are two possibilities:

- If each histogram overlaps only with one neighboring histogram, you 
*must* know the autocorrelation time of each window. This is often a 
problem in MD simulations, because there may be hidden slow transitions. 
In my experience, you always underestimate the autocorrelation time and 
as a consequence the statistical error. However, if you do know the 
autocorrelation time, then you can either (a) compute the PMF from 
blocks of the data (how you did), but this only works if the blocks are 
longer than the autocorrelation time or (b) use "g_wham -bs-method traj" 
to generate new "synthentic" histograms for bootstrapping (which 
incorporate the autocorrelation time). Important: You cannot do 
bootstrapping of complete histograms, because there is only one 
histogram at each window.


- If you have many histograms overlapping each other, or if you did 
umbrella sampling at each window multiple times, you can assume that the 
different histograms represent all possible histograms at the respective 
position of the reaction coordinate. Then, you can do bootstrapping of 
histograms with g_wham -bs-method b-hist. It is not obvious how many 
histograms you need at each position, but maybe 10 is a reasonable number.


Coming to your error from blocks of data (10-30, 30-50, 50-70, 70-100 
ns). The small error you get could mean two things:

a) you have a well-converged PMF (good)
b) you have long autocorrelations. Therefore, the histograms from the 
blocks are similar. Therefore, you underestimate the error (bad).


So you see, it is not trivial to estimate errors from umbrella sampling. 
My experience is that bootstrapping of histograms is more reliable, but 
it requires that you have multiple histograms at each position (and 
these histograms should be uncorrelated!!). But at least, this way you 
do not need to know the autocorrelation times, but instead "only" need 
to generate histograms which are independent. The latter is easier in 
practice, because independent simulations are more likely to be 
uncorrelated than frames *within* one simulation.


I hope this helps a bit.

Cheers,
Jochen


Am 2/19/13 3:22 PM, schrieb Steven Neumann:

Dear Gmx Users,

I run 10 US windows of 100 ns each - ion binding protein. I have a
great convergence of profiles and good windows overlap.I tried to see
PMF profiles from 10-30, 30-50, 50-70, 70-100 ns and they look very
similar (Max. error would be 0.2 kcal/mol). The overal deltaG is about
-5 kcal/mol.

When I use g_wham with -nBootsrap 200 and -bins 200 I get error bars
of -1.2 kcal/mol which is very significant.
How can I impove my error bars? Why they are so large?

Steven



--
---
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
---
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Re: [gmx-users] Error during npt equilibration in coarse grained simulation

[Justin Lemkul]

On 2/26/13 12:51 AM, Anu Chandran wrote:

  Sir,
I have tried Berendsen barostat for Pcoupl. Still I get the same error.



So have a look at the other recommendations on the page I linked.  Thermostat 
instability is just one possibility.  We have had numerous reports, just in the 
last week, of crashes with CG force fields during equilibration (hint: check the 
archives).  You probably need either better minimization or a shorter time step.


-Justin


On Mon, Feb 25, 2013 at 6:58 PM, Justin Lemkul  wrote:




On 2/25/13 12:16 AM, Anu Chandran wrote:


Dear users,
I am trying to do a coarse grained simulation of an octamer of a 350
residue protein in water using gromacs-4.5.3 using martini force field. I
got the following error when i started running NPT equilibration

"Step 32, time 0.64 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 16.561310, max 137.568573 (between atoms 626 and 627)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length

Step 32, time 0.64 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 438.087891, max 3717.233887 (between atoms 580 and 581)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
  626627  121.90.2705  36.7207  0.2650
  621622   90.00.2756   0.4600  0.2700
  624626   91.50.3368 269.7515  0.3300
  621623   90.00.2756   0.3172  0.2700
  620624   90.40.3164 432.6003  0.3100
  622623   90.00.2756   0.3991  0.2700
  618620   85.50.3164 477.1006  0.3100
  626627  121.90.2705  36.7206  0.2650
  615618   88.60.3164 211.2461  0.3100
  607610  141.30.3164  14.3253  0.3100

Step 32, time 0.64 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 134.347206, max 2000.691284 (between atoms 4949 and 4946)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
  610612  149.20.3164  17.6610  0.3100
  612614   89.70.3164   3.1394  0.3100
  614615  150.90.3164   9.9306  0.3100
  615618   88.60.3164 211.1131  0.3100
  618620   85.50.3164 477.0737  0.3100
  620624   90.40.3164 432.5994  0.3100
 4950   4949   75.80.3164 146.5132  0.3100
  624626   91.50.3368 269.7514  0.3300
 4952   4950  118.90.3164  14.6303  0.3100
  468469   90.00.2705  24.6834  0.2650
 4941   4939   90.00.3368   8.5601  0.3300
  585586   61.30.2756   0.3361  0.2700
 4944   4941   82.50.3164 206.9830  0.3100
  586587   90.10.2756   0.3137  0.2700
 4946   4944   90.00.3164 583.5660  0.3100
  606607   90.00.3368   6.6314  0.3300
 4949   4946   90.00.3164 620.5243  0.3100
  580581   91.90.4030 1003.9232  0.2700
 4954   4952   90.30.3164   1.6571  0.3100
  580582   89.80.2756 960.9988  0.2700
  582583   98.60.2756 592.0677  0.2700
  463464   90.00.2654   7.6858  0.2600
  581582   88.80.1280 193.0707  0.2700
  581583   91.30.2254 514.1149  0.2700
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)"


Energy minimization and the NVT equilibration ran without any error or
warning. The mdp file used is as shown below;

title= Martini
define   = -DPOSRES
integrator   = md
dt   = 0.02
nsteps   = 5
nstcomm  = 10
comm-grps=
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 1000
nstenergy= 100
nstxtcout= 1000
xtc_precision= 100
xtc-grps =
energygrps   = Protein W
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.4
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch  = 0.9
rvdw = 1.2
tcoupl   = v-rescale
tc-grps  = System
tau_t= 1.0
ref_t= 300
Pcoupl   = parrinello-rahman
Pcoupltype   = isotropic
tau_p= 5.0
compressibility  = 3e-4
ref_p= 1.0
gen_vel  = yes



If you ran NVT previously, regenerating velocities defeats that purpose
and perturbs the system unnecessarily.  Further, Parrinello-Rahman is not
very stabl

Re: [gmx-users] Error during npt equilibration in coarse grained simulation

[Anu Chandran]

 Sir,
I have tried Berendsen barostat for Pcoupl. Still I get the same error.

Thank you,

 regards,
 Anu


On Mon, Feb 25, 2013 at 6:58 PM, Justin Lemkul  wrote:

>
>
> On 2/25/13 12:16 AM, Anu Chandran wrote:
>
>> Dear users,
>> I am trying to do a coarse grained simulation of an octamer of a 350
>> residue protein in water using gromacs-4.5.3 using martini force field. I
>> got the following error when i started running NPT equilibration
>>
>> "Step 32, time 0.64 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 16.561310, max 137.568573 (between atoms 626 and 627)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>
>> Step 32, time 0.64 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 438.087891, max 3717.233887 (between atoms 580 and 581)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>  626627  121.90.2705  36.7207  0.2650
>>  621622   90.00.2756   0.4600  0.2700
>>  624626   91.50.3368 269.7515  0.3300
>>  621623   90.00.2756   0.3172  0.2700
>>  620624   90.40.3164 432.6003  0.3100
>>  622623   90.00.2756   0.3991  0.2700
>>  618620   85.50.3164 477.1006  0.3100
>>  626627  121.90.2705  36.7206  0.2650
>>  615618   88.60.3164 211.2461  0.3100
>>  607610  141.30.3164  14.3253  0.3100
>>
>> Step 32, time 0.64 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 134.347206, max 2000.691284 (between atoms 4949 and 4946)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>  610612  149.20.3164  17.6610  0.3100
>>  612614   89.70.3164   3.1394  0.3100
>>  614615  150.90.3164   9.9306  0.3100
>>  615618   88.60.3164 211.1131  0.3100
>>  618620   85.50.3164 477.0737  0.3100
>>  620624   90.40.3164 432.5994  0.3100
>> 4950   4949   75.80.3164 146.5132  0.3100
>>  624626   91.50.3368 269.7514  0.3300
>> 4952   4950  118.90.3164  14.6303  0.3100
>>  468469   90.00.2705  24.6834  0.2650
>> 4941   4939   90.00.3368   8.5601  0.3300
>>  585586   61.30.2756   0.3361  0.2700
>> 4944   4941   82.50.3164 206.9830  0.3100
>>  586587   90.10.2756   0.3137  0.2700
>> 4946   4944   90.00.3164 583.5660  0.3100
>>  606607   90.00.3368   6.6314  0.3300
>> 4949   4946   90.00.3164 620.5243  0.3100
>>  580581   91.90.4030 1003.9232  0.2700
>> 4954   4952   90.30.3164   1.6571  0.3100
>>  580582   89.80.2756 960.9988  0.2700
>>  582583   98.60.2756 592.0677  0.2700
>>  463464   90.00.2654   7.6858  0.2600
>>  581582   88.80.1280 193.0707  0.2700
>>  581583   91.30.2254 514.1149  0.2700
>> Wrote pdb files with previous and current coordinates
>> Wrote pdb files with previous and current coordinates
>> Segmentation fault (core dumped)"
>>
>>
>> Energy minimization and the NVT equilibration ran without any error or
>> warning. The mdp file used is as shown below;
>>
>> title= Martini
>> define   = -DPOSRES
>> integrator   = md
>> dt   = 0.02
>> nsteps   = 5
>> nstcomm  = 10
>> comm-grps=
>> nstxout  = 0
>> nstvout  = 0
>> nstfout  = 0
>> nstlog   = 1000
>> nstenergy= 100
>> nstxtcout= 1000
>> xtc_precision= 100
>> xtc-grps =
>> energygrps   = Protein W
>> nstlist  = 10
>> ns_type  = grid
>> pbc  = xyz
>> rlist= 1.4
>> coulombtype  = Shift
>> rcoulomb_switch  = 0.0
>> rcoulomb = 1.2
>> epsilon_r= 15
>> vdw_type = Shift
>> rvdw_switch  = 0.9
>> rvdw = 1.2
>> tcoupl   = v-rescale
>> tc-grps  = System
>> tau_t= 1.0
>> ref_t= 300
>> Pcoupl   = parrinello-rahman
>> Pcoupltype   = isotropic
>> tau_p= 5.0
>> compressibility  = 3e-4
>> ref_p= 1.0
>> gen_vel  = yes
>>
>
> If you ran NVT previously, regenerating velocities defeats that purpose
> and perturbs the system unnecessarily.  Further, Parrinello-Rahman is not
> very stable for initial equilibration; use Berendsen and then switch to P-R
> for data collec

Re: [gmx-users] Error during npt equilibration in coarse grained simulation

[Justin Lemkul]

On 2/25/13 12:16 AM, Anu Chandran wrote:

Dear users,
I am trying to do a coarse grained simulation of an octamer of a 350
residue protein in water using gromacs-4.5.3 using martini force field. I
got the following error when i started running NPT equilibration

"Step 32, time 0.64 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 16.561310, max 137.568573 (between atoms 626 and 627)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length

Step 32, time 0.64 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 438.087891, max 3717.233887 (between atoms 580 and 581)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 626627  121.90.2705  36.7207  0.2650
 621622   90.00.2756   0.4600  0.2700
 624626   91.50.3368 269.7515  0.3300
 621623   90.00.2756   0.3172  0.2700
 620624   90.40.3164 432.6003  0.3100
 622623   90.00.2756   0.3991  0.2700
 618620   85.50.3164 477.1006  0.3100
 626627  121.90.2705  36.7206  0.2650
 615618   88.60.3164 211.2461  0.3100
 607610  141.30.3164  14.3253  0.3100

Step 32, time 0.64 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 134.347206, max 2000.691284 (between atoms 4949 and 4946)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 610612  149.20.3164  17.6610  0.3100
 612614   89.70.3164   3.1394  0.3100
 614615  150.90.3164   9.9306  0.3100
 615618   88.60.3164 211.1131  0.3100
 618620   85.50.3164 477.0737  0.3100
 620624   90.40.3164 432.5994  0.3100
4950   4949   75.80.3164 146.5132  0.3100
 624626   91.50.3368 269.7514  0.3300
4952   4950  118.90.3164  14.6303  0.3100
 468469   90.00.2705  24.6834  0.2650
4941   4939   90.00.3368   8.5601  0.3300
 585586   61.30.2756   0.3361  0.2700
4944   4941   82.50.3164 206.9830  0.3100
 586587   90.10.2756   0.3137  0.2700
4946   4944   90.00.3164 583.5660  0.3100
 606607   90.00.3368   6.6314  0.3300
4949   4946   90.00.3164 620.5243  0.3100
 580581   91.90.4030 1003.9232  0.2700
4954   4952   90.30.3164   1.6571  0.3100
 580582   89.80.2756 960.9988  0.2700
 582583   98.60.2756 592.0677  0.2700
 463464   90.00.2654   7.6858  0.2600
 581582   88.80.1280 193.0707  0.2700
 581583   91.30.2254 514.1149  0.2700
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)"


Energy minimization and the NVT equilibration ran without any error or
warning. The mdp file used is as shown below;

title= Martini
define   = -DPOSRES
integrator   = md
dt   = 0.02
nsteps   = 5
nstcomm  = 10
comm-grps=
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 1000
nstenergy= 100
nstxtcout= 1000
xtc_precision= 100
xtc-grps =
energygrps   = Protein W
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.4
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch  = 0.9
rvdw = 1.2
tcoupl   = v-rescale
tc-grps  = System
tau_t= 1.0
ref_t= 300
Pcoupl   = parrinello-rahman
Pcoupltype   = isotropic
tau_p= 5.0
compressibility  = 3e-4
ref_p= 1.0
gen_vel  = yes


If you ran NVT previously, regenerating velocities defeats that purpose and 
perturbs the system unnecessarily.  Further, Parrinello-Rahman is not very 
stable for initial equilibration; use Berendsen and then switch to P-R for data 
collection.



gen_temp = 300
gen_seed = 473529
constraints  = none
constraint_algorithm = Lincs
unconstrained_start  = no
lincs_order  = 4
lincs_warnangle  = 30

Also the water box after energy minimization showed some gaps towards the
edge of the box when visualized using VMD.


can anybody please help me on how to overcome this error?



In addition to the above, see the standard advice for unstable s

[gmx-users] Error during npt equilibration in coarse grained simulation

[Anu Chandran]

Dear users,
I am trying to do a coarse grained simulation of an octamer of a 350
residue protein in water using gromacs-4.5.3 using martini force field. I
got the following error when i started running NPT equilibration

"Step 32, time 0.64 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 16.561310, max 137.568573 (between atoms 626 and 627)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 32, time 0.64 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 438.087891, max 3717.233887 (between atoms 580 and 581)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
626627  121.90.2705  36.7207  0.2650
621622   90.00.2756   0.4600  0.2700
624626   91.50.3368 269.7515  0.3300
621623   90.00.2756   0.3172  0.2700
620624   90.40.3164 432.6003  0.3100
622623   90.00.2756   0.3991  0.2700
618620   85.50.3164 477.1006  0.3100
626627  121.90.2705  36.7206  0.2650
615618   88.60.3164 211.2461  0.3100
607610  141.30.3164  14.3253  0.3100

Step 32, time 0.64 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 134.347206, max 2000.691284 (between atoms 4949 and 4946)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
610612  149.20.3164  17.6610  0.3100
612614   89.70.3164   3.1394  0.3100
614615  150.90.3164   9.9306  0.3100
615618   88.60.3164 211.1131  0.3100
618620   85.50.3164 477.0737  0.3100
620624   90.40.3164 432.5994  0.3100
   4950   4949   75.80.3164 146.5132  0.3100
624626   91.50.3368 269.7514  0.3300
   4952   4950  118.90.3164  14.6303  0.3100
468469   90.00.2705  24.6834  0.2650
   4941   4939   90.00.3368   8.5601  0.3300
585586   61.30.2756   0.3361  0.2700
   4944   4941   82.50.3164 206.9830  0.3100
586587   90.10.2756   0.3137  0.2700
   4946   4944   90.00.3164 583.5660  0.3100
606607   90.00.3368   6.6314  0.3300
   4949   4946   90.00.3164 620.5243  0.3100
580581   91.90.4030 1003.9232  0.2700
   4954   4952   90.30.3164   1.6571  0.3100
580582   89.80.2756 960.9988  0.2700
582583   98.60.2756 592.0677  0.2700
463464   90.00.2654   7.6858  0.2600
581582   88.80.1280 193.0707  0.2700
581583   91.30.2254 514.1149  0.2700
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)"


Energy minimization and the NVT equilibration ran without any error or
warning. The mdp file used is as shown below;

title= Martini
define   = -DPOSRES
integrator   = md
dt   = 0.02
nsteps   = 5
nstcomm  = 10
comm-grps=
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 1000
nstenergy= 100
nstxtcout= 1000
xtc_precision= 100
xtc-grps =
energygrps   = Protein W
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.4
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch  = 0.9
rvdw = 1.2
tcoupl   = v-rescale
tc-grps  = System
tau_t= 1.0
ref_t= 300
Pcoupl   = parrinello-rahman
Pcoupltype   = isotropic
tau_p= 5.0
compressibility  = 3e-4
ref_p= 1.0
gen_vel  = yes
gen_temp = 300
gen_seed = 473529
constraints  = none
constraint_algorithm = Lincs
unconstrained_start  = no
lincs_order  = 4
lincs_warnangle  = 30

Also the water box after energy minimization showed some gaps towards the
edge of the box when visualized using VMD.


can anybody please help me on how to overcome this error?


Thank you,
with regards,
Anu
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Re: [gmx-users] error in editconf

[Justin Lemkul]

On 2/19/13 4:53 AM, az kalsom wrote:

hi all,

i generated the ligand topology file by prodrg server and then i generated
the .out file from gaussain software aund used itp adjuster to adjsut the
charges in ligand itp file

but still i am getting the bad box error when i run the editconf command

why is this so what should i do to correct this ?



"Bad box" errors usually mean you don't have box vectors in the coordinate file 
or that the number of atoms specified in the .gro file is incorrect, leading to 
editconf reading a coordinate entry as box vectors.  Without the first 2 lines 
and last line of the .gro file, as well as the output of wc -l on the file, it's 
impossible to say what the real problem is.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Error Esitmation of replicates

[ravi sharma]

Dear all,


We have run of three temperatures simulation (unfolding) and three replicates 
of them. we are interested to calculate the experimental errors.
anyone has idea how do it?


regards,
Ravi

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Re: [gmx-users] Error in BlueGene

[Cintia C. Vequi-Suplicy]

Hello,

I am writing just to tell how the problem was solved.

I contact a person that works with the BlueGene cluster and he installed 
the Gromacs 4.6 in the cluster.
And all my problems were solved. I did not get the same error over and 
over again.


Apparently, it was some problem with the 4.5.5 version.

Thank you all for your help, I learned a lot with all the suggestions.

Cíntia


On 05/02/2013 13:10, Cintia C. Vequi-Suplicy wrote:

Mark,

Thank you for your answer.

I have already tried to run with several numbers of processors from 8 
to 512 and I always got the same error.


And I transfer the simulation to the BlueGene in two different ways. 
In both ways, I got the same error.

They were the following:

1) only using the .gro file after the simulation on my local cluster 
with the velocities, generate a new .tpr using the md.mdp I sent 
before. And the use this .tpr file to run in the bluegene. The 
commands were these:


grompp -f md.mdp -c min_dppc.gro  -p dppc512.top -o dppc10ns.tpr 
/*(this was done in my computer)


and then in the bgp, I submitted the following script:

#@ job_name = dppc_001ps
#@ comment = "bilayer continuacao gauss com cpi"
#@ error = $(job_name).$(jobid).out
#@ output = $(job_name).$(jobid).out
#@ environment = COPY_ALL
#@ wall_clock_limit = 80:00:00
#@ notification = error
#@ job_type = bluegene
#@ class = compute
#@ bg_size = 128
#@ queue

/bgsys/drivers/ppcfloor/bin/mpirun -np 512 -exe 
/opt/apps/gromacs/4.5.5/bin/mdrun -args " -s dppc10.tpr -v" -mode VN



2) I used the .tpr and the state.cpt from the simulation on my local 
cluster to restart the simulation on the bluegene with more nodes. And 
the script I used  was:


#@ job_name = gromacs_dppc
#@ comment = "bilayer"
#@ error = $(job_name).$(jobid).out
#@ output = $(job_name).$(jobid).out
#@ environment = COPY_ALL
#@ wall_clock_limit = 80:00:00
#@ notification = error
#@ job_type = bluegene
#@ class = compute
#@ bg_size = 128
#@ queue

/bgsys/drivers/ppcfloor/bin/mpirun -np 512 -exe 
/opt/apps/gromacs/4.5.5/bin/mdrun -args "-cpi state.cpt -s 
dppc_min.tpr -v " -mode VN



In both ways, I got the same error.

Cheers,
Cíntia


md.mdp

integrator   = md
tinit= 0.0
dt   = 0.002
nsteps   = 500
nstcomm  = 5
comm-grps= Other SOL

nstxout  = 1000
nstvout  = 1000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 1000
xtc-grps =
energygrps   = Other SOL

nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.4

coulombtype  = reaction-field
rcoulomb = 1.4
epsilon_rf   = 66

vdw_type = cut-off
rvdw = 1.4
DispCorr = No

tcoupl   = v-rescale
tc-grps  = Other SOL
tau_t= 0.4 0.4
ref_t= 296 296

Pcoupl   = berendsen
Pcoupltype   = semiisotropic
tau_p= 0.2 0.2
compressibility  = 4.51e-5 4.51e-5
ref_p= 1.0 1.0

constraints  = hbonds
constraint_algorithm = lincs



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Re: [gmx-users] Error: The Y-size of the box times the triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

[Justin Lemkul]

On 2/12/13 5:24 PM, Sonia Aguilera wrote:

Hi,

I was performing a NPT calculation, and I got this error:

The Y-size of the box (6.002812) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (1.000605)

I also tried to change the number of processors but I got the same error. My
system is a protein in vacuo. This is my mdp file (Taken from Justin
Lemkul's tutorial for FE calculations:

title= NPT equilibration
; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.002
nsteps   = 20; 00 ps
nstcomm  = 100
;Langevin dynamics
ld_seed  = -1
; Output control
nstxout  = 1000
nstvout  = 1000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 0
xtc-precision= 1000
; Neighborsearching and short-range nonbonded interactions
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.5
; Electrostatics
coulombtype  = PME
rcoulomb = 1.5
; van der Waals
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t= 1.0
ref_t= 300
; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman
tau_p= 0.5
compressibility  = 4.5e-05
ref_p= 1.0
; Do not generate velocities
gen_vel  = no
; options for bonds
constraints  = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Constrain the starting configuration
; since we are continuing from NVT
continuation = yes
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12


Can you please tell my what is wrong? I runned previous nvt, npt and md
simulation with the same box size and protein but in water. Is there any way
of solving this problem without affecting the accuracy of the simulation?



NPT doesn't make sense in vacuo.  The unit cell compresses around the protein, 
leaving you with periodicity artifacts and a quasi-crystalline environment.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Error: The Y-size of the box times the triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

[Sonia Aguilera]

Hi, 

I was performing a NPT calculation, and I got this error:

The Y-size of the box (6.002812) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (1.000605)

I also tried to change the number of processors but I got the same error. My
system is a protein in vacuo. This is my mdp file (Taken from Justin
Lemkul's tutorial for FE calculations:

title= NPT equilibration
; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.002
nsteps   = 20; 00 ps
nstcomm  = 100
;Langevin dynamics
ld_seed  = -1
; Output control
nstxout  = 1000
nstvout  = 1000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 0
xtc-precision= 1000
; Neighborsearching and short-range nonbonded interactions
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.5
; Electrostatics
coulombtype  = PME
rcoulomb = 1.5
; van der Waals
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t= 1.0
ref_t= 300
; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman
tau_p= 0.5
compressibility  = 4.5e-05
ref_p= 1.0
; Do not generate velocities
gen_vel  = no
; options for bonds
constraints  = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Constrain the starting configuration
; since we are continuing from NVT
continuation = yes
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12


Can you please tell my what is wrong? I runned previous nvt, npt and md
simulation with the same box size and protein but in water. Is there any way
of solving this problem without affecting the accuracy of the simulation?

Thank you in advance

Sonia Aguilera





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Re: [gmx-users] error in md.log files

[Justin Lemkul]

On 2/12/13 10:29 AM, vidhya sankar wrote:

Dear Justin Thank you for your reply,


I have set the Restraint  Along the Z Axis .  as follows

#ifdef POSRES_WATER
  ; Position restraint for each water oxygen
[ position_restraints ]
   i  funct   fcxfcyfcz
   11 0   0  100
   #endif


Are you using the correct define statement in the .mdp file, and is your #ifdef 
in the correct location in the topology ?

As you have Asked  above in previous mail i have used the

define=  -DPOSRES  -DPOSRES_WATERin my .mdp file  My question is


1) Should i use  -DPOSRES_WATER  statement or Not  in .mdp file  ?



If you want the restraint, then yes.  This seems correct.



Also I have used the #ifdef  statement in the correct location in the topology  
as follows

.

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
110  0 10
#endif


; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"



2) in  My md.log files  I have got following Lines At The end of Every 100 
steps  While it runs Smoothly Without Any Error .

Large VCM(group NA): -0.01457, -0.01793, -0.03262, Temp-cm: 
 inf
Large VCM(group NA): -0.00894, -0.07417, -0.08968, Temp-cm: 
 inf
Large VCM(group NA):  0.00260, -0.05862, -0.10835, Temp-cm: 
 inf
Large VCM(group NA):  0.02240,  0.06127, -0.08617, Temp-cm: 
 inf
Large VCM(group NA):  0.11406,  0.11506, -0.07386, Temp-cm: 
 inf
Large VCM(group NA):  0.16859,  0.05669, -0.03958, Temp-cm: 
 inf
Large VCM(group NA):  0.07832, -0.04243, -0.02288, Temp-cm: 
 inf
Large VCM(group NA): -0.05293, -0.02293, -0.03210, Temp-cm: 
 inf
Large VCM(group NA):  0.01289,  0.09823, -0.02071, Temp-cm: 
 inf
Large VCM(group NA):  0.09863,  0.18033,  0.03704, Temp-cm: 
 inf
Large VCM(group NA):  0.01632,  0.22306,  0.04888, Temp-cm: 
 inf
Large VCM(group NA): -0.04317,  0.22376, -0.02476, Temp-cm: 
 inf
Large VCM(group NA):  0.08154,  0.19584, -0.06280, Temp-cm: 
 inf
Large VCM(group NA):  0.23298,  0.14145,  0.00921, Temp-cm: 
 inf
Large VCM(group NA):  0.22764,  0.09442,  0.07858, Temp-cm: 
 inf
Large VCM(group NA):  0.09441,  0.07206,  0.02138, Temp-cm: 
 inf
Large VCM(group NA):  0.00187,  0.04563, -0.03987, Temp-cm: 
 inf
Large VCM(group NA):  0.05896,  0.00550,  0.02418, Temp-cm: 
 inf
Large VCM(group NA):  0.2,  0.04126,  0.11459, Temp-cm: 
 inf
DD  step 5199  vol min/aver 0.821  load imb.: force  1.3%

How to Eliminate The Above error ?



"Group NA" seems to imply that you are coupling solvent and ions to separate 
thermostats, which is a terrible idea.  The ions are moving separately from 
water and they are crashing into one another.  You may have to restrain the ions 
in some way if you are also restraining water to prevent such collisions.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] error in md.log files

[vidhya sankar]

Dear Justin Thank you for your reply,


   I have set the Restraint  Along the Z Axis .  as follows

#ifdef POSRES_WATER
 ; Position restraint for each water oxygen
   [ position_restraints ]
      i  funct       fcx        fcy        fcz
      1    1         0           0      100
  #endif


Are you using the correct define statement in the .mdp file, and is your #ifdef 
in the correct location in the topology ?

As you have Asked  above in previous mail i have used the 

define        =  -DPOSRES  -DPOSRES_WATER    in my .mdp file  My question is 


1) Should i use  -DPOSRES_WATER  statement or Not  in .mdp file  ?


Also I have used the #ifdef  statement in the correct location in the topology  
as follows 

.  

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcx    fcy    fcz
   1    1    0  0 10
#endif


; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"



2) in  My md.log files  I have got following Lines At The end of Every 100 
steps  While it runs Smoothly Without Any Error . 

Large VCM(group NA): -0.01457, -0.01793, -0.03262, Temp-cm: 
 inf
Large VCM(group NA): -0.00894, -0.07417, -0.08968, Temp-cm: 
 inf
Large VCM(group NA):  0.00260, -0.05862, -0.10835, Temp-cm: 
 inf
Large VCM(group NA):  0.02240,  0.06127, -0.08617, Temp-cm: 
 inf
Large VCM(group NA):  0.11406,  0.11506, -0.07386, Temp-cm: 
 inf
Large VCM(group NA):  0.16859,  0.05669, -0.03958, Temp-cm: 
 inf
Large VCM(group NA):  0.07832, -0.04243, -0.02288, Temp-cm: 
 inf
Large VCM(group NA): -0.05293, -0.02293, -0.03210, Temp-cm: 
 inf
Large VCM(group NA):  0.01289,  0.09823, -0.02071, Temp-cm: 
 inf
Large VCM(group NA):  0.09863,  0.18033,  0.03704, Temp-cm: 
 inf
Large VCM(group NA):  0.01632,  0.22306,  0.04888, Temp-cm: 
 inf
Large VCM(group NA): -0.04317,  0.22376, -0.02476, Temp-cm: 
 inf
Large VCM(group NA):  0.08154,  0.19584, -0.06280, Temp-cm: 
 inf
Large VCM(group NA):  0.23298,  0.14145,  0.00921, Temp-cm: 
 inf
Large VCM(group NA):  0.22764,  0.09442,  0.07858, Temp-cm: 
 inf
Large VCM(group NA):  0.09441,  0.07206,  0.02138, Temp-cm: 
 inf
Large VCM(group NA):  0.00187,  0.04563, -0.03987, Temp-cm: 
 inf
Large VCM(group NA):  0.05896,  0.00550,  0.02418, Temp-cm: 
 inf
Large VCM(group NA):  0.2,  0.04126,  0.11459, Temp-cm: 
 inf
DD  step 5199  vol min/aver 0.821  load imb.: force  1.3%

How to Eliminate The Above error ?

Thanks In Advance
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Re: [gmx-users] Error- Simulation box resizes during mdrun

[Justin Lemkul]

On 2/6/13 11:52 AM, Bharath K. Srikanth wrote:

Hi everyone,

Today, I was attempting a simulation of a system with a lipid bilayer, and
the size of my simulation box, obtained from a previous simulation, was 15
nm x 7.5 nm x 7.5 nm (15 nm being the direction perpendicular to the plane
of the bilayer). The bilayer consisted of 128 DOPC lipids and was located
at the centre of the box. I used periodic boundary conditions in all three
directions.

I then resized the box to 7.5 nm in all directions, using the editconf
-box option. After doing the requisite energy minimization steps, I ran
the simulation using mdrun. However, running the simulation caused the box
to gradually shrink in the y-direction (parallel to the plane of the
bilayer!) during the simulation, ultimately settling at around half the
original dimension. Is there anything I may have done that could cause
this effect? I'm thoroughly baffled.



What do you mean by "resized the box?"  Did you strip out water, adjust box 
vectors, re-solvate, equilibrate, etc?  What you're describing is very weird; 
pictures, plots, etc would help a lot here.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Error- Simulation box resizes during mdrun

[Bharath K. Srikanth]

Hi everyone,

Today, I was attempting a simulation of a system with a lipid bilayer, and
the size of my simulation box, obtained from a previous simulation, was 15
nm x 7.5 nm x 7.5 nm (15 nm being the direction perpendicular to the plane
of the bilayer). The bilayer consisted of 128 DOPC lipids and was located
at the centre of the box. I used periodic boundary conditions in all three
directions.

I then resized the box to 7.5 nm in all directions, using the editconf
-box option. After doing the requisite energy minimization steps, I ran
the simulation using mdrun. However, running the simulation caused the box
to gradually shrink in the y-direction (parallel to the plane of the
bilayer!) during the simulation, ultimately settling at around half the
original dimension. Is there anything I may have done that could cause
this effect? I'm thoroughly baffled.

Thanks!

Regards
Bharath

-- 
Bharath K Srikanth
IV Year B.Tech
Dept. of Chemical Engineering
Indian Institute of Technology, Guwahati
Ph: (+91) 88762 03224
E.mail: s.bhar...@iitg.ernet.in
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Re: [gmx-users] error in running command

[Justin Lemkul]

On 2/5/13 9:04 AM, Arunima Shilpi wrote:

Dear Sir/ Madam

I am using gromacs for simulation and has the following while running the command for 
"grompp"
Expected integer argument for option -maxwarn "".

I do not want use maxwarn to bypass the error.

I request you to kindly help me out to debug the error.


If you don't want to use -maxwarn, then omit it from your command.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Error in BlueGene

[Cintia C. Vequi-Suplicy]

Mark,

Thank you for your answer.

I have already tried to run with several numbers of processors from 8 to 
512 and I always got the same error.


And I transfer the simulation to the BlueGene in two different ways. In 
both ways, I got the same error.

They were the following:

1) only using the .gro file after the simulation on my local cluster 
with the velocities, generate a new .tpr using the md.mdp I sent before. 
And the use this .tpr file to run in the bluegene. The commands were these:


grompp -f md.mdp -c min_dppc.gro  -p dppc512.top -o dppc10ns.tpr /*(this 
was done in my computer)


and then in the bgp, I submitted the following script:

#@ job_name = dppc_001ps
#@ comment = "bilayer continuacao gauss com cpi"
#@ error = $(job_name).$(jobid).out
#@ output = $(job_name).$(jobid).out
#@ environment = COPY_ALL
#@ wall_clock_limit = 80:00:00
#@ notification = error
#@ job_type = bluegene
#@ class = compute
#@ bg_size = 128
#@ queue

/bgsys/drivers/ppcfloor/bin/mpirun -np 512 -exe 
/opt/apps/gromacs/4.5.5/bin/mdrun -args " -s dppc10.tpr -v" -mode VN



2) I used the .tpr and the state.cpt from the simulation on my local 
cluster to restart the simulation on the bluegene with more nodes. And 
the script I used  was:


#@ job_name = gromacs_dppc
#@ comment = "bilayer"
#@ error = $(job_name).$(jobid).out
#@ output = $(job_name).$(jobid).out
#@ environment = COPY_ALL
#@ wall_clock_limit = 80:00:00
#@ notification = error
#@ job_type = bluegene
#@ class = compute
#@ bg_size = 128
#@ queue

/bgsys/drivers/ppcfloor/bin/mpirun -np 512 -exe 
/opt/apps/gromacs/4.5.5/bin/mdrun -args "-cpi state.cpt -s dppc_min.tpr 
-v " -mode VN



In both ways, I got the same error.

Cheers,
Cíntia


md.mdp

integrator   = md
tinit= 0.0
dt   = 0.002
nsteps   = 500
nstcomm  = 5
comm-grps= Other SOL

nstxout  = 1000
nstvout  = 1000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 1000
xtc-grps =
energygrps   = Other SOL

nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.4

coulombtype  = reaction-field
rcoulomb = 1.4
epsilon_rf   = 66

vdw_type = cut-off
rvdw = 1.4
DispCorr = No

tcoupl   = v-rescale
tc-grps  = Other SOL
tau_t= 0.4 0.4
ref_t= 296 296

Pcoupl   = berendsen
Pcoupltype   = semiisotropic
tau_p= 0.2 0.2
compressibility  = 4.51e-5 4.51e-5
ref_p= 1.0 1.0

constraints  = hbonds
constraint_algorithm = lincs

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[gmx-users] error in running command

[Arunima Shilpi]

Dear Sir/ Madam

I am using gromacs for simulation and has the following while running the 
command for "grompp"
Expected integer argument for option -maxwarn "". 

I do not want use maxwarn to bypass the error.

I request you to kindly help me out to debug the error.
Regards
Arunima

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Re: [gmx-users] Error in BlueGene

[Mark Abraham]

On Mon, Feb 4, 2013 at 5:18 PM, Cintia C. Vequi-Suplicy wrote:

>
>
>
> Hello David,
>
> I think it is the pressure.
>

I would think the mentions of pressure are just one of the symptoms. See
http://www.gromacs.org/Documentation/Terminology/Blowing_Up.

You seem to have somewhat more than 100K atoms, which is a bit over 200
atoms/processor for 512 processors. That's down the low end of GROMACS
scaling limits. I asked you earlier to try running with the same number of
processors on the BlueGene as you do locally, and to report the command
lines you were using for the whole transfer and restart process. This will
allow us to see if the problem is in how DD is treating your system, or how
you are managing the transfer between hardware. Until then, nobody can tell
anything.

Mark
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Re: [gmx-users] Error in BlueGene

[Cintia C. Vequi-Suplicy]

Hello David,

I think it is the pressure.

Because the error starts with the message below.
But this only happens in the BlueGene cluster. In my local cluster it is
running fine for 60 ns.

Thank you,
Cintia

vol 0.71  imb F  1% vol 0.74  imb F  1% vol 0.73  imb F  1% vol 0.75
imb F  1% vol 0.74  vol 0.75  vol 0.74  vol 0.73  imb F  1% imb F  1%
imb F  1% imb F  1% step 3400, will finish Sat Feb  2 08:09:38 2013
vol 0.70  imb F  1% vol 0.75  vol 0.74  vol 0.74  vol 0.74  vol 0.73
imb F  1% imb F  1% imb F  1% imb F  1% imb F  1% vol 0.74 imb F  1% vol
0.73  imb F  1% step 3500, will finish Sat Feb  2 08:07:49 2013
vol 0.73  imb F  1% vol 0.71  imb F  1% vol 0.74  imb F  1% vol 0.74
vol 0.74  imb F  1% vol 0.74  imb F  1% imb F  1% vol 0.75 imb F  1% vol
0.74  imb F  1% step 3600, will finish Sat Feb  2 08:06:01 2013
Warning: 1-4 interaction between 7552 and 7556 at distance 6.386 which
is larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38174 1.38174
1.4951

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38167 1.38167
1.49502

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38127 1.38127
1.49449

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38206 1.38206
1.49552

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38219 1.38219
1.49569

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38212 1.38212
1.4956

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38215 1.38215
1.49563

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38223 1.38223
1.49573

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38228 1.38228
1.4958

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38227 1.38227
1.49578

Step 3616  Warning: pressure scaling more than 1%, mu: 1.37921 1.37921
1.49181

Step 3616  Warning: pressure scaling more than 1%, mu: 1.3794 1.3794 1.49206

Step 3616  Warning: pressure scaling more than 1%, mu: 1.37967 1.37967
1.49242

Step 3616  Warning: pressure scaling more than 1%, mu: 1.37928 1.37928
1.49191

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38003 1.38003
1.49289

Step 3616  Warning: pressure scaling more than 1%, mu: 1.37973 1.37973
1.4925

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38187 1.38187
1.49527

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38164 1.38164
1.49498

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38183 1.38183
1.49522

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38181 1.38181
1.4952

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38222 1.38222
1.49572

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38229 1.38229
1.49582

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38234 1.38234
1.49588

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38216 1.38216
1.49564

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38221 1.38221
1.49571

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38226 1.38226
1.49578

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38226 1.38226
1.49577

Step 3616  Warning: pressure scaling more than 1%, mu: 1.3822 1.3822 1.4957

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38241 1.38241
1.49597

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38218 1.38218
1.49568

Step 3616  Warning: pressure scaling more than 1%, mu: 1.3822 1.3822 1.4957

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38213 1.38213
1.49561

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38213 1.38213
1.49561

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38221 1.38221
1.49571

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38222 1.38222
1.49573

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38229 1.38229
1.49581

Step 3616  Warning: pressure scaling more than 1%, mu: 1.37951 1.37951
1.49221

Step 3616  Warning: pressure scaling more than 1%, mu: 1.3815 1.3815 1.49479

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38153 1.38153
1.49483

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38153 1.38153
1.49483

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38215 1.38215
1.49564

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38225 1.38225
1.49576

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38228 1.38228
1.4958

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38226 1.38226
1.49577

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38216 1.38216
1.49565

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38229 1.38229
1.49581

Step 3616  Warning: pressure scaling more than 1%, mu: 1.3823 1.3823 1.49582

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38226 1.38226
1.49578

Step 3616  Warning: pressure sc

Re: [gmx-users] Error in BlueGene

[Ricardo O. S. Soares]

Hello Cíntia,






On 02/01/2013 04:19 PM, Cintia C. Vequi-Suplicy wrote:

Hello Ricardo,

I tried to decrease the integration time but I got the same error.
The system is running fine in my local core.

I have two questions:

1) What do you mean by "I balance the domain decomposition for the 
larger number of core"?


When you run at your local hardware, the 8 cores handles your system 
differently than the 1024, 2048  (or more) cores in bluegene. So you 
must balance the number of cores with your system size. If you try to 
run a small system in too many cores, an error may appear:


http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

So you must decrease their number, or assign different numbers of cores 
only for PME (mdrun options). There's also the scalability/performance 
issue






2) Are you running simulations at Bluegene P at Rice University?



Yes!


Thank you,
Cíntia


On 30/01/2013 20:48, Ricardo Soares wrote:

Hello,

before submitting to Bluegene, I always test the system in my local 8 
core
cpu, and if it works, it will also work in Bluegene, as long as I 
balance the
domain decomposition for the larger number of cores. If your system 
insists in

exploding, even after energy minimization, you could try to decrease the
integration timestep (dt) to something lower than 2 fs, maybe to 1fs 
or, in

some cases even 0.5 fs. Did you tried that?

Cheers,

Ricardo.



On Wed, 30 Jan 2013 15:44:53 -0200, Cintia C. Vequi-Suplicy wrote

Mark,

Thank you for your answer.

I did an energy minimization with the file em.mdp (below) and then I
did a  40 ns simulation with the same md.mdp I send before. These
two steps were done in my local cluster. After that I took the
configuration for the simulation in the bluegene and I got these
error. I notice that the step that the error occurs depends on the
number of nodes I use. I am also including the end of the min.out file.

I also tried others integrators for the energy minimization but I
always get the same error.

Thank you again,
Cíntia

---
em.mdp

integrator   = steep
tinit= 0.0
dt   = 0.002
nsteps   = 500
nstcomm  = 1
comm-grps= Other SOL

nstxout  = 100
nstvout  = 100
nstfout  = 0
nstlog   = 100
nstenergy= 100
nstxtcout= 100
xtc_precision= 100
xtc-grps =
energygrps   = Other SOL

nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.4

coulombtype  = reaction-field
rcoulomb = 1.4
epsilon_rf   = 66

vdw_type = cut-off
rvdw = 1.4
DispCorr = No

constraints  = none
---
min.out
...
Step= 5192, Dmax= 1.9e-11 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5193, Dmax= 9.5e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5194, Dmax= 4.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5195, Dmax= 2.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5196, Dmax= 2.8e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5197, Dmax= 1.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5198, Dmax= 1.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 5199 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -1.79302464181879e+06
Maximum force =  6.65022934447791e+02 on atom 22015
Norm of force =  4.90065871184878e+00

gcq#0: Thanx for Using GROMACS - Have a Nice Day
---



 ---
 md.mdp file


 integrator   = md
 tinit= 0.0
 dt   = 0.002
 nsteps   = 500
 nstcomm  = 5
 comm-grps= Other SOL

 nstxout  = 1000
 nstvout  = 1000
 nstfout  = 0
 nstlog   = 1000
 nstenergy= 1000
 nstxtcout= 1000
 xtc_precision= 1000
 xtc-grps =
 energygrps   = Other SOL

 nstlist  = 5
 ns_type

Re: [gmx-users] Error in BlueGene

[Cintia C. Vequi-Suplicy]

Hello Ricardo,

I tried to decrease the integration time but I got the same error.
The system is running fine in my local core.

I have two questions:

1) What do you mean by "I balance the domain decomposition for the 
larger number of core"?

2) Are you running simulations at Bluegene P at Rice University?

Thank you,
Cíntia


On 30/01/2013 20:48, Ricardo Soares wrote:

Hello,

before submitting to Bluegene, I always test the system in my local 8 core
cpu, and if it works, it will also work in Bluegene, as long as I balance the
domain decomposition for the larger number of cores. If your system insists in
exploding, even after energy minimization, you could try to decrease the
integration timestep (dt) to something lower than 2 fs, maybe to 1fs or, in
some cases even 0.5 fs. Did you tried that?

Cheers,

Ricardo.



On Wed, 30 Jan 2013 15:44:53 -0200, Cintia C. Vequi-Suplicy wrote

Mark,

Thank you for your answer.

I did an energy minimization with the file em.mdp (below) and then I
did a  40 ns simulation with the same md.mdp I send before. These
two steps were done in my local cluster. After that I took the
configuration for the simulation in the bluegene and I got these
error. I notice that the step that the error occurs depends on the
number of nodes I use. I am also including the end of the min.out file.

I also tried others integrators for the energy minimization but I
always get the same error.

Thank you again,
Cíntia

---
em.mdp

integrator   = steep
tinit= 0.0
dt   = 0.002
nsteps   = 500
nstcomm  = 1
comm-grps= Other SOL

nstxout  = 100
nstvout  = 100
nstfout  = 0
nstlog   = 100
nstenergy= 100
nstxtcout= 100
xtc_precision= 100
xtc-grps =
energygrps   = Other SOL

nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.4

coulombtype  = reaction-field
rcoulomb = 1.4
epsilon_rf   = 66

vdw_type = cut-off
rvdw = 1.4
DispCorr = No

constraints  = none
---
min.out
...
Step= 5192, Dmax= 1.9e-11 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5193, Dmax= 9.5e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5194, Dmax= 4.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5195, Dmax= 2.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5196, Dmax= 2.8e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5197, Dmax= 1.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5198, Dmax= 1.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 5199 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -1.79302464181879e+06
Maximum force =  6.65022934447791e+02 on atom 22015
Norm of force =  4.90065871184878e+00

gcq#0: Thanx for Using GROMACS - Have a Nice Day
---



 ---
 md.mdp file


 integrator   = md
 tinit= 0.0
 dt   = 0.002
 nsteps   = 500
 nstcomm  = 5
 comm-grps= Other SOL

 nstxout  = 1000
 nstvout  = 1000
 nstfout  = 0
 nstlog   = 1000
 nstenergy= 1000
 nstxtcout= 1000
 xtc_precision= 1000
 xtc-grps =
 energygrps   = Other SOL

 nstlist  = 5
 ns_type  = grid
 pbc  = xyz
 rlist= 1.4

 coulombtype  = reaction-field
 rcoulomb = 1.4
 epsilon_rf   = 66

 vdw_type = cut-off
 rvdw = 1.4
 DispCorr = No

 tcoupl   = v-rescale
 tc-grps  = Other SOL
 tau_t= 0.4 0.4
 ref_t= 296 296

 Pcoupl   = berendsen
 Pcoupltype   = semiisotropic
 tau_p= 0.2 0.2
 compressibility  = 4.51e-5 4.51e-5
 ref_p 

Re: [gmx-users] Error in BlueGene

[David van der Spoel]

On 2013-01-30 23:48, Ricardo Soares wrote:

Hello,

before submitting to Bluegene, I always test the system in my local 8 core
cpu, and if it works, it will also work in Bluegene, as long as I balance the
domain decomposition for the larger number of cores. If your system insists in
exploding, even after energy minimization, you could try to decrease the
integration timestep (dt) to something lower than 2 fs, maybe to 1fs or, in
some cases even 0.5 fs. Did you tried that?


And check the energies.
Which term causes the crash?


Cheers,

Ricardo.



On Wed, 30 Jan 2013 15:44:53 -0200, Cintia C. Vequi-Suplicy wrote

Mark,

Thank you for your answer.

I did an energy minimization with the file em.mdp (below) and then I
did a  40 ns simulation with the same md.mdp I send before. These
two steps were done in my local cluster. After that I took the
configuration for the simulation in the bluegene and I got these
error. I notice that the step that the error occurs depends on the
number of nodes I use. I am also including the end of the min.out file.

I also tried others integrators for the energy minimization but I
always get the same error.

Thank you again,
Cíntia

---
em.mdp

integrator   = steep
tinit= 0.0
dt   = 0.002
nsteps   = 500
nstcomm  = 1
comm-grps= Other SOL

nstxout  = 100
nstvout  = 100
nstfout  = 0
nstlog   = 100
nstenergy= 100
nstxtcout= 100
xtc_precision= 100
xtc-grps =
energygrps   = Other SOL

nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.4

coulombtype  = reaction-field
rcoulomb = 1.4
epsilon_rf   = 66

vdw_type = cut-off
rvdw = 1.4
DispCorr = No

constraints  = none
---
min.out
...
Step= 5192, Dmax= 1.9e-11 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5193, Dmax= 9.5e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5194, Dmax= 4.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5195, Dmax= 2.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5196, Dmax= 2.8e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5197, Dmax= 1.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5198, Dmax= 1.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 5199 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -1.79302464181879e+06
Maximum force =  6.65022934447791e+02 on atom 22015
Norm of force =  4.90065871184878e+00

gcq#0: Thanx for Using GROMACS - Have a Nice Day
---




 ---
 md.mdp file


 integrator   = md
 tinit= 0.0
 dt   = 0.002
 nsteps   = 500
 nstcomm  = 5
 comm-grps= Other SOL

 nstxout  = 1000
 nstvout  = 1000
 nstfout  = 0
 nstlog   = 1000
 nstenergy= 1000
 nstxtcout= 1000
 xtc_precision= 1000
 xtc-grps =
 energygrps   = Other SOL

 nstlist  = 5
 ns_type  = grid
 pbc  = xyz
 rlist= 1.4

 coulombtype  = reaction-field
 rcoulomb = 1.4
 epsilon_rf   = 66

 vdw_type = cut-off
 rvdw = 1.4
 DispCorr = No

 tcoupl   = v-rescale
 tc-grps  = Other SOL
 tau_t= 0.4 0.4
 ref_t= 296 296

 Pcoupl   = berendsen
 Pcoupltype   = semiisotropic
 tau_p= 0.2 0.2
 compressibility  = 4.51e-5 4.51e-5
 ref_p= 1.0 1.0

 constraints  = hbonds
 constraint_algorithm = lincs



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http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
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Re: [gmx-users] Error in BlueGene

[Ricardo Soares]

Hello,

before submitting to Bluegene, I always test the system in my local 8 core
cpu, and if it works, it will also work in Bluegene, as long as I balance the
domain decomposition for the larger number of cores. If your system insists in
exploding, even after energy minimization, you could try to decrease the
integration timestep (dt) to something lower than 2 fs, maybe to 1fs or, in
some cases even 0.5 fs. Did you tried that?

Cheers,

Ricardo.



On Wed, 30 Jan 2013 15:44:53 -0200, Cintia C. Vequi-Suplicy wrote
> Mark,
> 
> Thank you for your answer.
> 
> I did an energy minimization with the file em.mdp (below) and then I 
> did a  40 ns simulation with the same md.mdp I send before. These 
> two steps were done in my local cluster. After that I took the 
> configuration for the simulation in the bluegene and I got these 
> error. I notice that the step that the error occurs depends on the 
> number of nodes I use. I am also including the end of the min.out file.
> 
> I also tried others integrators for the energy minimization but I 
> always get the same error.
> 
> Thank you again,
> Cíntia
> 
> ---
> em.mdp
> 
> integrator   = steep
> tinit= 0.0
> dt   = 0.002
> nsteps   = 500
> nstcomm  = 1
> comm-grps= Other SOL
> 
> nstxout  = 100
> nstvout  = 100
> nstfout  = 0
> nstlog   = 100
> nstenergy= 100
> nstxtcout= 100
> xtc_precision= 100
> xtc-grps =
> energygrps   = Other SOL
> 
> nstlist  = 5
> ns_type  = grid
> pbc  = xyz
> rlist= 1.4
> 
> coulombtype  = reaction-field
> rcoulomb = 1.4
> epsilon_rf   = 66
> 
> vdw_type = cut-off
> rvdw = 1.4
> DispCorr = No
> 
> constraints  = none
> ---
> min.out
> ...
> Step= 5192, Dmax= 1.9e-11 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Step= 5193, Dmax= 9.5e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Step= 5194, Dmax= 4.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Step= 5195, Dmax= 2.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Step= 5196, Dmax= 2.8e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Step= 5197, Dmax= 1.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Step= 5198, Dmax= 1.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 10
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> 
> writing lowest energy coordinates.
> 
> Steepest Descents converged to machine precision in 5199 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -1.79302464181879e+06
> Maximum force =  6.65022934447791e+02 on atom 22015
> Norm of force =  4.90065871184878e+00
> 
> gcq#0: Thanx for Using GROMACS - Have a Nice Day
> ---
> 
> >
> >
> > ---
> > md.mdp file
> >
> >
> > integrator   = md
> > tinit= 0.0
> > dt   = 0.002
> > nsteps   = 500
> > nstcomm  = 5
> > comm-grps= Other SOL
> >
> > nstxout  = 1000
> > nstvout  = 1000
> > nstfout  = 0
> > nstlog   = 1000
> > nstenergy= 1000
> > nstxtcout= 1000
> > xtc_precision= 1000
> > xtc-grps =
> > energygrps   = Other SOL
> >
> > nstlist  = 5
> > ns_type  = grid
> > pbc  = xyz
> > rlist= 1.4
> >
> > coulombtype  = reaction-field
> > rcoulomb = 1.4
> > epsilon_rf   = 66
> >
> > vdw_type = cut-off
> > rvdw = 1.4
> > DispCorr = No
> >
> > tcoupl   = v-rescale
> > tc-grps  = Other SOL
> > tau_t= 0.4 0.4
> > ref_t= 296 296
> >
> > Pcoupl   = berendsen
> > Pcoupltype   = semiisotropic
> > tau_p= 0.2 0.2
> > compressibility  = 4.51e-5 4.51e-5
> > ref_p= 1.0 1.0
> >
> > constraints  = 

Re: [gmx-users] Error in BlueGene

[Cintia C. Vequi-Suplicy]

Mark,

Thank you for your answer.

I did an energy minimization with the file em.mdp (below) and then I did 
a  40 ns simulation with the same md.mdp I send before. These two steps 
were done in my local cluster.
After that I took the configuration for the simulation in the bluegene 
and I got these error. I notice that the step that the error occurs 
depends on the number of nodes I use.

I am also including the end of the min.out file.

I also tried others integrators for the energy minimization but I always 
get the same error.


Thank you again,
Cíntia


---
em.mdp

integrator   = steep
tinit= 0.0
dt   = 0.002
nsteps   = 500
nstcomm  = 1
comm-grps= Other SOL

nstxout  = 100
nstvout  = 100
nstfout  = 0
nstlog   = 100
nstenergy= 100
nstxtcout= 100
xtc_precision= 100
xtc-grps =
energygrps   = Other SOL

nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.4

coulombtype  = reaction-field
rcoulomb = 1.4
epsilon_rf   = 66

vdw_type = cut-off
rvdw = 1.4
DispCorr = No

constraints  = none
---
min.out
...
Step= 5192, Dmax= 1.9e-11 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015
Step= 5193, Dmax= 9.5e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015
Step= 5194, Dmax= 4.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015
Step= 5195, Dmax= 2.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015
Step= 5196, Dmax= 2.8e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015
Step= 5197, Dmax= 1.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015
Step= 5198, Dmax= 1.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 5199 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -1.79302464181879e+06
Maximum force =  6.65022934447791e+02 on atom 22015
Norm of force =  4.90065871184878e+00

gcq#0: Thanx for Using GROMACS - Have a Nice Day
---




---
md.mdp file


integrator   = md
tinit= 0.0
dt   = 0.002
nsteps   = 500
nstcomm  = 5
comm-grps= Other SOL

nstxout  = 1000
nstvout  = 1000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 1000
xtc-grps =
energygrps   = Other SOL

nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.4

coulombtype  = reaction-field
rcoulomb = 1.4
epsilon_rf   = 66

vdw_type = cut-off
rvdw = 1.4
DispCorr = No

tcoupl   = v-rescale
tc-grps  = Other SOL
tau_t= 0.4 0.4
ref_t= 296 296

Pcoupl   = berendsen
Pcoupltype   = semiisotropic
tau_p= 0.2 0.2
compressibility  = 4.51e-5 4.51e-5
ref_p= 1.0 1.0

constraints  = hbonds
constraint_algorithm = lincs





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[gmx-users] Error in BlueGene

[Cintia C. Vequi-Suplicy]

Hello,

I am having some problems to run my system in a bluegene cluster.
I am running a bilayer simulation. The simulation runs very well in my 
local cluster.


After 50ns of simulation on my local cluster with 8 nodes, I got the 
configurations and tried to run it in a bluegene with 512 nodes.
But I always get the same error (the whole output error is below as also 
the md.mdp file):

"
---
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 4124

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
"

Can anyone help me?
Thank you,
Cíntia


---
md.mdp file


integrator   = md
tinit= 0.0
dt   = 0.002
nsteps   = 500
nstcomm  = 5
comm-grps= Other SOL

nstxout  = 1000
nstvout  = 1000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 1000
xtc-grps =
energygrps   = Other SOL

nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.4

coulombtype  = reaction-field
rcoulomb = 1.4
epsilon_rf   = 66

vdw_type = cut-off
rvdw = 1.4
DispCorr = No

tcoupl   = v-rescale
tc-grps  = Other SOL
tau_t= 0.4 0.4
ref_t= 296 296

Pcoupl   = berendsen
Pcoupltype   = semiisotropic
tau_p= 0.2 0.2
compressibility  = 4.51e-5 4.51e-5
ref_p= 1.0 1.0

constraints  = hbonds
constraint_algorithm = lincs
---
error.log

vol 0.73  imb F  1% vol 0.71  imb F  1% vol 0.74  imb F  1% vol 0.74  
vol 0.74  imb F  1% vol 0.74  imb F  1% imb F  1% vol 0.75 imb F  1% vol 
0.74  imb F  1% step 3600, will finish Sat Feb  2 08:06:01 2013
Warning: 1-4 interaction between 7552 and 7556 at distance 6.386 which 
is larger than the 1-4 table size 2.400 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38174 1.38174 
1.4951


...

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38219 1.38219 
1.49568
Warning: 1-4 interaction between 7556 and 7559 at distance 13.605 which 
is larger than the 1-4 table size 2.400 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

step 3618: Water molecule starting at atom 92582 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 3618: Water molecule starting at atom 81278 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 3618: Water molecule starting at atom 72206 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 3618: Water molecule starting at atom 58769 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 7757 and 7762 at distance 591.859 which 
is larger than the 1-4 table size 2.400 nm
Warning: 1-4 interaction between 1301 and 1306 at distance 34172.198 
which is larger than the 1-4 table size 2.400 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

step 3619: Water molecule starting at atom 70238 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 3619: Water molecule starting at atom 63254 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

...

Wrote pdb files with previous and current coordinates

Step 3620:
The charge gro

Re: [gmx-users] error

[Justin Lemkul]

On 1/29/13 11:01 AM, az kalsom wrote:

hi,

i am using the following
comamnd

  pdb2gmx -ff amber99sb -f proteinamber.pdb -o  protei2.pdb -p protein.top
-water spce -ignh

and gets the error

Fatal error:
Residue 2 named GLU of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

how to rename it ?



You may or may not have a naming issue.  pdb2gmx is telling you that the 
expected atom (CG) is missing from the input file.  If you have incomplete 
residues, you will need to use some external (non-Gromacs) modeling software to 
rebuild the missing elements of the input file.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
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[gmx-users] error

[az kalsom]

hi,

i am using the following
comamnd

 pdb2gmx -ff amber99sb -f proteinamber.pdb -o  protei2.pdb -p protein.top
-water spce -ignh

and gets the error

Fatal error:
Residue 2 named GLU of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

how to rename it ?

regards
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] error about pbc

[Justin Lemkul]

On 1/28/13 10:29 AM, Kieu Thu Nguyen wrote:

I reduced time step in equi.mdp file to 20 ps. But the system is still not
balance. Should i continue reduce time step below 20 ps value ? Thanks so
much for any suggestion about appropriate time step value !



The first step I would take is to keep halving the time step until the system is 
stable, then increase to the desired value after you've achieved a stable system.


-Justin


On Mon, Jan 28, 2013 at 12:53 PM, Kieu Thu Nguyen wrote:


Thank Justin and Tsjerk so much for your help !
I will try smaller time step. And i hope it work :-)

Regards,
KT


On Mon, Jan 28, 2013 at 10:19 AM, Tsjerk Wassenaar wrote:


Well, 20-30 fs is fine with Martini. But you may have to take care
initially, and start with a smaller time step.

Cheers,

Tsjerk

On Mon, Jan 28, 2013 at 3:11 AM, Justin Lemkul  wrote:




On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote:


@Justin,
Fmax=8.0226669e+00



OK, that looks good.


  the system includes protein, lipid, water, ion Cl-


em.mdp file is

integrator   = steep
tinit= 0.0
dt   = 0.02
nsteps   = 5
nstcomm  = 1
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 1000
nstlist  = 1
ns_type  = grid
pbc  = xyz
rlist= 1.4
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch  = 0.9
rvdw = 1.2
DispCorr = No
tcoupl   = no
pcoupl   = no
gen_vel  = no
constraints  = none
constraint_algorithm = Lincs
continuation = no
lincs_order  = 4
lincs_warnangle  = 30


equi.mdp file is

integrator   = md
tinit= 0.0
dt   = 0.03



Does a smaller time step work?  I know the whole point of a MARTINI
simulation is to use a 20-40 fs time step, but in my (very very limited)
experience, nothing over 20 fs is consistently stable.  Perhaps others

with

better experience can offer pointers.

-Justin


  nsteps   = 300

nstcomm  = 1
comm-grps =
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 100
xtc-grps =
energygrps   =
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.2
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch  = 0.9
rvdw = 1.2
DispCorr = No
tcoupl   = Berendsen
tc-grps  = Protein DSPC Ion_W
tau_t= 1.5 1.5 1.5
ref_t= 310 310 310
Pcoupl   = Berendsen
Pcoupltype   = semiisotropic
tau_p= 3.0 3.0
compressibility  = 3e-4 3e-4
ref_p= 1.0 1.0
gen_vel  = no
constraints  = none
constraint_algorithm = Lincs
continuation = no
lincs_order  = 4
lincs_warnangle  = 30

Thanks so much for any help !
Regards,
KT


On Sun, Jan 27, 2013 at 8:26 AM, Justin Lemkul 

wrote:





On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote:

  Thank Tsjerk so much !

But after being minimized 5 steps and equilibrated 90 ns, there

are

some bonds in the system that rotate more than 30 degrees.
I applied tips for blew up system as you advised. But the system does
not
achieve balance.
Should i carry out more many steps for minimization ? or minimize

many

times ? to get more equilibrated system.


  I would say that 5 steps of minimization is far more than is

normally
necessary.  What Fmax do you achieve at the end of EM?  What is in the
system? What is in your .mdp file?  Systems can randomly crash if the
model
physics breaks due to incorrect .mdp settings or an unstable topology.

-Justin


   On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar <

tsje...@gmail.com



wrote:




   Hi KT,



This is caused by another problem. Your system blew up. Check

messages

before this one, and check the log for LINCS warnings.

Cheers,

Tsjerk

On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen <
kieuthu2...@gmail.com

  wrote:




   Dear All,



My MD simulation  has an error

Warning: Only triclinic boxes with the first vector parallel to the

  x-axis


  and the second vector in the xy-plane 

Re: [gmx-users] error about pbc

[Kieu Thu Nguyen]

I reduced time step in equi.mdp file to 20 ps. But the system is still not
balance. Should i continue reduce time step below 20 ps value ? Thanks so
much for any suggestion about appropriate time step value !

Regards,
KT


On Mon, Jan 28, 2013 at 12:53 PM, Kieu Thu Nguyen wrote:

> Thank Justin and Tsjerk so much for your help !
> I will try smaller time step. And i hope it work :-)
>
> Regards,
> KT
>
>
> On Mon, Jan 28, 2013 at 10:19 AM, Tsjerk Wassenaar wrote:
>
>> Well, 20-30 fs is fine with Martini. But you may have to take care
>> initially, and start with a smaller time step.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Mon, Jan 28, 2013 at 3:11 AM, Justin Lemkul  wrote:
>>
>> >
>> >
>> > On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote:
>> >
>> >> @Justin,
>> >> Fmax=8.0226669e+00
>> >>
>> >
>> > OK, that looks good.
>> >
>> >
>> >  the system includes protein, lipid, water, ion Cl-
>> >>
>> >> em.mdp file is
>> >>
>> >> integrator   = steep
>> >> tinit= 0.0
>> >> dt   = 0.02
>> >> nsteps   = 5
>> >> nstcomm  = 1
>> >> nstxout  = 5000
>> >> nstvout  = 5000
>> >> nstfout  = 0
>> >> nstlog   = 1000
>> >> nstenergy= 1000
>> >> nstxtcout= 1000
>> >> xtc_precision= 1000
>> >> nstlist  = 1
>> >> ns_type  = grid
>> >> pbc  = xyz
>> >> rlist= 1.4
>> >> coulombtype  = Shift
>> >> rcoulomb_switch  = 0.0
>> >> rcoulomb = 1.2
>> >> epsilon_r= 15
>> >> vdw_type = Shift
>> >> rvdw_switch  = 0.9
>> >> rvdw = 1.2
>> >> DispCorr = No
>> >> tcoupl   = no
>> >> pcoupl   = no
>> >> gen_vel  = no
>> >> constraints  = none
>> >> constraint_algorithm = Lincs
>> >> continuation = no
>> >> lincs_order  = 4
>> >> lincs_warnangle  = 30
>> >>
>> >>
>> >> equi.mdp file is
>> >>
>> >> integrator   = md
>> >> tinit= 0.0
>> >> dt   = 0.03
>> >>
>> >
>> > Does a smaller time step work?  I know the whole point of a MARTINI
>> > simulation is to use a 20-40 fs time step, but in my (very very limited)
>> > experience, nothing over 20 fs is consistently stable.  Perhaps others
>> with
>> > better experience can offer pointers.
>> >
>> > -Justin
>> >
>> >
>> >  nsteps   = 300
>> >> nstcomm  = 1
>> >> comm-grps =
>> >> nstxout  = 5000
>> >> nstvout  = 5000
>> >> nstfout  = 0
>> >> nstlog   = 1000
>> >> nstenergy= 1000
>> >> nstxtcout= 1000
>> >> xtc_precision= 100
>> >> xtc-grps =
>> >> energygrps   =
>> >> nstlist  = 10
>> >> ns_type  = grid
>> >> pbc  = xyz
>> >> rlist= 1.2
>> >> coulombtype  = Shift
>> >> rcoulomb_switch  = 0.0
>> >> rcoulomb = 1.2
>> >> epsilon_r= 15
>> >> vdw_type = Shift
>> >> rvdw_switch  = 0.9
>> >> rvdw = 1.2
>> >> DispCorr = No
>> >> tcoupl   = Berendsen
>> >> tc-grps  = Protein DSPC Ion_W
>> >> tau_t= 1.5 1.5 1.5
>> >> ref_t= 310 310 310
>> >> Pcoupl   = Berendsen
>> >> Pcoupltype   = semiisotropic
>> >> tau_p= 3.0 3.0
>> >> compressibility  = 3e-4 3e-4
>> >> ref_p= 1.0 1.0
>> >> gen_vel  = no
>> >> constraints  = none
>> >> constraint_algorithm = Lincs
>> >> continuation = no
>> >> lincs_order  = 4
>> >> lincs_warnangle  = 30
>> >>
>> >> Thanks so much for any help !
>> >> Regards,
>> >> KT
>> >>
>> >>
>> >> On Sun, Jan 27, 2013 at 8:26 AM, Justin Lemkul 
>> wrote:
>> >>
>> >>
>> >>>
>> >>> On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote:
>> >>>
>> >>>  Thank Tsjerk so much !
>>  But after being minimized 5 steps and equilibrated 90 ns, there
>> are
>>  some bonds in the system that rotate more than 30 degrees.
>>  I applied tips for blew up system as you advised. But the system does
>>  not
>>  achieve balance.
>>  Should i carry out more many steps for minimization ? or minimize
>> many
>>  times ? to get more equilibrated system.
>> 
>> 
>>   I would say that 5 steps of minimization is far more than is
>> >>> normally
>> >>> necessary.  What Fmax do you achieve at the end of EM?  What is in the
>> >>> system? What is in your .mdp file?  Systems can randomly crash if the
>> >>> model
>> >>> p

Re: [gmx-users] error about pbc

[Kieu Thu Nguyen]

Thank Justin and Tsjerk so much for your help !
I will try smaller time step. And i hope it work :-)

Regards,
KT


On Mon, Jan 28, 2013 at 10:19 AM, Tsjerk Wassenaar wrote:

> Well, 20-30 fs is fine with Martini. But you may have to take care
> initially, and start with a smaller time step.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Jan 28, 2013 at 3:11 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote:
> >
> >> @Justin,
> >> Fmax=8.0226669e+00
> >>
> >
> > OK, that looks good.
> >
> >
> >  the system includes protein, lipid, water, ion Cl-
> >>
> >> em.mdp file is
> >>
> >> integrator   = steep
> >> tinit= 0.0
> >> dt   = 0.02
> >> nsteps   = 5
> >> nstcomm  = 1
> >> nstxout  = 5000
> >> nstvout  = 5000
> >> nstfout  = 0
> >> nstlog   = 1000
> >> nstenergy= 1000
> >> nstxtcout= 1000
> >> xtc_precision= 1000
> >> nstlist  = 1
> >> ns_type  = grid
> >> pbc  = xyz
> >> rlist= 1.4
> >> coulombtype  = Shift
> >> rcoulomb_switch  = 0.0
> >> rcoulomb = 1.2
> >> epsilon_r= 15
> >> vdw_type = Shift
> >> rvdw_switch  = 0.9
> >> rvdw = 1.2
> >> DispCorr = No
> >> tcoupl   = no
> >> pcoupl   = no
> >> gen_vel  = no
> >> constraints  = none
> >> constraint_algorithm = Lincs
> >> continuation = no
> >> lincs_order  = 4
> >> lincs_warnangle  = 30
> >>
> >>
> >> equi.mdp file is
> >>
> >> integrator   = md
> >> tinit= 0.0
> >> dt   = 0.03
> >>
> >
> > Does a smaller time step work?  I know the whole point of a MARTINI
> > simulation is to use a 20-40 fs time step, but in my (very very limited)
> > experience, nothing over 20 fs is consistently stable.  Perhaps others
> with
> > better experience can offer pointers.
> >
> > -Justin
> >
> >
> >  nsteps   = 300
> >> nstcomm  = 1
> >> comm-grps =
> >> nstxout  = 5000
> >> nstvout  = 5000
> >> nstfout  = 0
> >> nstlog   = 1000
> >> nstenergy= 1000
> >> nstxtcout= 1000
> >> xtc_precision= 100
> >> xtc-grps =
> >> energygrps   =
> >> nstlist  = 10
> >> ns_type  = grid
> >> pbc  = xyz
> >> rlist= 1.2
> >> coulombtype  = Shift
> >> rcoulomb_switch  = 0.0
> >> rcoulomb = 1.2
> >> epsilon_r= 15
> >> vdw_type = Shift
> >> rvdw_switch  = 0.9
> >> rvdw = 1.2
> >> DispCorr = No
> >> tcoupl   = Berendsen
> >> tc-grps  = Protein DSPC Ion_W
> >> tau_t= 1.5 1.5 1.5
> >> ref_t= 310 310 310
> >> Pcoupl   = Berendsen
> >> Pcoupltype   = semiisotropic
> >> tau_p= 3.0 3.0
> >> compressibility  = 3e-4 3e-4
> >> ref_p= 1.0 1.0
> >> gen_vel  = no
> >> constraints  = none
> >> constraint_algorithm = Lincs
> >> continuation = no
> >> lincs_order  = 4
> >> lincs_warnangle  = 30
> >>
> >> Thanks so much for any help !
> >> Regards,
> >> KT
> >>
> >>
> >> On Sun, Jan 27, 2013 at 8:26 AM, Justin Lemkul  wrote:
> >>
> >>
> >>>
> >>> On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote:
> >>>
> >>>  Thank Tsjerk so much !
>  But after being minimized 5 steps and equilibrated 90 ns, there
> are
>  some bonds in the system that rotate more than 30 degrees.
>  I applied tips for blew up system as you advised. But the system does
>  not
>  achieve balance.
>  Should i carry out more many steps for minimization ? or minimize many
>  times ? to get more equilibrated system.
> 
> 
>   I would say that 5 steps of minimization is far more than is
> >>> normally
> >>> necessary.  What Fmax do you achieve at the end of EM?  What is in the
> >>> system? What is in your .mdp file?  Systems can randomly crash if the
> >>> model
> >>> physics breaks due to incorrect .mdp settings or an unstable topology.
> >>>
> >>> -Justin
> >>>
> >>>
> >>>   On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar <
> tsje...@gmail.com
> >>>
>  wrote:
> >
> 
>    Hi KT,
> 
> >
> > This is caused by another problem. Your system blew up. Check
> messages
> > before this one, and check the log for LINCS warnings.
> >
> > Cheers,
> >
> > Tsjerk
> >>

Re: [gmx-users] error about pbc

[Tsjerk Wassenaar]

Well, 20-30 fs is fine with Martini. But you may have to take care
initially, and start with a smaller time step.

Cheers,

Tsjerk

On Mon, Jan 28, 2013 at 3:11 AM, Justin Lemkul  wrote:

>
>
> On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote:
>
>> @Justin,
>> Fmax=8.0226669e+00
>>
>
> OK, that looks good.
>
>
>  the system includes protein, lipid, water, ion Cl-
>>
>> em.mdp file is
>>
>> integrator   = steep
>> tinit= 0.0
>> dt   = 0.02
>> nsteps   = 5
>> nstcomm  = 1
>> nstxout  = 5000
>> nstvout  = 5000
>> nstfout  = 0
>> nstlog   = 1000
>> nstenergy= 1000
>> nstxtcout= 1000
>> xtc_precision= 1000
>> nstlist  = 1
>> ns_type  = grid
>> pbc  = xyz
>> rlist= 1.4
>> coulombtype  = Shift
>> rcoulomb_switch  = 0.0
>> rcoulomb = 1.2
>> epsilon_r= 15
>> vdw_type = Shift
>> rvdw_switch  = 0.9
>> rvdw = 1.2
>> DispCorr = No
>> tcoupl   = no
>> pcoupl   = no
>> gen_vel  = no
>> constraints  = none
>> constraint_algorithm = Lincs
>> continuation = no
>> lincs_order  = 4
>> lincs_warnangle  = 30
>>
>>
>> equi.mdp file is
>>
>> integrator   = md
>> tinit= 0.0
>> dt   = 0.03
>>
>
> Does a smaller time step work?  I know the whole point of a MARTINI
> simulation is to use a 20-40 fs time step, but in my (very very limited)
> experience, nothing over 20 fs is consistently stable.  Perhaps others with
> better experience can offer pointers.
>
> -Justin
>
>
>  nsteps   = 300
>> nstcomm  = 1
>> comm-grps =
>> nstxout  = 5000
>> nstvout  = 5000
>> nstfout  = 0
>> nstlog   = 1000
>> nstenergy= 1000
>> nstxtcout= 1000
>> xtc_precision= 100
>> xtc-grps =
>> energygrps   =
>> nstlist  = 10
>> ns_type  = grid
>> pbc  = xyz
>> rlist= 1.2
>> coulombtype  = Shift
>> rcoulomb_switch  = 0.0
>> rcoulomb = 1.2
>> epsilon_r= 15
>> vdw_type = Shift
>> rvdw_switch  = 0.9
>> rvdw = 1.2
>> DispCorr = No
>> tcoupl   = Berendsen
>> tc-grps  = Protein DSPC Ion_W
>> tau_t= 1.5 1.5 1.5
>> ref_t= 310 310 310
>> Pcoupl   = Berendsen
>> Pcoupltype   = semiisotropic
>> tau_p= 3.0 3.0
>> compressibility  = 3e-4 3e-4
>> ref_p= 1.0 1.0
>> gen_vel  = no
>> constraints  = none
>> constraint_algorithm = Lincs
>> continuation = no
>> lincs_order  = 4
>> lincs_warnangle  = 30
>>
>> Thanks so much for any help !
>> Regards,
>> KT
>>
>>
>> On Sun, Jan 27, 2013 at 8:26 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote:
>>>
>>>  Thank Tsjerk so much !
 But after being minimized 5 steps and equilibrated 90 ns, there are
 some bonds in the system that rotate more than 30 degrees.
 I applied tips for blew up system as you advised. But the system does
 not
 achieve balance.
 Should i carry out more many steps for minimization ? or minimize many
 times ? to get more equilibrated system.


  I would say that 5 steps of minimization is far more than is
>>> normally
>>> necessary.  What Fmax do you achieve at the end of EM?  What is in the
>>> system? What is in your .mdp file?  Systems can randomly crash if the
>>> model
>>> physics breaks due to incorrect .mdp settings or an unstable topology.
>>>
>>> -Justin
>>>
>>>
>>>   On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar >>
 wrote:
>

   Hi KT,

>
> This is caused by another problem. Your system blew up. Check messages
> before this one, and check the log for LINCS warnings.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen <
> kieuthu2...@gmail.com
>
>  wrote:
>>
>>
>   Dear All,
>
>>
>> My MD simulation  has an error
>>
>> Warning: Only triclinic boxes with the first vector parallel to the
>>
>>  x-axis
>
>  and the second vector in the xy-plane are supported.
>>Box (3x3):
>>   Box[0]={ nan,  nan,  nan}
>>   Box[1]={ nan,  

Re: [gmx-users] error about pbc

[Justin Lemkul]

On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote:

@Justin,
Fmax=8.0226669e+00


OK, that looks good.


the system includes protein, lipid, water, ion Cl-

em.mdp file is

integrator   = steep
tinit= 0.0
dt   = 0.02
nsteps   = 5
nstcomm  = 1
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 1000
nstlist  = 1
ns_type  = grid
pbc  = xyz
rlist= 1.4
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch  = 0.9
rvdw = 1.2
DispCorr = No
tcoupl   = no
pcoupl   = no
gen_vel  = no
constraints  = none
constraint_algorithm = Lincs
continuation = no
lincs_order  = 4
lincs_warnangle  = 30


equi.mdp file is

integrator   = md
tinit= 0.0
dt   = 0.03


Does a smaller time step work?  I know the whole point of a MARTINI simulation 
is to use a 20-40 fs time step, but in my (very very limited) experience, 
nothing over 20 fs is consistently stable.  Perhaps others with better 
experience can offer pointers.


-Justin


nsteps   = 300
nstcomm  = 1
comm-grps =
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 100
xtc-grps =
energygrps   =
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.2
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch  = 0.9
rvdw = 1.2
DispCorr = No
tcoupl   = Berendsen
tc-grps  = Protein DSPC Ion_W
tau_t= 1.5 1.5 1.5
ref_t= 310 310 310
Pcoupl   = Berendsen
Pcoupltype   = semiisotropic
tau_p= 3.0 3.0
compressibility  = 3e-4 3e-4
ref_p= 1.0 1.0
gen_vel  = no
constraints  = none
constraint_algorithm = Lincs
continuation = no
lincs_order  = 4
lincs_warnangle  = 30

Thanks so much for any help !
Regards,
KT


On Sun, Jan 27, 2013 at 8:26 AM, Justin Lemkul  wrote:




On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote:


Thank Tsjerk so much !
But after being minimized 5 steps and equilibrated 90 ns, there are
some bonds in the system that rotate more than 30 degrees.
I applied tips for blew up system as you advised. But the system does not
achieve balance.
Should i carry out more many steps for minimization ? or minimize many
times ? to get more equilibrated system.



I would say that 5 steps of minimization is far more than is normally
necessary.  What Fmax do you achieve at the end of EM?  What is in the
system? What is in your .mdp file?  Systems can randomly crash if the model
physics breaks due to incorrect .mdp settings or an unstable topology.

-Justin


  On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar 
wrote:


  Hi KT,


This is caused by another problem. Your system blew up. Check messages
before this one, and check the log for LINCS warnings.

Cheers,

Tsjerk

On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen 
wrote:



  Dear All,


My MD simulation  has an error

Warning: Only triclinic boxes with the first vector parallel to the


x-axis


and the second vector in the xy-plane are supported.
   Box (3x3):
  Box[0]={ nan,  nan,  nan}
  Box[1]={ nan,  nan,  nan}
  Box[2]={ nan,  nan,  nan}
   Can not fix pbc.

I searched on Gromacs-errors web, but i did not see this error.
How can i fix it ?

Thanks and regards,
KT
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--
Tsjer

Re: [gmx-users] error about pbc

[Kieu Thu Nguyen]

@Justin,
Fmax=8.0226669e+00
the system includes protein, lipid, water, ion Cl-

em.mdp file is

integrator   = steep
tinit= 0.0
dt   = 0.02
nsteps   = 5
nstcomm  = 1
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 1000
nstlist  = 1
ns_type  = grid
pbc  = xyz
rlist= 1.4
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch  = 0.9
rvdw = 1.2
DispCorr = No
tcoupl   = no
pcoupl   = no
gen_vel  = no
constraints  = none
constraint_algorithm = Lincs
continuation = no
lincs_order  = 4
lincs_warnangle  = 30


equi.mdp file is

integrator   = md
tinit= 0.0
dt   = 0.03
nsteps   = 300
nstcomm  = 1
comm-grps =
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 100
xtc-grps =
energygrps   =
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.2
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch  = 0.9
rvdw = 1.2
DispCorr = No
tcoupl   = Berendsen
tc-grps  = Protein DSPC Ion_W
tau_t= 1.5 1.5 1.5
ref_t= 310 310 310
Pcoupl   = Berendsen
Pcoupltype   = semiisotropic
tau_p= 3.0 3.0
compressibility  = 3e-4 3e-4
ref_p= 1.0 1.0
gen_vel  = no
constraints  = none
constraint_algorithm = Lincs
continuation = no
lincs_order  = 4
lincs_warnangle  = 30

Thanks so much for any help !
Regards,
KT


On Sun, Jan 27, 2013 at 8:26 AM, Justin Lemkul  wrote:

>
>
> On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote:
>
>> Thank Tsjerk so much !
>> But after being minimized 5 steps and equilibrated 90 ns, there are
>> some bonds in the system that rotate more than 30 degrees.
>> I applied tips for blew up system as you advised. But the system does not
>> achieve balance.
>> Should i carry out more many steps for minimization ? or minimize many
>> times ? to get more equilibrated system.
>>
>>
> I would say that 5 steps of minimization is far more than is normally
> necessary.  What Fmax do you achieve at the end of EM?  What is in the
> system? What is in your .mdp file?  Systems can randomly crash if the model
> physics breaks due to incorrect .mdp settings or an unstable topology.
>
> -Justin
>
>
>  On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar > >wrote:
>>
>>  Hi KT,
>>>
>>> This is caused by another problem. Your system blew up. Check messages
>>> before this one, and check the log for LINCS warnings.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen >>
 wrote:

>>>
>>>  Dear All,

 My MD simulation  has an error

 Warning: Only triclinic boxes with the first vector parallel to the

>>> x-axis
>>>
 and the second vector in the xy-plane are supported.
   Box (3x3):
  Box[0]={ nan,  nan,  nan}
  Box[1]={ nan,  nan,  nan}
  Box[2]={ nan,  nan,  nan}
   Can not fix pbc.

 I searched on Gromacs-errors web, but i did not see this error.
 How can i fix it ?

 Thanks and regards,
 KT
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-users
 * Please search the archive at
 http://www.gromacs.org/**Support/Mailing_Lists/Searchbefore
  posting!
 * Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 * Can't post? Read 
 http://www.gromacs.org/**Support/Mailing_Lists


>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>> post-doctoral researcher
>>> Biocomputing Group
>>> Department of Biolog