Re: [gmx-users] mdrun error

[Justin Lemkul]

On 7/21/13 12:18 AM, Collins Nganou wrote:

Dear Users,

when trying to run the following command:
mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb
I have received the error below.



Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision)
Starting 2 threads

---
Program mdrun, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 6005

Fatal error:
Domain decomposition does not support simple neighbor searching, use grid
searching or use particle decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I am looking any suggestion that can help me to overcome this error.



Not all combinations of options are compatible, and mdrun already told you 
exactly what to do.  If you want to use DD, you can't use "nstype = simple," so 
you have to invoke mdrun -pd in this case or otherwise switch to "nstype = 
grid."  How you proceed depends on what you're trying to achieve with your .mdp 
settings.


-Justin

--
==

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[gmx-users] mdrun error

[Collins Nganou]

Dear Users,

when trying to run the following command:
mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb
I have received the error below.



Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision)
Starting 2 threads

---
Program mdrun, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 6005

Fatal error:
Domain decomposition does not support simple neighbor searching, use grid
searching or use particle decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I am looking any suggestion that can help me to overcome this error.

Best regards

Albert Collins
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Re: [gmx-users] mdrun error

[Justin Lemkul]

On 8/9/12 1:40 PM, Shima Arasteh wrote:

Dear gmx users,

Would be this error (as you see here) a symptom of blowing up of a system? Or 
just .mdp options should be changed?

Fatal error:
1 of the 16625 bonded interactions could not be calculated because some atoms 
involved moved further apart than the multi-body cut-off distance (0.817695 nm) 
or the two-body cut-off distance (1 nm), see option -rdd, for pairs and 
tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors




Any time something moves too far, it's a case of blowing up.

-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] mdrun error

[Shima Arasteh]

Dear gmx users,

Would be this error (as you see here) a symptom of blowing up of a system? Or 
just .mdp options should be changed?

Fatal error:
1 of the 16625 bonded interactions could not be calculated because some atoms 
involved moved further apart than the multi-body cut-off distance (0.817695 nm) 
or the two-body cut-off distance (1 nm), see option -rdd, for pairs and 
tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



Thanks for your suggestions.


Sincerely,
Shima
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Re: [gmx-users] mdrun : error

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello,
I am trying to do equilibration for my system (solvent + solute). I am
geting the following error. If I run solvent and solute molecules
separately, its run well. For mixture I am getting following error.
What this error means.

Fatal error:
1 of the 22334 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck



Search the list archive.  This has been asked and answered several times, so 
you'll likely find something useful.  Also, take mdrun's advice and read about 
the options it's telling you.


-Justin


NIlesh



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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] mdrun : error

[Nilesh Dhumal]

Hello,
I am trying to do equilibration for my system (solvent + solute). I am
geting the following error. If I run solvent and solute molecules
separately, its run well. For mixture I am getting following error.
What this error means.

Fatal error:
1 of the 22334 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck

NIlesh

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Re: [gmx-users] Mdrun error

[Mark Abraham]

Cíntia C. Vequi-Suplicy wrote:

Hello Justin,

I used Gromacs 4.0.5 and the error was gone. Thank you.

But now I have another problem when using mdrun_d. I gave the comand:

mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log  &

And first I got  a lot of output on the shell window and I think it is 
strange. This output should be on a file or not?


No, this output to stdout is normal. 3.3.3 does that too. Roughly the 
same content got written to the .log file. It sounds like you should do 
some tutorial material to get used to the GROMACS workflow.



And  after a few seconds I got an error which says:

t = 0.052 ps: Water molecule starting at atom 17276 can not be settled.
Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step26b.pdb to ./#step26b.pdb.2#

Back Off! I just backed up step26c.pdb to ./#step26c.pdb.2#
Wrote pdb files with previous and current coordinates
MPI process rank 0 (n0, p23764) caught a SIGSEGV.


See 
http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings


You should do some searching on the wiki/web to help diagnose your own 
problems before asking here :-) You'll learn more about problems you've 
solved yourself :-)


Mark
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[gmx-users] Mdrun error

Hello Justin,

I used Gromacs 4.0.5 and the error was gone. Thank you.

But now I have another problem when using mdrun_d. I gave the comand:

mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log  &

And first I got  a lot of output on the shell window and I think it is 
strange. This output should be on a file or not?

And  after a few seconds I got an error which says:

t = 0.052 ps: Water molecule starting at atom 17276 can not be settled.
Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step26b.pdb to ./#step26b.pdb.2#

Back Off! I just backed up step26c.pdb to ./#step26c.pdb.2#
Wrote pdb files with previous and current coordinates
MPI process rank 0 (n0, p23764) caught a SIGSEGV.

Can you help me?

Thank you
Cíntia C. Vequi-Suplicy
Biophysics Group
Physics Institute
São Paulo University

Justin A. Lemkul wrote:



Cíntia C. Vequi-Suplicy wrote:

Hello,

I am trying to simulate a lipid membrane with Gromacs. I am trying to
generate the *.tpr file o run the simulation, but every time I use the
command grompp I got the following error:

checking input for internal consistency...
...ling /usr/bin/cpp
: No such file or directory
cpp exit code: 32512
dppc128.top > gromppzJXISa'cpp
' command is defined in the .mdp file
*
* Important: if you do not have a c-preprocessor installed, *
* you MUST run grompp with the "-pp" command line option*
* in place of the "-p" option.  *
*
processing topology...
processing coordinates...

---
Program grompp, VERSION 3.3.3
Source code file: ../../../../src/kernel/grompp.c, line: 469

Fatal error:
number of coordinates in coordinate file (dppc128.gro, 17365)
   does not match topology (dppc128.top, 0)
---

"One Cross Each" (Monty Python)

I don´t where the problem is, I've already checked the cpp compiler and
it installed in the /usr/bin/cpp, as I put in the .mdp file. In the
topology file I have the following lines:



Have you tried the advice from grompp to use -pp instead of -p?

General advice for this problem can be found here:

http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology 



Also an option is to upgrade to the most recent version of Gromacs 
(4.0.5), which does not require cpp.


-Justin


;
;File 'dppc128.top' was generated
;By user: onbekend (0)
;On host: onbekend
;At date: Tue Aug 18 10:02:52 2009
;
;This is your topology file
;Pure DPPC bilayer with 128 lipids and 3655 water molecules
;
; The force field files to be include
#include "ffoplsaa.itp"
; Include DPPC topology
#include "dppc.itp"
#include "lipid.itp"
#include "spc.itp"

[ molecules ]
; Compound   #mol
DPP  128
SOL  3655

If anyone can help It will be very nice,

Thank you very much so far,
Cíntia C. Vequi-Suplicy
Biophysics Group
Physics Institute
São Paulo University
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Re: [gmx-users] mdrun error

[Justin A. Lemkul]

Pawan Kumar wrote:

probably a bad starting structure...
check this website for  pressure scaling warning : 
http://wiki.gromacs.org/index.php/Errors




Also,

compressibility =  4.575e-4

is of the wrong magnitude for water.  Should be e-5.

-Justin


regards,
pawan

On Mon, Apr 27, 2009 at 5:21 PM, Sheetal Arora 
mailto:sheetal.aror...@gmail.com>> wrote:


I am trying to run the simulation of protein ligand complex.
But after running the mdrun by giving command-"grompp –f md.
mdp –c pr.gro –p trp.top –o md.tpr "
and then "nohup mdrun –deffnm md & "
the md.log file is showing the following message-
Step 11  Warning: pressure scaling more than 1%, mu: 1.01684 1.01684
1.01684

Step 13  Warning: pressure scaling more than 1%, mu: 0.947161
0.947161 0.947161

Step 14  Warning: pressure scaling more than 1%, mu: 1.01207 1.01207
1.01207

Step 15  Warning: pressure scaling more than 1%, mu: 1.18248 1.18248
1.18248

Step 16  Warning: pressure scaling more than 1%, mu: 0.867467
0.867467 0.867467

Step 16, time 0.032 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.099556 (between atoms 1396 and 1398) rms 0.028595
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 21 23   30.80.1740   0.1569  0.1470
 38 40   32.00.1740   0.1583  0.1470
 54 56   33.00.1740   0.1588  0.1470
 56 57   30.60.1810   0.1623  0.1530
 67 69   31.40.1740   0.1568  0.1470
104106   32.60.1740   0.1588  0.1470
106107   31.10.1811   0.1632  0.1530
216218   31.80.1741   0.1584  0.1470
I am attaching my md.mdp file.Please help me in this regard.

-- 
Sheetal Arora

M.Tech(Biotechnology & Medical Engg)

NIT Rourkela

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] mdrun error

[Pawan Kumar]

probably a bad starting structure...
check this website for  pressure scaling warning :
http://wiki.gromacs.org/index.php/Errors

regards,
pawan

On Mon, Apr 27, 2009 at 5:21 PM, Sheetal Arora wrote:

> I am trying to run the simulation of protein ligand complex.
> But after running the mdrun by giving command-"grompp –f md.
> mdp –c pr.gro –p trp.top –o md.tpr "
> and then "nohup mdrun –deffnm md & "
> the md.log file is showing the following message-
> Step 11  Warning: pressure scaling more than 1%, mu: 1.01684 1.01684
> 1.01684
>
> Step 13  Warning: pressure scaling more than 1%, mu: 0.947161 0.947161
> 0.947161
>
> Step 14  Warning: pressure scaling more than 1%, mu: 1.01207 1.01207
> 1.01207
>
> Step 15  Warning: pressure scaling more than 1%, mu: 1.18248 1.18248
> 1.18248
>
> Step 16  Warning: pressure scaling more than 1%, mu: 0.867467 0.867467
> 0.867467
>
> Step 16, time 0.032 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.099556 (between atoms 1396 and 1398) rms 0.028595
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>  21 23   30.80.1740   0.1569  0.1470
>  38 40   32.00.1740   0.1583  0.1470
>  54 56   33.00.1740   0.1588  0.1470
>  56 57   30.60.1810   0.1623  0.1530
>  67 69   31.40.1740   0.1568  0.1470
> 104106   32.60.1740   0.1588  0.1470
> 106107   31.10.1811   0.1632  0.1530
> 216218   31.80.1741   0.1584  0.1470
> I am attaching my md.mdp file.Please help me in this regard.
>
> --
> Sheetal Arora
> M.Tech(Biotechnology & Medical Engg)
>
> NIT Rourkela
>
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[gmx-users] mdrun error

[Sheetal Arora]

I am trying to run the simulation of protein ligand complex.
But after running the mdrun by giving command-"grompp –f md.
mdp –c pr.gro –p trp.top –o md.tpr "
and then "nohup mdrun –deffnm md & "
the md.log file is showing the following message-
Step 11  Warning: pressure scaling more than 1%, mu: 1.01684 1.01684 1.01684

Step 13  Warning: pressure scaling more than 1%, mu: 0.947161 0.947161
0.947161

Step 14  Warning: pressure scaling more than 1%, mu: 1.01207 1.01207 1.01207

Step 15  Warning: pressure scaling more than 1%, mu: 1.18248 1.18248 1.18248

Step 16  Warning: pressure scaling more than 1%, mu: 0.867467 0.867467
0.867467

Step 16, time 0.032 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.099556 (between atoms 1396 and 1398) rms 0.028595
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 21 23   30.80.1740   0.1569  0.1470
 38 40   32.00.1740   0.1583  0.1470
 54 56   33.00.1740   0.1588  0.1470
 56 57   30.60.1810   0.1623  0.1530
 67 69   31.40.1740   0.1568  0.1470
104106   32.60.1740   0.1588  0.1470
106107   31.10.1811   0.1632  0.1530
216218   31.80.1741   0.1584  0.1470
I am attaching my md.mdp file.Please help me in this regard.

-- 
Sheetal Arora
M.Tech(Biotechnology & Medical Engg)

NIT Rourkela


md.mdp
Description: Binary data
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Re: [gmx-users] mdrun error

[Mark Abraham]

supti mukherjee wrote:

Dear all,
I am doing a protein simulation for 20ns in single processor machine. 


You may wish to avoid using MPI versions of GROMACS on a 
single-processor machine.


after 11.1ns when I am trying to rerun mdrun its coming out with the 
following error.

--
Inner product between old and new vector <= 0.0!
constraint #0 atoms 1 and 2
Warning: 1-4 interaction between 1 and 7 at distance inf 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
MPI process rank 0 (n0, p20175) caught a SIGSEGV.
-
Can anybody please give me some clue to solve this?


See 
http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off


Mark
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[gmx-users] mdrun error

[supti mukherjee]

Dear all,
I am doing a protein simulation for 20ns in single processor machine. after
11.1ns when I am trying to rerun mdrun its coming out with the following
error.
--
Inner product between old and new vector <= 0.0!
constraint #0 atoms 1 and 2
Warning: 1-4 interaction between 1 and 7 at distance inf 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
MPI process rank 0 (n0, p20175) caught a SIGSEGV.
-
Can anybody please give me some clue to solve this?
Thanks in advance
Supti Mukhopadhyay
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RE: [gmx-users] mdrun error

[pragya chohan]

hi 
i tried to run the simulation with single alamethicin molecule but i am getting 
the same error as i was getting earlier.
Warning: 1-4 interaction between 164 and>> 169 at distance 3.430 which is 
larger than the 1-4 table size 1.000 nm.
I used the command 
 $ genbox -cp alamethicin.gro -cs popc.gro -o system.gro 
my pdb file at 164 to 169 is:
ATOM 164 CZ PHL 21 44.000 52.840 35.170 1.00 0.00
ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00
ATOM 166 CX PHL 21 38.140 50.450 37.160 1.00 0.00
ATOM 167 OY PHL 21 37.940 49.350 38.060 1.00 0.00
ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00
ATOM 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00.
This is occuring at the start of equillibration step . I have not done any 
simulation as yet. 
I also tried pre-equillibrating the protein and directly simulating by restrain 
but that also is not working.

I cannot figure out the problem. Please help

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Virginia>>> Tech> Blacksburg, VA> [EMAIL PROTECTED] | (540) 231-9080>> 
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= 
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Graduate Research Assistant> Department of Biochemistry> Virginia Tech> 
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Re: [gmx-users] mdrun error

[Mark Abraham]

pragya chohan wrote:

Hi justin
I placed POPC membrane in a box too of same dimension as the box of 
alamethicin and centred it too so that alamethicin is placed correctly 
in the membrane.

I am attaching the pdb please have a look.
Any help would be appreciated


Check out http://wiki.gromacs.org/index.php/Membrane_Simulations

Mark
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RE: [gmx-users] mdrun error

[Justin A. Lemkul]

Pragya,

I just realized that I may have read your message incorrectly.  If you'd like to
send me your PDB file off-list, I'd be happy to have a look.

-Justin

Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:

> Quoting pragya chohan <[EMAIL PROTECTED]>:
>
> > Hi justin
> > I placed POPC membrane in a box too of same dimension as the box of
> > alamethicin and centred it too so that alamethicin is placed correctly in
> the
> > membrane.
> > I am attaching the pdb please have a look.Any help would be appreciated
>
> Looks like the listserv ate the PDB file, but from your description it sounds
> like you've generated some severe atomic overlap.  Simply pasting coordinates
> of a protein into a membrane is sure to cause bad contacts.  The proper
> procedure would be to create a cavity within the membrane and place the
> protein
> in it (i.e., make_hole.pl, inflategro, as I previously suggested), or using
> genbox, which you originally said you did.  Try this (assuming you have the
> box
> dimensions correct):
>
> $ genbox -cp alamethicin.gro -cs popc.gro -o system.gro
>
> -Justin
>
> >
> > Pragya
> >
> >
> >
> > > Date: Sat, 10 Nov 2007 12:42:01 -0500> From: [EMAIL PROTECTED]> To:
> > gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Quoting
> pragya
> > chohan <[EMAIL PROTECTED]>:> > > Thanks Justin for your reply. I am
> > generating the starting structure through> > genbox.> > I added popc as
> > solvent around alamethicin after aligning alamethicin in a> > box and
> > centering it in the box and followed same procedure for popc also. Do> >
> you
> > have any better way?> >> > In theory, that should work just fine, but I
> don't
> > understand what you mean by> "followed the same procedure for popc." What
> did
> > you do there? The first part> should be all you need (alamethicin in the
> box,
> > solvated with popc).> > Alternatively, you can use make_hole.pl or the
> > inflategro script available> through Peter Tieleman's site:> >
> > http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis> > -Justin> >
> >>
> > >> > > Date: Sat, 10 Nov 2007 10:22:45 -0500> From: [EMAIL PROTECTED]> To:> 
> > >> > > >
> > gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Since> >
> > alamethicin works on its own, it suggests to me that the introduction of>>
> >
> > alamethicin into POPC is what's causing the problem, and judging by the>> >
> > enormous potential energies and forces, it appears to be bad
> > contacts/atomic>> > overlap (at least, that's been the cause of problems in
> > my experience). How>> > are you generating your starting structure?> >
> > -Justin> > >> > Thanks for> > your help. I figured the problem out but am
> > getting an error> > again. I have> > alamethicin in popc and water. Since
> > alamethicin has some non> > standard> > residue i made topology file in
> text
> > editor and ran mdrun with only> >> > alamethicin. It went fine. But when i
> am
> > tring to minimize alamethicin in> >> > popc mdrum probably does not
> recognize
> > the starting of second chain and> > gives> > me following error:> >> >
> > Warning: 1-4 interaction between 164 and> > 169 at distance 3.430 which is>
> >
> > larger than the 1-4 table size 1.000 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> > Step= 1,
> > Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09,> > atom=> > 2441> >
> > Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax=> > 1.82388e+08, atom=> >
> > 12852> > Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09> > Fmax= 7.44135e+07,
> > atom= 262> > Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09> > Fmax=
> > 4.32188e+07, atom= 260> > Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09> >
> > Fmax= 2.77292e+07, atom= 262> > Step= 6, Dmax= 2.5e-02 nm, Epot=
> 1.83083e+09>
> > > Fmax= 1.89783e+07, atom= 258> > Step= 7, Dmax= 3.0e-02 nm, Epot=
> > 1.81606e+09> > Fmax= 9.97167e+06, atom= 253> > Step= 8, Dmax= 3.6e-02 nm,
> > Epot= 1.79660e+09> > Fmax= 2.09557e+07, atom=

RE: [gmx-users] mdrun error

[Justin A. Lemkul]

Quoting pragya chohan <[EMAIL PROTECTED]>:

> Hi justin
> I placed POPC membrane in a box too of same dimension as the box of
> alamethicin and centred it too so that alamethicin is placed correctly in the
> membrane.
> I am attaching the pdb please have a look.Any help would be appreciated

Looks like the listserv ate the PDB file, but from your description it sounds
like you've generated some severe atomic overlap.  Simply pasting coordinates
of a protein into a membrane is sure to cause bad contacts.  The proper
procedure would be to create a cavity within the membrane and place the protein
in it (i.e., make_hole.pl, inflategro, as I previously suggested), or using
genbox, which you originally said you did.  Try this (assuming you have the box
dimensions correct):

$ genbox -cp alamethicin.gro -cs popc.gro -o system.gro

-Justin

>
> Pragya
>
>
>
> > Date: Sat, 10 Nov 2007 12:42:01 -0500> From: [EMAIL PROTECTED]> To:
> gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Quoting pragya
> chohan <[EMAIL PROTECTED]>:> > > Thanks Justin for your reply. I am
> generating the starting structure through> > genbox.> > I added popc as
> solvent around alamethicin after aligning alamethicin in a> > box and
> centering it in the box and followed same procedure for popc also. Do> > you
> have any better way?> >> > In theory, that should work just fine, but I don't
> understand what you mean by> "followed the same procedure for popc." What did
> you do there? The first part> should be all you need (alamethicin in the box,
> solvated with popc).> > Alternatively, you can use make_hole.pl or the
> inflategro script available> through Peter Tieleman's site:> >
> http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis> > -Justin> > >>
> >> > > Date: Sat, 10 Nov 2007 10:22:45 -0500> From: [EMAIL PROTECTED]> To:> >
> gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Since> >
> alamethicin works on its own, it suggests to me that the introduction of>> >
> alamethicin into POPC is what's causing the problem, and judging by the>> >
> enormous potential energies and forces, it appears to be bad
> contacts/atomic>> > overlap (at least, that's been the cause of problems in
> my experience). How>> > are you generating your starting structure?> >
> -Justin> > >> > Thanks for> > your help. I figured the problem out but am
> getting an error> > again. I have> > alamethicin in popc and water. Since
> alamethicin has some non> > standard> > residue i made topology file in text
> editor and ran mdrun with only> >> > alamethicin. It went fine. But when i am
> tring to minimize alamethicin in> >> > popc mdrum probably does not recognize
> the starting of second chain and> > gives> > me following error:> >> >
> Warning: 1-4 interaction between 164 and> > 169 at distance 3.430 which is> >
> larger than the 1-4 table size 1.000 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> > Step= 1,
> Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09,> > atom=> > 2441> >
> Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax=> > 1.82388e+08, atom=> >
> 12852> > Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09> > Fmax= 7.44135e+07,
> atom= 262> > Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09> > Fmax=
> 4.32188e+07, atom= 260> > Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09> >
> Fmax= 2.77292e+07, atom= 262> > Step= 6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09>
> > Fmax= 1.89783e+07, atom= 258> > Step= 7, Dmax= 3.0e-02 nm, Epot=
> 1.81606e+09> > Fmax= 9.97167e+06, atom= 253> > Step= 8, Dmax= 3.6e-02 nm,
> Epot= 1.79660e+09> > Fmax= 2.09557e+07, atom= 258> > Step= 9, Dmax= 4.3e-02
> nm, Epot= 1.78793e+09> > Fmax= 1.63547e+07, atom= 259> > Step= 10, Dmax=
> 5.2e-02 nm, Epot= 1.77532e+09> > Fmax= 7.54157e+06, atom=> > 12539> > Step=
> 11, Dmax= 6.2e-02 nm, Epot=> > 1.74488e+09 Fmax= 7.42417e+06, atom=> > 12539>
> > Step= 12, Dmax= 7.4e-02 nm,> > Epot= 1.70998e+09 Fmax= 7.28331e+06, atom=>
> > 12539> > Step= 13, Dmax=> > 8.9e-02 nm, Epot= 1.66920e+09 Fmax=
> 7.11508e+06, atom=> > 12539> > Wrote pdb> > files with previous and current
> coordinates> >> > Back Off! I just b

RE: [gmx-users] mdrun error

[pragya chohan]

Hi justin 
I placed POPC membrane in a box too of same dimension as the box of alamethicin 
and centred it too so that alamethicin is placed correctly in the membrane. 
I am attaching the pdb please have a look.Any help would be appreciated
 
Pragya



> Date: Sat, 10 Nov 2007 12:42:01 -0500> From: [EMAIL PROTECTED]> To: 
> gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Quoting pragya 
> chohan <[EMAIL PROTECTED]>:> > > Thanks Justin for your reply. I am 
> generating the starting structure through> > genbox.> > I added popc as 
> solvent around alamethicin after aligning alamethicin in a> > box and 
> centering it in the box and followed same procedure for popc also. Do> > you 
> have any better way?> >> > In theory, that should work just fine, but I don't 
> understand what you mean by> "followed the same procedure for popc." What did 
> you do there? The first part> should be all you need (alamethicin in the box, 
> solvated with popc).> > Alternatively, you can use make_hole.pl or the 
> inflategro script available> through Peter Tieleman's site:> > 
> http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis> > -Justin> > >> 
> >> > > Date: Sat, 10 Nov 2007 10:22:45 -0500> From: [EMAIL PROTECTED]> To:> > 
> gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Since> > 
> alamethicin works on its own, it suggests to me that the introduction of>> > 
> alamethicin into POPC is what's causing the problem, and judging by the>> > 
> enormous potential energies and forces, it appears to be bad 
> contacts/atomic>> > overlap (at least, that's been the cause of problems in 
> my experience). How>> > are you generating your starting structure?> > 
> -Justin> > >> > Thanks for> > your help. I figured the problem out but am 
> getting an error> > again. I have> > alamethicin in popc and water. Since 
> alamethicin has some non> > standard> > residue i made topology file in text 
> editor and ran mdrun with only> >> > alamethicin. It went fine. But when i am 
> tring to minimize alamethicin in> >> > popc mdrum probably does not recognize 
> the starting of second chain and> > gives> > me following error:> >> > 
> Warning: 1-4 interaction between 164 and> > 169 at distance 3.430 which is> > 
> larger than the 1-4 table size 1.000 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> > Step= 1, 
> Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09,> > atom=> > 2441> > 
> Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax=> > 1.82388e+08, atom=> > 
> 12852> > Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09> > Fmax= 7.44135e+07, 
> atom= 262> > Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09> > Fmax= 
> 4.32188e+07, atom= 260> > Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09> > 
> Fmax= 2.77292e+07, atom= 262> > Step= 6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09> 
> > Fmax= 1.89783e+07, atom= 258> > Step= 7, Dmax= 3.0e-02 nm, Epot= 
> 1.81606e+09> > Fmax= 9.97167e+06, atom= 253> > Step= 8, Dmax= 3.6e-02 nm, 
> Epot= 1.79660e+09> > Fmax= 2.09557e+07, atom= 258> > Step= 9, Dmax= 4.3e-02 
> nm, Epot= 1.78793e+09> > Fmax= 1.63547e+07, atom= 259> > Step= 10, Dmax= 
> 5.2e-02 nm, Epot= 1.77532e+09> > Fmax= 7.54157e+06, atom=> > 12539> > Step= 
> 11, Dmax= 6.2e-02 nm, Epot=> > 1.74488e+09 Fmax= 7.42417e+06, atom=> > 12539> 
> > Step= 12, Dmax= 7.4e-02 nm,> > Epot= 1.70998e+09 Fmax= 7.28331e+06, atom=> 
> > 12539> > Step= 13, Dmax=> > 8.9e-02 nm, Epot= 1.66920e+09 Fmax= 
> 7.11508e+06, atom=> > 12539> > Wrote pdb> > files with previous and current 
> coordinates> >> > Back Off! I just backed up> > step13.pdb to 
> ./#step13.pdb.1#> >> > Back Off! I just backed up step14.pdb to> > 
> ./#step14.pdb.1#> > Wrote pdb files with previous and current coordinates> 
> >>> > > my pdb file at 164 to 169 is:> > ATOM 164 CZ PHL 21 44.000 52.840 
> 35.170> > 1.00 0.00> > ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00> > 
> ATOM 166 CX> > PHL 21 38.140 50.450 37.160 1.00 0.00> > ATOM 167 OY PHL 21 
> 37.940 49.350> > 38.060 1.00 0.00> > ATOM 168 HY PHL 21 37.040 48.940 37.950 
> 1

RE: [gmx-users] mdrun error

[Justin A. Lemkul]

Quoting pragya chohan <[EMAIL PROTECTED]>:

> Thanks Justin for your reply. I am generating the starting structure through
> genbox.
> I added popc as solvent around alamethicin after aligning alamethicin in a
> box and centering it in the box and followed same procedure for popc also. Do
> you have any better way?
>

In theory, that should work just fine, but I don't understand what you mean by
"followed the same procedure for popc."  What did you do there?  The first part
should be all you need (alamethicin in the box, solvated with popc).

Alternatively, you can use make_hole.pl or the inflategro script available
through Peter Tieleman's site:

http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis

-Justin

>
>
> > Date: Sat, 10 Nov 2007 10:22:45 -0500> From: [EMAIL PROTECTED]> To:
> gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Since
> alamethicin works on its own, it suggests to me that the introduction of>
> alamethicin into POPC is what's causing the problem, and judging by the>
> enormous potential energies and forces, it appears to be bad contacts/atomic>
> overlap (at least, that's been the cause of problems in my experience). How>
> are you generating your starting structure?> > -Justin> > >> > Thanks for
> your help. I figured the problem out but am getting an error> > again. I have
> alamethicin in popc and water. Since alamethicin has some non> > standard
> residue i made topology file in text editor and ran mdrun with only> >
> alamethicin. It went fine. But when i am tring to minimize alamethicin in> >
> popc mdrum probably does not recognize the starting of second chain and
> gives> > me following error:> >> > Warning: 1-4 interaction between 164 and
> 169 at distance 3.430 which is> > larger than the 1-4 table size 1.000 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> > Step= 1, Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09,
> atom=> > 2441> > Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax=
> 1.82388e+08, atom=> > 12852> > Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09
> Fmax= 7.44135e+07, atom= 262> > Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09
> Fmax= 4.32188e+07, atom= 260> > Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09
> Fmax= 2.77292e+07, atom= 262> > Step= 6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09
> Fmax= 1.89783e+07, atom= 258> > Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81606e+09
> Fmax= 9.97167e+06, atom= 253> > Step= 8, Dmax= 3.6e-02 nm, Epot= 1.79660e+09
> Fmax= 2.09557e+07, atom= 258> > Step= 9, Dmax= 4.3e-02 nm, Epot= 1.78793e+09
> Fmax= 1.63547e+07, atom= 259> > Step= 10, Dmax= 5.2e-02 nm, Epot= 1.77532e+09
> Fmax= 7.54157e+06, atom=> > 12539> > Step= 11, Dmax= 6.2e-02 nm, Epot=
> 1.74488e+09 Fmax= 7.42417e+06, atom=> > 12539> > Step= 12, Dmax= 7.4e-02 nm,
> Epot= 1.70998e+09 Fmax= 7.28331e+06, atom=> > 12539> > Step= 13, Dmax=
> 8.9e-02 nm, Epot= 1.66920e+09 Fmax= 7.11508e+06, atom=> > 12539> > Wrote pdb
> files with previous and current coordinates> >> > Back Off! I just backed up
> step13.pdb to ./#step13.pdb.1#> >> > Back Off! I just backed up step14.pdb to
> ./#step14.pdb.1#> > Wrote pdb files with previous and current coordinates> >>
> > my pdb file at 164 to 169 is:> > ATOM 164 CZ PHL 21 44.000 52.840 35.170
> 1.00 0.00> > ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00> > ATOM 166 CX
> PHL 21 38.140 50.450 37.160 1.00 0.00> > ATOM 167 OY PHL 21 37.940 49.350
> 38.060 1.00 0.00> > ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00> > ATOM
> 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00> >> > I think it is not
> recognising different chain. Am i right? Please help me.> >
> _> > Check
> out some new online services at Windows Live Ideas—so new they haven’t> >
> even been officially released yet.> >>
>
http://www.msnspecials.in/windowslive/___>
> > gmx-users mailing list gmx-users@gromacs.org> >
> http://www.gromacs.org/mailman/listinfo/gmx-users> > Please search the
> archive at http://www.gromacs.org/search before posting!> > Please don't post
> (un)subscribe requests to the list. Use the> > www interface or send it to
> [EMAIL PROTECTED]> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php> >> 

RE: [gmx-users] mdrun error

[pragya chohan]

Thanks Justin for your reply. I am generating the starting structure through 
genbox.
I added popc as solvent around alamethicin after aligning alamethicin in a box 
and centering it in the box and followed same procedure for popc also. Do you 
have any better way?



> Date: Sat, 10 Nov 2007 10:22:45 -0500> From: [EMAIL PROTECTED]> To: 
> gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Since 
> alamethicin works on its own, it suggests to me that the introduction of> 
> alamethicin into POPC is what's causing the problem, and judging by the> 
> enormous potential energies and forces, it appears to be bad contacts/atomic> 
> overlap (at least, that's been the cause of problems in my experience). How> 
> are you generating your starting structure?> > -Justin> > >> > Thanks for 
> your help. I figured the problem out but am getting an error> > again. I have 
> alamethicin in popc and water. Since alamethicin has some non> > standard 
> residue i made topology file in text editor and ran mdrun with only> > 
> alamethicin. It went fine. But when i am tring to minimize alamethicin in> > 
> popc mdrum probably does not recognize the starting of second chain and 
> gives> > me following error:> >> > Warning: 1-4 interaction between 164 and 
> 169 at distance 3.430 which is> > larger than the 1-4 table size 1.000 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> > Step= 1, Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09, 
> atom=> > 2441> > Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax= 
> 1.82388e+08, atom=> > 12852> > Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09 
> Fmax= 7.44135e+07, atom= 262> > Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09 
> Fmax= 4.32188e+07, atom= 260> > Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09 
> Fmax= 2.77292e+07, atom= 262> > Step= 6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09 
> Fmax= 1.89783e+07, atom= 258> > Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81606e+09 
> Fmax= 9.97167e+06, atom= 253> > Step= 8, Dmax= 3.6e-02 nm, Epot= 1.79660e+09 
> Fmax= 2.09557e+07, atom= 258> > Step= 9, Dmax= 4.3e-02 nm, Epot= 1.78793e+09 
> Fmax= 1.63547e+07, atom= 259> > Step= 10, Dmax= 5.2e-02 nm, Epot= 1.77532e+09 
> Fmax= 7.54157e+06, atom=> > 12539> > Step= 11, Dmax= 6.2e-02 nm, Epot= 
> 1.74488e+09 Fmax= 7.42417e+06, atom=> > 12539> > Step= 12, Dmax= 7.4e-02 nm, 
> Epot= 1.70998e+09 Fmax= 7.28331e+06, atom=> > 12539> > Step= 13, Dmax= 
> 8.9e-02 nm, Epot= 1.66920e+09 Fmax= 7.11508e+06, atom=> > 12539> > Wrote pdb 
> files with previous and current coordinates> >> > Back Off! I just backed up 
> step13.pdb to ./#step13.pdb.1#> >> > Back Off! I just backed up step14.pdb to 
> ./#step14.pdb.1#> > Wrote pdb files with previous and current coordinates> >> 
> > my pdb file at 164 to 169 is:> > ATOM 164 CZ PHL 21 44.000 52.840 35.170 
> 1.00 0.00> > ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00> > ATOM 166 CX 
> PHL 21 38.140 50.450 37.160 1.00 0.00> > ATOM 167 OY PHL 21 37.940 49.350 
> 38.060 1.00 0.00> > ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00> > ATOM 
> 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00> >> > I think it is not 
> recognising different chain. Am i right? Please help me.> > 
> _> > Check 
> out some new online services at Windows Live Ideas—so new they haven’t> > 
> even been officially released yet.> >> 
> http://www.msnspecials.in/windowslive/___>
>  > gmx-users mailing list gmx-users@gromacs.org> > 
> http://www.gromacs.org/mailman/listinfo/gmx-users> > Please search the 
> archive at http://www.gromacs.org/search before posting!> > Please don't post 
> (un)subscribe requests to the list. Use the> > www interface or send it to 
> [EMAIL PROTECTED]> > Can't post? Read 
> http://www.gromacs.org/mailing_lists/users.php> >> > > > 
> => > Justin A. 
> Lemkul> Graduate Research Assistant> Department of Biochemistry> Virginia 
> Tech> Blacksburg, VA> [EMAIL PROTECTED] | (540) 231-9080> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> > 
> => 
> ___> gmx-users 

RE: [gmx-users] mdrun error

[Justin A. Lemkul]

Since alamethicin works on its own, it suggests to me that the introduction of
alamethicin into POPC is what's causing the problem, and judging by the
enormous potential energies and forces, it appears to be bad contacts/atomic
overlap (at least, that's been the cause of problems in my experience).  How
are you generating your starting structure?

-Justin

>
> Thanks for your help. I figured the problem out but am getting an error
> again. I have alamethicin in popc and water. Since alamethicin has some non
> standard residue i made topology file in text editor and ran mdrun with only
> alamethicin. It went fine. But when i am tring to minimize alamethicin in
> popc mdrum probably does not recognize the starting of second chain and gives
> me following error:
>
> Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is
> larger than the 1-4 table size 1.000 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
> Step=1, Dmax= 1.0e-02 nm, Epot=  3.25524e+09 Fmax= 1.00321e+09, atom=
> 2441
> Step=2, Dmax= 1.2e-02 nm, Epot=  2.21743e+09 Fmax= 1.82388e+08, atom=
> 12852
> Step=3, Dmax= 1.4e-02 nm, Epot=  1.95672e+09 Fmax= 7.44135e+07, atom= 262
> Step=4, Dmax= 1.7e-02 nm, Epot=  1.88109e+09 Fmax= 4.32188e+07, atom= 260
> Step=5, Dmax= 2.1e-02 nm, Epot=  1.84989e+09 Fmax= 2.77292e+07, atom= 262
> Step=6, Dmax= 2.5e-02 nm, Epot=  1.83083e+09 Fmax= 1.89783e+07, atom= 258
> Step=7, Dmax= 3.0e-02 nm, Epot=  1.81606e+09 Fmax= 9.97167e+06, atom= 253
> Step=8, Dmax= 3.6e-02 nm, Epot=  1.79660e+09 Fmax= 2.09557e+07, atom= 258
> Step=9, Dmax= 4.3e-02 nm, Epot=  1.78793e+09 Fmax= 1.63547e+07, atom= 259
> Step=   10, Dmax= 5.2e-02 nm, Epot=  1.77532e+09 Fmax= 7.54157e+06, atom=
> 12539
> Step=   11, Dmax= 6.2e-02 nm, Epot=  1.74488e+09 Fmax= 7.42417e+06, atom=
> 12539
> Step=   12, Dmax= 7.4e-02 nm, Epot=  1.70998e+09 Fmax= 7.28331e+06, atom=
> 12539
> Step=   13, Dmax= 8.9e-02 nm, Epot=  1.66920e+09 Fmax= 7.11508e+06, atom=
> 12539
> Wrote pdb files with previous and current coordinates
>
> Back Off! I just backed up step13.pdb to ./#step13.pdb.1#
>
> Back Off! I just backed up step14.pdb to ./#step14.pdb.1#
> Wrote pdb files with previous and current coordinates
>
> my pdb file at 164 to 169 is:
> ATOM164  CZ  PHL21  44.000  52.840  35.170  1.00  0.00
> ATOM165  HZ  PHL21  44.990  53.260  35.090  1.00  0.00
> ATOM166  CX  PHL21  38.140  50.450  37.160  1.00  0.00
> ATOM167  OY  PHL21  37.940  49.350  38.060  1.00  0.00
> ATOM168  HY  PHL21  37.040  48.940  37.950  1.00  0.00
> ATOM169  CA  ACE22  53.840  44.410  66.930  1.00  0.00
>
> I think it is not recognising different chain. Am i right? Please help me.
> _
> Check out some new online services at Windows Live Ideas—so new they haven’t
> even been officially released yet.
>
http://www.msnspecials.in/windowslive/___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
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>



=

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

=
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RE: [gmx-users] mdrun error

[pragya chohan]

> Date: Fri, 9 Nov 2007 09:01:48 -0500> 
From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] 
mdrun error>> Check out the wiki at:>> 
http://wiki.gromacs.org/index.php/Errors#LINCS_warnings>> Alternatively, search 
the list for some of my posts from around a year ago - NVT> and minimization of 
a lipid bilayer (or search for my name, they should come up> as well). I 
suspect you have bad contacts in your starting structure.>> -Justin>> Quoting 
pragya chohan :>>>>> hi i am trying to run mdrun for protein in membrane 
system. When i run mdrun>> i get a warning>>>> Step -2, time -0.002 (ps) LINCS 
WARNING>> relative constraint deviation after LINCS:>> max 2.144082 (between 
atoms 12433 and 12434) rms 0.216090>> bonds that rotated more than 30 
degrees:>> atom 1 atom 2 angle previous, current, constraint length>> 11761 
11762 90.0 0.1633 0.2387 0.1000>> 11929 11930 31.7 0.1633 0.1000 0.1000>> 12097 
12098 90.0 0.1632 0.1041 0.1000>> 12265 12266 90.0 0.1633 0.2266 0.1000>> 12433 
12434 90.0 0.1633 0.3144 0.1000>> starting mdrun 'alamethicin in popc'>> 500 
steps, 0.5 ps.>>>> Warning: 1-4 interaction between 115 and 136 at distance 
1.144 which is>> larger t>> han the 1-4 table size 1.000 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>>>> Step 0, time 0 
(ps) LINCS WARNING>> relative constraint deviation after LINCS:>> max inf 
(between atoms 12007 and 12008) rms inf>> bonds that rotated more than 30 
degrees:>> atom 1 atom 2 angle previous, current, constraint length>> 11619 
11620 90.0 0.1000 0.1411 0.1000>> 11633 11634 90.0 0.1000 13155507200. 
0.1000>> 11640 11641 90.0 0.1000 0.1214 0.1000>> .>> 12619 12620 90.0 
0.1080 0.1447 0.1080>> Wrote pdb files with previous and current coordinates>> 
step 0Segmentation fault>> I am using shake in my mdp file. I want to restrain 
water.>>>> my mdp file is:>> title = popc128a>> integrator = md>> define = 
-DFLEX_SPC>> dt = 0.001>> nsteps = 500>> nstxout = 500>> ns_type = grid>> pbc = 
xyz>> constraints = hbonds>> constraints_algorithm= shake>> coulombtype = PME>> 
vdwtype = cut-off>> rcoloumb = 1.0>> nstlist = 10.0>> Tcoupl = no>> pcoupl = 
no>> compressibility = 4.5e-5>> gen_temp = 300>> gen_vel = no>> Please help.>> 
Thanks in advance.>> 
_>> Check out 
some new online services at Windows Live Ideas—so new they haven’t>> even been 
officially released yet.>>> 
http://www.msnspecials.in/windowslive/___>>
 gmx-users mailing list gmx-users@gromacs.org>> 
http://www.gromacs.org/mailman/listinfo/gmx-users>> Please search the archive 
at http://www.gromacs.org/search before posting!>> Please don't post 
(un)subscribe requests to the list. Use the>> www interface or send it to 
[EMAIL PROTECTED]>> Can't post? Read 
http://www.gromacs.org/mailing_lists/users.php>>>>>> 
=>> Justin A. Lemkul> 
Graduate Research Assistant> Department of Biochemistry> Virginia Tech> 
Blacksburg, VA> [EMAIL PROTECTED] | (540) 231-9080> 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/>> 
=> 
___> gmx-users mailing list 
gmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> 
Please search the archive at http://www.gromacs.org/search before posting!> 
Please don't post (un)subscribe requests to the list. Use the> www interface or 
send it to [EMAIL PROTECTED]> Can't post? Read 
http://www.gromacs.org/mailing_lists/users.php

Thanks for your help. I figured the problem out but am getting an error again. 
I have alamethicin in popc and water. Since alamethicin has some non standard 
residue i made topology file in text editor and ran mdrun with only 
alamethicin. It went fine. But when i am tring to minimize alamethicin in popc 
mdrum probably does not recognize the starting of second chain and gives me 
following error:

Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is larger 
than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase tab

Re: [gmx-users] mdrun error

[Mark Abraham]

>
> hi i am trying to run mdrun for protein in membrane system. When i run
> mdrun i get a warning

Check out the wiki link Justin provided. Also read
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and make
sure your setup regime is reasonable.

Also, when you run grompp, pay attention to the warning messages. You'll
get at least one for this .mdp file.

> my mdp file is:
> title= popc128a
> integrator   = md
> define   = -DFLEX_SPC
> dt   = 0.001
> nsteps   = 500
> nstxout  = 500
> ns_type  = grid
> pbc  = xyz
> constraints  = hbonds
> constraints_algorithm= shake
> coulombtype  = PME
> vdwtype  = cut-off
> rcoloumb = 1.0
> nstlist  = 10.0
> Tcoupl   = no
> pcoupl   = no
> compressibility  = 4.5e-5
> gen_temp = 300
> gen_vel  = no
> Please help.
> Thanks in advance.

Mark

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Re: [gmx-users] mdrun error

[Justin A. Lemkul]

Check out the wiki at:

http://wiki.gromacs.org/index.php/Errors#LINCS_warnings

Alternatively, search the list for some of my posts from around a year ago - NVT
and minimization of a lipid bilayer (or search for my name, they should come up
as well).  I suspect you have bad contacts in your starting structure.

-Justin

Quoting pragya chohan <[EMAIL PROTECTED]>:

>
> hi i am trying to run mdrun for protein in membrane system. When i run mdrun
> i get a warning
>
> Step -2, time -0.002 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 2.144082 (between atoms 12433 and 12434) rms 0.216090
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   11761  11762   90.00.1633   0.2387  0.1000
>   11929  11930   31.70.1633   0.1000  0.1000
>   12097  12098   90.00.1632   0.1041  0.1000
>   12265  12266   90.00.1633   0.2266  0.1000
>   12433  12434   90.00.1633   0.3144  0.1000
> starting mdrun 'alamethicin in popc'
> 500 steps,  0.5 ps.
>
> Warning: 1-4 interaction between 115 and 136 at distance 1.144 which is
> larger t
> han the 1-4 table size 1.000 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
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max inf (between atoms 12007 and 12008) rms inf
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   11619  11620   90.00.1000   0.1411  0.1000
>   11633  11634   90.00.1000 13155507200.  0.1000
>   11640  11641   90.00.1000   0.1214  0.1000
> .
>   12619  12620   90.00.1080   0.1447  0.1080
> Wrote pdb files with previous and current coordinates
> step 0Segmentation fault
> I am using shake in my mdp file. I want to restrain water.
>
> my mdp file is:
> title= popc128a
> integrator   = md
> define   = -DFLEX_SPC
> dt   = 0.001
> nsteps   = 500
> nstxout  = 500
> ns_type  = grid
> pbc  = xyz
> constraints  = hbonds
> constraints_algorithm= shake
> coulombtype  = PME
> vdwtype  = cut-off
> rcoloumb = 1.0
> nstlist  = 10.0
> Tcoupl   = no
> pcoupl   = no
> compressibility  = 4.5e-5
> gen_temp = 300
> gen_vel  = no
> Please help.
> Thanks in advance.
> _
> Check out some new online services at Windows Live Ideas—so new they haven’t
> even been officially released yet.
>
http://www.msnspecials.in/windowslive/___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



=

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

=
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[gmx-users] mdrun error

[pragya chohan]

hi i am trying to run mdrun for protein in membrane system. When i run mdrun i 
get a warning

Step -2, time -0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 2.144082 (between atoms 12433 and 12434) rms 0.216090
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  11761  11762   90.00.1633   0.2387  0.1000
  11929  11930   31.70.1633   0.1000  0.1000
  12097  12098   90.00.1632   0.1041  0.1000
  12265  12266   90.00.1633   0.2266  0.1000
  12433  12434   90.00.1633   0.3144  0.1000
starting mdrun 'alamethicin in popc'
500 steps,  0.5 ps.

Warning: 1-4 interaction between 115 and 136 at distance 1.144 which is larger t
han the 1-4 table size 1.000 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

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max inf (between atoms 12007 and 12008) rms inf
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  11619  11620   90.00.1000   0.1411  0.1000
  11633  11634   90.00.1000 13155507200.  0.1000
  11640  11641   90.00.1000   0.1214  0.1000
.
  12619  12620   90.00.1080   0.1447  0.1080
Wrote pdb files with previous and current coordinates
step 0Segmentation fault
I am using shake in my mdp file. I want to restrain water.

my mdp file is:
title= popc128a
integrator   = md
define   = -DFLEX_SPC
dt   = 0.001
nsteps   = 500
nstxout  = 500
ns_type  = grid
pbc  = xyz
constraints  = hbonds
constraints_algorithm= shake
coulombtype  = PME
vdwtype  = cut-off
rcoloumb = 1.0
nstlist  = 10.0
Tcoupl   = no
pcoupl   = no
compressibility  = 4.5e-5
gen_temp = 300
gen_vel  = no
Please help.
Thanks in advance.
_
Check out some new online services at Windows Live Ideas—so new they haven’t 
even been officially released yet.
http://www.msnspecials.in/windowslive/___
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Re: [gmx-users] mdrun error after 2.6nS

[Mark Abraham]

Blaise Mathias-Costa wrote:
Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone 
through that web site and it doesn't say anything very specific, for 
example if the system is not minimized properly it should have 
complained at the beginning, but the problem arises after 2.6nS!


No. The numerical equations are well-defined whether or not you 
minimize. Whether the system is numerically or physically stable is 
another matter, and things could fairly easily take many picoseconds to 
nanoseconds in a feedback loop to get bad enough to cause LINCS warnings.


The website can't be more specific, because proper system preparation is 
a bit of dark art and system-dependent.


I have searched in the archive, when somebody had similar problem with 
PR run David suggested to look for the "center-of-mass motion removal", 
to give POPC+Protein, but I dont have POPC in my system. In another case 
advised to reduce the time step, does it mean that I should reduce the 
time step from 0.002 to 0.001 and do the simulations from the beginning?


Yes. Making the integration time step smaller can help you relax away 
from bad numerical space into good ones... once equilibrated you can 
then try relaxing the time step back to 2fs.


Another suggestion was the computing power may not be sufficient, but I 
don't think this will be applicable for me, b'se I am running in 8 nodes 
each node is with 4 processors, and the unit cell size is ~96000 atoms 
in total.
 
What could be the most appropriate way to solve this problem?  Many 
thanks in  advance!


Find a reasonable equilibration protocol in the literature for a system 
similar to yours, try it out, and experiment.


Mark
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Re: [gmx-users] mdrun error after 2.6nS

[Tsjerk Wassenaar]

Hi Blaise,

Check for the first occurrence of the error in the log file and match the
atom numbers against your .gro file to see which residue is involved from
the beginning. Also, do you have non-standard residues/metal ions? Tell more
about the system and what you're trying to do.

Best,

Tsjerk

On 10/3/07, Blaise Mathias-Costa <[EMAIL PROTECTED]> wrote:
>
> Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone
> through that web site and it doesn't say anything very specific, for example
> if the system is not minimized properly it should have complained at the
> beginning, but the problem arises after 2.6nS!
> I have searched in the archive, when somebody had similar problem with PR
> run David suggested to look for the "center-of-mass motion removal", to give
> POPC+Protein, but I dont have POPC in my system. In another case advised to
> reduce the time step, does it mean that I should reduce the time step from
> 0.002 to 0.001 and do the simulations from the beginning?
>
> Another suggestion was the computing power may not be sufficient, but I
> don't think this will be applicable for me, b'se I am running in 8 nodes
> each node is with 4 processors, and the unit cell size is ~96000 atoms in
> total.
>
> What could be the most appropriate way to solve this problem?  Many thanks
> in  advance!
>
> Kind Regards,
> Blaise
>
> Blaise Mathias Costa, PhD
> Department of Pharmacology and Experimental Neuroscience
> University of Nebraska Medical Center
> Omaha, NE 68198-5800, USA.
> Tel: 001 402 559 7132
>
> [EMAIL PROTECTED] wrote: -
>
> To: Discussion list for GROMACS users 
> From: Mark Abraham <[EMAIL PROTECTED]>
> Sent by: [EMAIL PROTECTED]
> Date: 10/02/2007 12:29PM
> Subject: Re: [gmx-users] mdrun error after 2.6nS
>
> Blaise Mathias-Costa wrote:
> > Hi all,
> >
> > The mdrun stopped  after 2.6nS  after writing this error:
> > Step 1321571, time 2643.14 (ps)  LINCS WARNING
>
> See http://wiki.gromacs.org/index.php/Errors#LINCS_warnings
>
> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] mdrun error after 2.6nS

[Blaise Mathias-Costa]

Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone through that web site and it doesn't say anything very specific, for example if the system is not minimized properly it should have complained at the beginning, but the problem arises after 2.6nS! I have searched in the archive, when somebody had similar problem with PR run David suggested to look for the "center-of-mass motion removal", to give POPC+Protein, but I dont have POPC in my system. In another case advised to reduce the time step, does it mean that I should reduce the time step from 0.002 to 0.001 and do the simulations from the beginning?  Another suggestion was the computing power may not be sufficient, but I don't think this will be applicable for me, b'se I am running in 8 nodes each node is with 4 processors, and the unit cell size is ~96000 atoms in total. What could be the most appropriate way to solve this problem?  Many thanks in  advance! Kind Regards,BlaiseBlaise Mathias Costa, PhDDepartment of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical CenterOmaha, NE 68198-5800, USA.Tel: 001 402 559 7132 [EMAIL PROTECTED] wrote: -To: Discussion list for GROMACS users From: Mark Abraham <[EMAIL PROTECTED]>Sent by: [EMAIL PROTECTED]Date: 10/02/2007 12:29PMSubject: Re: [gmx-users] mdrun error after 2.6nSBlaise Mathias-Costa wrote:> Hi all,> > The mdrun stopped  after 2.6nS  after writing this error:> Step 1321571, time 2643.14 (ps)  LINCS WARNINGSee http://wiki.gromacs.org/index.php/Errors#LINCS_warningsMark___gmx-users mailing list    gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php___
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Re: [gmx-users] mdrun error after 2.6nS

[Mark Abraham]

Blaise Mathias-Costa wrote:

Hi all,

The mdrun stopped  after 2.6nS  after writing this error:
Step 1321571, time 2643.14 (ps)  LINCS WARNING


See http://wiki.gromacs.org/index.php/Errors#LINCS_warnings

Mark
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Re: [gmx-users] mdrun error after 2.6nS

[Tsjerk Wassenaar]

Hi Blaise,

You'd better look in the log file where this starts. I bet it's either
Lys-NH3+ or phosphate (ATP?) spinning like crazy. Check the archive for
solutions.

Best,

Tsjerk

On 10/2/07, Blaise Mathias-Costa <[EMAIL PROTECTED]> wrote:
>
> Hi all,
>
> The mdrun stopped  after 2.6nS  after writing this error:
> Step 1321571, time 2643.14 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 2.814066 (between atoms 2742 and 2745) rms 0.041434
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   2742   2743   90.10.1728   0.0946  0.1000
>   2742   2744   90.00.1010   0.2410  0.1000
>   2742   2745   90.00.1675   0.3814  0.1000
>
> like this for 100s of times..
>
> here is the md.mdp file:
> cpp  = cpp
> include  = -I../top
> define   =
> integrator  = md
> dt= 0.002
> comm_grps= Protein
> nstcomm   = 1
> nsteps  = 250
> nstxout = 5000
> nstvout = 5000
> nstlog   = 5000
> nstenergy  = 500
> nstxtcout   = 250
> xtc_grps = Protein
> energygrps  = Protein non-protein
> nstlist= 10
>
>
> Blaise Mathias Costa, PhD
> Department of Pharmacology and Experimental Neuroscience
> University of Nebraska Medical Center
> Omaha, NE 68198-5800, USA.
> Tel: 001 402 559 7132
>
> ___
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] mdrun error after 2.6nS

[Blaise Mathias-Costa]

Hi all,The mdrun stopped  after 2.6nS  after writing this error:Step 1321571, time 2643.14 (ps)  LINCS WARNINGrelative constraint deviation after LINCS:max 2.814066 (between atoms 2742 and 2745) rms 0.041434bonds that rotated more than 30 degrees: atom 1 atom 2  angle  previous, current, constraint length  2742   2743   90.1    0.1728   0.0946      0.1000  2742   2744   90.0    0.1010   0.2410      0.1000  2742   2745   90.0    0.1675   0.3814      0.1000like this for 100s of times..here is the md.mdp file:cpp                      = cppinclude                  = -I../topdefine                   =integrator  = mddt                        = 0.002comm_grps= Proteinnstcomm   = 1nsteps  = 250nstxout = 5000nstvout = 5000nstlog                   = 5000nstenergy  = 500nstxtcout   = 250xtc_grps = Proteinenergygrps  = Protein non-proteinnstlist                    = 10 Blaise Mathias Costa, PhDDepartment of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical CenterOmaha, NE 68198-5800, USA.Tel: 001 402 559 7132 ___
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Re: [gmx-users] mdrun error during pr

[Yang Ye]

Hi,

What's settings for tc-grps, tau_t and ref_t in your mdp files?

Regards,
Yang Ye

On 1/2/2007 8:59 PM, Dhananjay wrote:

Hello all,

I have minimized the pdb file and wish to do mdrun for position 
restrain dynamics. 
For this when I run grompp programm, it is showing error as follows. I 
don't understand why it is showing this error:


processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
Reading position restraint coords from 2HT1_b4pr.gro
renumbering atomtypes...
converting bonded parameters...
#  G96ANGLES:   9382
#  PDIHS:   3544
#  IDIHS:   2984
#   LJ14:   10898
# POSRES:   5054
# CONSTR:   6472
# SETTLE:   25639
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file 
/users/soft/GromacsSingle/share/gromacs/top/aminoacids.dat

There are: 25641  OTHER residues
There are:   648PROTEIN residues
There are: 0DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 10 elements
---
Program grompp, VERSION 3.3
Source code file: readir.c, line: 1131

Fatal error:
Not enough ref_t and tau_t values!
---

"I was detained, I was restrained" (The Smiths)



Please anybody tell me what is wrong here ?
for the reference I have attached pr.mdp file

Thanking you in advance..


-- Dhananjay


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Re: [gmx-users] mdrun error during pr

[Tsjerk Wassenaar]

Hi Dhananjay,

Happy new year :)

Just what it says: not enough ref_t and tau_t values. You use
"Protein" and "Sol" as temperature coupling groups, but likely, you
also have ions in your system, which are not coupled now. You may want
to use "Protein" and "Non-Protein" in stead. In case you have some non
standard groups (modified amino acid, ligands, cofactors), you need to
use an index group. Do not think of giving a cofactor/ligand/small
group of ions a private heat bath. Check the archives using "Not
enough ref_t and tau_t values" as search string, or simply ref_t and
tau_t. You should've done that before posting, really, because this
issue has been dealt with several times already, including
explanations of why not giving private heat baths.

Cheers,

Tsjerk


On 1/2/07, Dhananjay <[EMAIL PROTECTED]> wrote:

Hello all,

I have minimized the pdb file and wish to do mdrun for position restrain
dynamics.
For this when I run grompp programm, it is showing error as follows. I don't
understand why it is showing this error:

processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
Reading position restraint coords from 2HT1_b4pr.gro
renumbering atomtypes...
converting bonded parameters...
#  G96ANGLES:   9382
#  PDIHS:   3544
#  IDIHS:   2984
#   LJ14:   10898
# POSRES:   5054
# CONSTR:   6472
# SETTLE:   25639
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file
/users/soft/GromacsSingle/share/gromacs/top/aminoacids.dat
There are: 25641  OTHER residues
There are:   648PROTEIN residues
There are: 0DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 10 elements
---
Program grompp, VERSION 3.3
Source code file: readir.c, line: 1131

Fatal error:
Not enough ref_t and tau_t values!
---

"I was detained, I was restrained" (The Smiths)



Please anybody tell me what is wrong here ?
for the reference I have attached pr.mdp file

Thanking you in advance..


-- Dhananjay

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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] mdrun error during pr

[Dhananjay]

Hello all,

I have minimized the pdb file and wish to do mdrun for position restrain
dynamics.
For this when I run grompp programm, it is showing error as follows. I don't
understand why it is showing this error:

processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
Reading position restraint coords from 2HT1_b4pr.gro
renumbering atomtypes...
converting bonded parameters...
#  G96ANGLES:   9382
#  PDIHS:   3544
#  IDIHS:   2984
#   LJ14:   10898
# POSRES:   5054
# CONSTR:   6472
# SETTLE:   25639
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file
/users/soft/GromacsSingle/share/gromacs/top/aminoacids.dat
There are: 25641  OTHER residues
There are:   648PROTEIN residues
There are: 0DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 10 elements
---
Program grompp, VERSION 3.3
Source code file: readir.c, line: 1131

Fatal error:
Not enough ref_t and tau_t values!
---

"I was detained, I was restrained" (The Smiths)



Please anybody tell me what is wrong here ?
for the reference I have attached pr.mdp file

Thanking you in advance..


-- Dhananjay


pr.mdp
Description: Binary data
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Re: [gmx-users] mdrun error

[Mahnam]

In God We Trust
Hello proof David van der Spoel 

Thank you very much for your guides and your reply.

Sincerely yours
Karim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University 
P.O.box 13145-1384
Tehran 
Iran 
http://www.ibb.ut.ac.ir/



-Original Message-
From: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users 
Date: Thu, 15 Jun 2006 12:00:35 +0200
Subject: Re: [gmx-users] mdrun error

> Mahnam wrote:
> > 
> > In God We Trust
> > Hi Dr Biswas
> > Thank you for your guids.Excuse me for many question. I am using a 
> > serial version of CPMD. I made cpmdmpi script and corrected the path
> of 
> > cpmd.x ( /root/CPMD-3.11.1/SOURCE/cpmd.x  CPMD_inp.run.),but when I
> run 
> > rgmx script , mdrun says:
> >  
> >  GROMACS awaits QM-result for present step ==
> > /root/CPMD-3.11.1/SOURCE/cpmd.x: error while loading shared
> libraries: 
> > libsvml.so: cannot open shared object file: No such file or directory
> >  
> >  
> Locate this file libsvml.so on your machine and make sure it is the
> path 
> for the linker (edit /etc/ld.so.conf and run ldconfig).
> 
> You probably want to install the CPMD package somewhere more logical 
> like /usr/local
> 
> 
> 
> > I attached my cpmdmpi to this mail .Would appreciate if you got any
> more 
> > ideas what went wrong.
> > Thank you very much in advance for your kindness and your reply.
> > Sincerely yours
> > Karim Mahnam
> > Institute of  Biochemistry  and  Biophysics (IBB)
> > Tehran University
> > P.O.box 13145-1384
> > Tehran
> > Iran
> > http://www.ibb.ut.ac.ir/
> > 
> > 
> >
> ---
> -
> > 
> > #! /bin/sh
> > /root/CPMD-3.11.1/SOURCE/cpmd.x CPMD_inp.run
> > 
> > 
> >
> ---
> -
> > 
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> 
> 
> -- 
> David.
> ___
> _
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone:   46 18 471 4205  fax: 46 18 511 755
> [EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
> +++
> +
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Re: [gmx-users] mdrun error

[David van der Spoel]

Mahnam wrote:


In God We Trust
Hi Dr Biswas
Thank you for your guids.Excuse me for many question. I am using a 
serial version of CPMD. I made cpmdmpi script and corrected the path of 
cpmd.x ( /root/CPMD-3.11.1/SOURCE/cpmd.x  CPMD_inp.run.),but when I run 
rgmx script , mdrun says:
 
 GROMACS awaits QM-result for present step ==
/root/CPMD-3.11.1/SOURCE/cpmd.x: error while loading shared libraries: 
libsvml.so: cannot open shared object file: No such file or directory
 
 
Locate this file libsvml.so on your machine and make sure it is the path 
for the linker (edit /etc/ld.so.conf and run ldconfig).


You probably want to install the CPMD package somewhere more logical 
like /usr/local




I attached my cpmdmpi to this mail .Would appreciate if you got any more 
ideas what went wrong.

Thank you very much in advance for your kindness and your reply.
Sincerely yours
Karim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University
P.O.box 13145-1384
Tehran
Iran
http://www.ibb.ut.ac.ir/




#! /bin/sh
/root/CPMD-3.11.1/SOURCE/cpmd.x CPMD_inp.run




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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] mdrun error

[Mahnam]

In God We Trust
Hi Dr Biswas Thank you for your guids.Excuse me for many question. 
I am using a serial version of CPMD. I made cpmdmpi script and corrected the 
path of cpmd.x ( /root/CPMD-3.11.1/SOURCE/cpmd.x  CPMD_inp.run.),but 
when I run rgmx script , mdrun says:  GROMACS awaits 
QM-result for present step ==/root/CPMD-3.11.1/SOURCE/cpmd.x: 
error while loading shared libraries: libsvml.so: cannot open shared object 
file: No such file or directory  I attached my cpmdmpi 
to this mail .Would appreciate if you got any more ideas what went wrong. 
Thank you very much in advance for your kindness and your reply.
Sincerely yoursKarim MahnamInstitute of  Biochemistry  
and  Biophysics (IBB)Tehran University P.O.box 13145-1384
Tehran Iran 
http://www.ibb.ut.ac.ir/

#! /bin/sh
/root/CPMD-3.11.1/SOURCE/cpmd.x CPMD_inp.run
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Re: [gmx-users] mdrun error with QM/MM with Gromacs-CPMD

[Pradip Kumar Biswas]

Hi Maham,

You need to edit the script 'cpmdmpi' so that it does have the path to access the cpmd.x from your working folder. The error message is due to that; it is not being able to access cpmd.x.

1. If you are using a serial version of CPMD then create a script 'cpmdmpi' with the following line:

/.../.../cpmd.x CPMD_inp.run

where you must replace the .../../ with the proper path where you have your cpmd.x.

2. If you are using a parallel version of CPMD then edit the existing cpmdmpi script accordingly by replacing the paths like:
/Users/biswas/host_file   so that it refers to your host_file and  ~/bin/cpmd_mpi.x  so that it referes to the path og your cpmd.x (Note that here I renamed the mpi version of CPMD executable cpmd.x as cpmd_mpi.x; you do not need to do that; you can maintain cpmd.x). 

best wishes,
pb


--
Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
http://comppsi.csuohio.edu/groups/people/biswas.html
On Jun 14, 2006, at 10:29 AM, Mahnam wrote:

In God We Trust
Hello Dr Biswas 
Yes, our  run created  the output.pdb2gmx, output.grompp_em and output.mdrun_em. Output.pdb2gmx and output.grompp_em  haven't any error message but output.mdrun_em has an error .I attached it to this mail.  
Thank you very much in advance for your kindness and your reply.
Sincerely yours
Karim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University 
P.O.box 13145-1384
Tehran 
Iran 
http://www.ibb.ut.ac.ir/
 
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[gmx-users] mdrun error

[Mahnam]

In God We Trust
Hello Dr Biswas Yes, our  run created  the 
output.pdb2gmx, output.grompp_em and output.mdrun_em. Output.pdb2gmx and 
output.grompp_em  haven't any error message but output.mdrun_em has an 
error .I attached it to this mail.  Thank you very much in advance 
for your kindness and your reply.Sincerely yoursKarim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)Tehran 
University P.O.box 13145-1384Tehran Iran http://www.ibb.ut.ac.ir/
 



output.mdrun_em
Description: Binary data
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[gmx-users] Mdrun Error

[Venky]

Hi gmx-users,

I am setting up a membrane inserted protein simulation.
The protein is mutated at a specific place and attached to a label and
this is inserted into the POPC membrane (434 lipids). The label is a
small molecule whose force field params were generated on PRODRG
server.
Everything was setup fine but when I try running the energy
minimisation I get the following error



Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 3179 ]
Please report this to the mailing list (gmx-users@gromacs.org)
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What does it mean and how to go about correcting it? Thanks in advance.

Venks



--
Venky Krishnamani
Graduate Student,
Dr. Janos K. Lanyi Lab
Univerisity of California, Irvine
Irvine, CA
(949) 202-9466
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