[gmx-users] Pulling

[Kieu Thu Nguyen]

Dear users,

I have a sytem including protein, lipids, and water. My protein is in
center of the box. Now i want it stays at one side of the box. Which tool
or command should i use to pull the protein to a any mong muốn location ?

Thankful for any help !
Thu
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Re: [gmx-users] PBC problem

[Tsjerk Wassenaar]

Hi Yutian Yang,

Yes. That is, if the chain is interacting with itself. If it remains curled
up, then it won't be a problem.

Cheers,

Tsjerk


On Thu, Jun 27, 2013 at 10:10 PM, Yutian Yang  wrote:

> Hi all,
>
> I have a question about PBC. If I have a polymer chain that is longer than
> the box length, will the properties of the chain change because the tail of
> the chain may interact with the head of the chain due to PBC? Thank you!
>
> Yutian
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Re: [gmx-users] clarification of equation 4.65

[Mark Abraham]

Seems plausible, but someone would have to double-check the trig. Or
make a test case where theta is 0, and then see whether C4 changes the
potential in a rerun (should be minus) or not (not). Code's in
src/kernel/convparm.c.

Mark

On Thu, Jun 27, 2013 at 8:46 PM, Christopher Neale
 wrote:
> Dear Users:
>
> can anybody confirm that there is a mistake in equation 4.65 on page 82 of 
> the manual for version 4.6.1?
>
> Specifically, I think that the final term should be C4*(1-cos(4*theta)) and 
> not C4*(1+cos(4*theta)) where the difference is the sign of the cosine term ?
>
> Thank you,
> Chris.
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[gmx-users] PBC problem

[Yutian Yang]

Hi all, 

I have a question about PBC. If I have a polymer chain that is longer than the 
box length, will the properties of the chain change because the tail of the 
chain may interact with the head of the chain due to PBC? Thank you! 

Yutian
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Re: [gmx-users] Gromacs 4.5.4 and Gromacs 4.5.5 give different results

[Sapna Sarupria]

I have tried the same with Berendsen and it still crashes. I have seen this
happen before in some other versions compatibility too (I have an old post
about it in the mailing list).

Thanks for the response!


On Thu, Jun 27, 2013 at 3:21 PM, Justin Lemkul  wrote:

>
>
> On 6/27/13 3:16 PM, Sapna Sarupria wrote:
>
>> Thanks Justin for the response. I thought of that too but was not sure if
>> that could alone be attributed to the crash. There is no obvious reason
>> why
>> it should happen given Gromacs has typically been quite stable. This is
>> quite a straightforward system...but perhaps it is the version. I am able
>> to run other simulations in this version with similar set up and
>> therefore,
>> I wonder what is going wrong.
>>
>>
> Without an actual backtrace from gdb, there's not much to go on, but then
> too, the development team isn't going to try to fix anything about 4.5.4
> that presumably has already been fixed.  The most obvious culprit in the
> .mdp file below is the combination of velocity generation and Nose-Hoover;
> it's not a very stable combination.
>
> -Justin
>
>
>> On Thu, Jun 27, 2013 at 3:05 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 6/27/13 2:30 PM, sarupria wrote:
>>>
>>>  Hello all,

 I have a naphthalene + water system which I want to run a NPT simulation
 of.
 The system has been energy mininimized. When I run the NPT simulation
 using
 gromacs 4.5.5 the simulation runs fine, but when I attempt to run the
 same
 simulation using 4.5.4 it crashes with lincs error.  We have tried
 various
 things like energy minimizing multiple times using 4.5.4 but it still
 crashes. I have also changed the thermostat and barostat to Berendsen,
 the
 problem persists.

 Has anything changed between the two versions that could lead to this
 trouble? I am pasted the mdp file below and also the last few lines of
 the
 error message I get from Gromacs 4.5.4.


  Well, according to the release notes (http://www.gromacs.org/About_**
>>> ** 
>>> Gromacs/Release_Notes/Versions_4.5.x>> gromacs.org/About_Gromacs/**Release_Notes/Versions_4.5.x
>>> >)**,
>>>  in version 4.5.5:
>>>
>>> "Many small fixes which avoid termination with fatal errors or crashes in
>>> mdrun and tools."
>>>
>>> Small bugs are constantly getting fixed.  I see no compelling reason to
>>> use an outdated version (4.5.4) when a slightly less outdated version
>>> (4.5.5) works correctly.
>>>
>>> -Justin
>>>
>>>
>>>   Thanks for your help.
>>>
 Sapna

  MDP FILE *
 title   =  NPH + water  ; a string
 dt  =  0.002; time step
 nsteps  =  1250  ; number of steps
 comm-grps   =  system
 comm-mode   =  Linear
 nstcomm =  10   ; reset c.o.m. motion
 nstxout =  000  ; write coords
 nstvout =  000  ; write velocities
 nstlog  =  2500 ; print to logfile
 nstenergy   =  500  ; print energies
 xtc_grps=  System
 nstxtcout   =  1000
 nstlist =  10   ; update pairlist
 ns_type =  grid ; pairlist method
 coulombtype =  PME
 rvdw=  1.00 ; cut-off for vdw
 rcoulomb=  1.00 ; cut-off for coulomb
 rlist   =  1.00 ; cut-off for coulomb
 Tcoupl  =  Nose-Hoover
 ref_t   =  280.0
 tc-grps =  System
 tau_t   =  0.5
 DispCorr=  EnerPres ; long range correction
 gen_vel =  yes   ; generate init. vel
 gen_temp=  280  ; init. temp.
 gen_seed=  372340   ; random seed
 constraints =  h-bonds   ; constraining bonds
 with H
 constraint_algorithm = lincs
 refcoord-scaling=  no
 Pcoupl  =  Parrinello-Rahman
 Pcoupltype  =  isotropic; pressure geometry
 tau_p   =  1.0  ; p-coupoling time
 compressibility =  4.5e-5   ; compressibility
 ref_p   =  1.0  ; ref pressure
 nsttcouple  =  1
 nstpcouple  =  1
 * END MDP File ***

 *** Error Message *
 Program mdrun_sp, VERSION 4.5.4
 Source code file: constr.c, line: 176

 Fatal error:
 Too many LIN

Re: [gmx-users] Gromacs 4.5.4 and Gromacs 4.5.5 give different results

[Justin Lemkul]

On 6/27/13 3:16 PM, Sapna Sarupria wrote:

Thanks Justin for the response. I thought of that too but was not sure if
that could alone be attributed to the crash. There is no obvious reason why
it should happen given Gromacs has typically been quite stable. This is
quite a straightforward system...but perhaps it is the version. I am able
to run other simulations in this version with similar set up and therefore,
I wonder what is going wrong.



Without an actual backtrace from gdb, there's not much to go on, but then too, 
the development team isn't going to try to fix anything about 4.5.4 that 
presumably has already been fixed.  The most obvious culprit in the .mdp file 
below is the combination of velocity generation and Nose-Hoover; it's not a very 
stable combination.


-Justin



On Thu, Jun 27, 2013 at 3:05 PM, Justin Lemkul  wrote:




On 6/27/13 2:30 PM, sarupria wrote:


Hello all,

I have a naphthalene + water system which I want to run a NPT simulation
of.
The system has been energy mininimized. When I run the NPT simulation
using
gromacs 4.5.5 the simulation runs fine, but when I attempt to run the same
simulation using 4.5.4 it crashes with lincs error.  We have tried various
things like energy minimizing multiple times using 4.5.4 but it still
crashes. I have also changed the thermostat and barostat to Berendsen, the
problem persists.

Has anything changed between the two versions that could lead to this
trouble? I am pasted the mdp file below and also the last few lines of the
error message I get from Gromacs 4.5.4.



Well, according to the release notes (http://www.gromacs.org/About_**
Gromacs/Release_Notes/**Versions_4.5.x),
in version 4.5.5:

"Many small fixes which avoid termination with fatal errors or crashes in
mdrun and tools."

Small bugs are constantly getting fixed.  I see no compelling reason to
use an outdated version (4.5.4) when a slightly less outdated version
(4.5.5) works correctly.

-Justin


  Thanks for your help.

Sapna

 MDP FILE *
title   =  NPH + water  ; a string
dt  =  0.002; time step
nsteps  =  1250  ; number of steps
comm-grps   =  system
comm-mode   =  Linear
nstcomm =  10   ; reset c.o.m. motion
nstxout =  000  ; write coords
nstvout =  000  ; write velocities
nstlog  =  2500 ; print to logfile
nstenergy   =  500  ; print energies
xtc_grps=  System
nstxtcout   =  1000
nstlist =  10   ; update pairlist
ns_type =  grid ; pairlist method
coulombtype =  PME
rvdw=  1.00 ; cut-off for vdw
rcoulomb=  1.00 ; cut-off for coulomb
rlist   =  1.00 ; cut-off for coulomb
Tcoupl  =  Nose-Hoover
ref_t   =  280.0
tc-grps =  System
tau_t   =  0.5
DispCorr=  EnerPres ; long range correction
gen_vel =  yes   ; generate init. vel
gen_temp=  280  ; init. temp.
gen_seed=  372340   ; random seed
constraints =  h-bonds   ; constraining bonds
with H
constraint_algorithm = lincs
refcoord-scaling=  no
Pcoupl  =  Parrinello-Rahman
Pcoupltype  =  isotropic; pressure geometry
tau_p   =  1.0  ; p-coupoling time
compressibility =  4.5e-5   ; compressibility
ref_p   =  1.0  ; ref pressure
nsttcouple  =  1
nstpcouple  =  1
* END MDP File ***

*** Error Message *
Program mdrun_sp, VERSION 4.5.4
Source code file: constr.c, line: 176

Fatal error:
Too many LINCS warnings (4811)
If you know what you are doing you can adjust the lincs warning threshold
in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the
GROMACS
website at 
http://www.gromacs.org/**Documentation/Errors
--**-


*** End Error Message *



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=

Re: [gmx-users] Gromacs 4.5.4 and Gromacs 4.5.5 give different results

[Sapna Sarupria]

Thanks Justin for the response. I thought of that too but was not sure if
that could alone be attributed to the crash. There is no obvious reason why
it should happen given Gromacs has typically been quite stable. This is
quite a straightforward system...but perhaps it is the version. I am able
to run other simulations in this version with similar set up and therefore,
I wonder what is going wrong.


On Thu, Jun 27, 2013 at 3:05 PM, Justin Lemkul  wrote:

>
>
> On 6/27/13 2:30 PM, sarupria wrote:
>
>> Hello all,
>>
>> I have a naphthalene + water system which I want to run a NPT simulation
>> of.
>> The system has been energy mininimized. When I run the NPT simulation
>> using
>> gromacs 4.5.5 the simulation runs fine, but when I attempt to run the same
>> simulation using 4.5.4 it crashes with lincs error.  We have tried various
>> things like energy minimizing multiple times using 4.5.4 but it still
>> crashes. I have also changed the thermostat and barostat to Berendsen, the
>> problem persists.
>>
>> Has anything changed between the two versions that could lead to this
>> trouble? I am pasted the mdp file below and also the last few lines of the
>> error message I get from Gromacs 4.5.4.
>>
>>
> Well, according to the release notes (http://www.gromacs.org/About_**
> Gromacs/Release_Notes/**Versions_4.5.x),
> in version 4.5.5:
>
> "Many small fixes which avoid termination with fatal errors or crashes in
> mdrun and tools."
>
> Small bugs are constantly getting fixed.  I see no compelling reason to
> use an outdated version (4.5.4) when a slightly less outdated version
> (4.5.5) works correctly.
>
> -Justin
>
>
>  Thanks for your help.
>> Sapna
>>
>>  MDP FILE *
>> title   =  NPH + water  ; a string
>> dt  =  0.002; time step
>> nsteps  =  1250  ; number of steps
>> comm-grps   =  system
>> comm-mode   =  Linear
>> nstcomm =  10   ; reset c.o.m. motion
>> nstxout =  000  ; write coords
>> nstvout =  000  ; write velocities
>> nstlog  =  2500 ; print to logfile
>> nstenergy   =  500  ; print energies
>> xtc_grps=  System
>> nstxtcout   =  1000
>> nstlist =  10   ; update pairlist
>> ns_type =  grid ; pairlist method
>> coulombtype =  PME
>> rvdw=  1.00 ; cut-off for vdw
>> rcoulomb=  1.00 ; cut-off for coulomb
>> rlist   =  1.00 ; cut-off for coulomb
>> Tcoupl  =  Nose-Hoover
>> ref_t   =  280.0
>> tc-grps =  System
>> tau_t   =  0.5
>> DispCorr=  EnerPres ; long range correction
>> gen_vel =  yes   ; generate init. vel
>> gen_temp=  280  ; init. temp.
>> gen_seed=  372340   ; random seed
>> constraints =  h-bonds   ; constraining bonds
>> with H
>> constraint_algorithm = lincs
>> refcoord-scaling=  no
>> Pcoupl  =  Parrinello-Rahman
>> Pcoupltype  =  isotropic; pressure geometry
>> tau_p   =  1.0  ; p-coupoling time
>> compressibility =  4.5e-5   ; compressibility
>> ref_p   =  1.0  ; ref pressure
>> nsttcouple  =  1
>> nstpcouple  =  1
>> * END MDP File ***
>>
>> *** Error Message *
>> Program mdrun_sp, VERSION 4.5.4
>> Source code file: constr.c, line: 176
>>
>> Fatal error:
>> Too many LINCS warnings (4811)
>> If you know what you are doing you can adjust the lincs warning threshold
>> in
>> your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at 
>> http://www.gromacs.org/**Documentation/Errors
>> --**-
>>
>>
>> *** End Error Message *
>>
>>
>>
>> --
>> View this message in context: http://gromacs.5086.x6.nabble.**
>> com/Gromacs-4-5-4-and-Gromacs-**4-5-5-give-different-results-**
>> tp5009424.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>>
>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
>

Re: [gmx-users] Gromacs 4.5.4 and Gromacs 4.5.5 give different results

[Justin Lemkul]

On 6/27/13 2:30 PM, sarupria wrote:

Hello all,

I have a naphthalene + water system which I want to run a NPT simulation of.
The system has been energy mininimized. When I run the NPT simulation using
gromacs 4.5.5 the simulation runs fine, but when I attempt to run the same
simulation using 4.5.4 it crashes with lincs error.  We have tried various
things like energy minimizing multiple times using 4.5.4 but it still
crashes. I have also changed the thermostat and barostat to Berendsen, the
problem persists.

Has anything changed between the two versions that could lead to this
trouble? I am pasted the mdp file below and also the last few lines of the
error message I get from Gromacs 4.5.4.



Well, according to the release notes 
(http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x), in version 
4.5.5:


"Many small fixes which avoid termination with fatal errors or crashes in mdrun 
and tools."


Small bugs are constantly getting fixed.  I see no compelling reason to use an 
outdated version (4.5.4) when a slightly less outdated version (4.5.5) works 
correctly.


-Justin


Thanks for your help.
Sapna

 MDP FILE *
title   =  NPH + water  ; a string
dt  =  0.002; time step
nsteps  =  1250  ; number of steps
comm-grps   =  system
comm-mode   =  Linear
nstcomm =  10   ; reset c.o.m. motion
nstxout =  000  ; write coords
nstvout =  000  ; write velocities
nstlog  =  2500 ; print to logfile
nstenergy   =  500  ; print energies
xtc_grps=  System
nstxtcout   =  1000
nstlist =  10   ; update pairlist
ns_type =  grid ; pairlist method
coulombtype =  PME
rvdw=  1.00 ; cut-off for vdw
rcoulomb=  1.00 ; cut-off for coulomb
rlist   =  1.00 ; cut-off for coulomb
Tcoupl  =  Nose-Hoover
ref_t   =  280.0
tc-grps =  System
tau_t   =  0.5
DispCorr=  EnerPres ; long range correction
gen_vel =  yes   ; generate init. vel
gen_temp=  280  ; init. temp.
gen_seed=  372340   ; random seed
constraints =  h-bonds   ; constraining bonds with H
constraint_algorithm = lincs
refcoord-scaling=  no
Pcoupl  =  Parrinello-Rahman
Pcoupltype  =  isotropic; pressure geometry
tau_p   =  1.0  ; p-coupoling time
compressibility =  4.5e-5   ; compressibility
ref_p   =  1.0  ; ref pressure
nsttcouple  =  1
nstpcouple  =  1
* END MDP File ***

*** Error Message *
Program mdrun_sp, VERSION 4.5.4
Source code file: constr.c, line: 176

Fatal error:
Too many LINCS warnings (4811)
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


*** End Error Message *



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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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[gmx-users] clarification of equation 4.65

[Christopher Neale]

Dear Users:

can anybody confirm that there is a mistake in equation 4.65 on page 82 of the 
manual for version 4.6.1?

Specifically, I think that the final term should be C4*(1-cos(4*theta)) and not 
C4*(1+cos(4*theta)) where the difference is the sign of the cosine term ?

Thank you,
Chris.
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[gmx-users] Gromacs 4.5.4 and Gromacs 4.5.5 give different results

[sarupria]

Hello all, 

I have a naphthalene + water system which I want to run a NPT simulation of.
The system has been energy mininimized. When I run the NPT simulation using
gromacs 4.5.5 the simulation runs fine, but when I attempt to run the same
simulation using 4.5.4 it crashes with lincs error.  We have tried various
things like energy minimizing multiple times using 4.5.4 but it still
crashes. I have also changed the thermostat and barostat to Berendsen, the
problem persists. 

Has anything changed between the two versions that could lead to this
trouble? I am pasted the mdp file below and also the last few lines of the
error message I get from Gromacs 4.5.4. 

Thanks for your help. 
Sapna 

 MDP FILE * 
title   =  NPH + water  ; a string 
dt  =  0.002; time step 
nsteps  =  1250  ; number of steps 
comm-grps   =  system 
comm-mode   =  Linear 
nstcomm =  10   ; reset c.o.m. motion 
nstxout =  000  ; write coords 
nstvout =  000  ; write velocities 
nstlog  =  2500 ; print to logfile 
nstenergy   =  500  ; print energies 
xtc_grps=  System 
nstxtcout   =  1000 
nstlist =  10   ; update pairlist 
ns_type =  grid ; pairlist method 
coulombtype =  PME 
rvdw=  1.00 ; cut-off for vdw 
rcoulomb=  1.00 ; cut-off for coulomb 
rlist   =  1.00 ; cut-off for coulomb 
Tcoupl  =  Nose-Hoover 
ref_t   =  280.0 
tc-grps =  System 
tau_t   =  0.5   
DispCorr=  EnerPres ; long range correction 
gen_vel =  yes   ; generate init. vel 
gen_temp=  280  ; init. temp. 
gen_seed=  372340   ; random seed 
constraints =  h-bonds   ; constraining bonds with H 
constraint_algorithm = lincs 
refcoord-scaling=  no 
Pcoupl  =  Parrinello-Rahman 
Pcoupltype  =  isotropic; pressure geometry 
tau_p   =  1.0  ; p-coupoling time 
compressibility =  4.5e-5   ; compressibility 
ref_p   =  1.0  ; ref pressure 
nsttcouple  =  1 
nstpcouple  =  1 
* END MDP File *** 

*** Error Message * 
Program mdrun_sp, VERSION 4.5.4 
Source code file: constr.c, line: 176 

Fatal error: 
Too many LINCS warnings (4811) 
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file 
or set the environment variable GMX_MAXCONSTRWARN to -1, 
but normally it is better to fix the problem 
For more information and tips for troubleshooting, please check the GROMACS 
website at http://www.gromacs.org/Documentation/Errors
--- 


*** End Error Message * 



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Re: [gmx-users] multiple chain restrain problem

[Albert]

On 06/27/2013 01:50 PM, Justin Lemkul wrote:


Then select by residue number.  Note that genrestr will only work for 
the first molecule, since position restraint numbering is based on the 
[moleculetype] numbering, not the coordinate file numbering.


-Justin



thank you very much for kind advices.

I solved this by extracting each chain into indivisual coordinate and 
make restrain based on them.


best
Albert
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Re: [gmx-users] Visualize Protein ligand complex

[Tsjerk Wassenaar]

Hi Sainitin,

You can extract only the protein and ligand, using a suitable index file,
or you can limit the number of frames.

Cheers,

Tsjerk


On Thu, Jun 27, 2013 at 5:36 PM, Thales Kronenberger <
kronenberg...@gmail.com> wrote:

> Don't you wanna try to use the VMD
>
> use vmd xxx.gro yyy.trr and then you could highlight your ligand
>
>
>
>
> 2013/6/27 Sainitin Donakonda 
>
> > Hi,
> >
> > I simulated protein ligand complex for 20 ns  now i want to visualize
> this
> > complex after simulation in pymol.To look ligand interactions with
> protein
> > binding site
> >
> > I tried trjconv to convert .xtc trajectory to .pdb but xtc file is too
> huge
> > with solvent molecules so pymol couldnot visualize complex
> >
> > Can anybody tell me command how to visualize protein ligand complex
> > trajectory in pymol
> >
> > Thanks,
> > Sainitin
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] still dealing with GFP-like chromophore with LINCS warnings

[Baptiste Demoulin]

I did experience some troubles using Parrinello-Rahman after an
equilibration with Berendsen. Trying many different time-constant was the
solution ( I had to shift this constant from 10 ps for Berendsen to 5 ps
for PR). Did you try to change it ? I do not know the fundamental reasons
for this problem, though...

Baptiste


2013/6/27 Anna Marabotti 

> Dear gmx-users,
> I'm still dealing with the problem of GFP-like chromophore. To be honest,
> with the help of another gmx user, I was able to obtain the topology of my
> chromophore, in protonated and unprotonated form, and I started performing
> the simulations. For the protonated chromophore, all worked well, and I
> obtained my simulations without many problems.
>
> Instead, I'm experimenting problems with the protein containing the
> unprotonated form. In particular, when I started calculating the production
> run, using in the .mdp files exactly the same parameters used for the
> protonated form, I started obtaining a lot of LINCS warnings and production
> of a lot of stepX.pdb files. This happened only during the production
> run, whereas I have no errors during minimization and position-restrained
> dynamics. The minimization step seems to be OK and I did not further
> continue with it (I set emtol=500 and emstep=0.01; the result of
> minimization was:
>
> Steepest Descents converged to Fmax < 500 in 2114 steps
>
> Potential Energy= -6.84833590617959e+05
>
> Maximum force=4.57025361763790e+02 on atom 2129
>
> Norm of force=9.42624640937790e+00
>
> that seems pretty good for me.)
>
> I tried to overcome the problem by using longer PR-MD (100 ps instead of
> 10 for NVT; 1 ns instead of 100 ps for NPT) but it doesn't work, despite
> the fact that the energies and all other factors (temperature, pressure)
> are really stable during PR-MD. I also watched the trajectory using VMD
> but, apart from parts of protein crossing periodic boundaries (a thing that
> I see regularly in my simulations), I don't see anything "strange" (like
> system exploding). Apparently, it simply stops, and that's all.
>
> Other things that trouble me are:
> 1) I checked the atoms with LINCS warning, and I see that not only those
> atoms belonging to chromophore are perturbed, but also other atoms in the
> backbone of the protein (mainly CA-C-N; many of them, but not all, are
> spatially close to chromophore).
> 2) during these production runs I also experimented many hardware problems
> (power outages) and software problems (bad job schedulation, problems in
> core communications etc) and I don't understand if these problems could
> affect the results of my simulation in this way. I ask this because my
> first production run was stopped because of a power outage, and in the .log
> file I saw a lot of errors very early; when the machine turned on, I resent
> exactly the same dynamics, and the errors were far later than before (in
> the first run, they came across 5 ns; in the second run not before 20 ns).
> 3) Last thing: when I started the production run, I switched the pressure
> coupling from Berendsen to Parrinello-Rahman (obviously not giving the .edr
> file to grompp for the creation of the full.tpr file) (on the contrary, the
> temperature coupling was left V-rescale both in PR-Md and production run).
> Can this switch perturb the system?
>
> My question is: do I have to suppose that the unprotonated form of
> chromophore is badly parametrized, and this can influence all the rest of
> the protein in this way? If yes, why nothing happens when I do PR-MD? If
> not, do I have simply to perform a very very very long stabilization, do I
> have to perform a deeper minimization, do I have to avoid switching from
> Berendsen to Parrinello? What do you suggest me to do?
>
> Thanks a lot
> Anna
>
> --
> __**
> Anna Marabotti, Ph.D.
> Assistant Professor
> Department of Chemistry and Biology
> University of Salerno
> Via Giovanni Paolo II, 132
> 84084 Fisciano (SA)
> Italy
> Phone: +39 089 969583
> Fax: +39 089 969603
> E-mail: amarabo...@unisa.it
> Skype: annam1972
> Web page: 
> http://www.unisa.it/docenti/**annamarabotti/index
>
> "Indifference is the eighth deadly sin" (don Andrea Gallo)
>
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htt

Re: [gmx-users] Visualize Protein ligand complex

[Thales Kronenberger]

Don't you wanna try to use the VMD

use vmd xxx.gro yyy.trr and then you could highlight your ligand




2013/6/27 Sainitin Donakonda 

> Hi,
>
> I simulated protein ligand complex for 20 ns  now i want to visualize this
> complex after simulation in pymol.To look ligand interactions with protein
> binding site
>
> I tried trjconv to convert .xtc trajectory to .pdb but xtc file is too huge
> with solvent molecules so pymol couldnot visualize complex
>
> Can anybody tell me command how to visualize protein ligand complex
> trajectory in pymol
>
> Thanks,
> Sainitin
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Protein RMSD high

[tarak karmakar]

No, it's not at all significant in my problem as the loop is not part of
the active site, way far at the two termini. I have plotted the RMSD in
presence and absence of the loop. In absence of the loop rmsd is coming
around 0.3 nm.
Thanks Mark

Tarak


On Thu, Jun 27, 2013 at 2:37 PM, Mark Abraham wrote:

> Your call. Is that motion significant to what you are trying to report
> by your observation of the RMSD?
>
> Mark
>
> On Thu, Jun 27, 2013 at 9:03 AM, tarak karmakar 
> wrote:
> > Dear All,
> >
> > While simulating a protein, I see the rmsd fluctuates around a mean of
> 0.6
> > nm. I carefully looked at the trajectory (VMD movie) and saw there are
> two
> > flexible terminii fluctuating with a very high amplitude contributing to
> > the high value of RMSD. Is it ok to report this problem with this RMSD
> > value?
> >
> > Thanks
> > Tarak
> > --
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Re: [gmx-users] Installation on Ubuntu 12.04LTS

[Szilárd Páll]

On Thu, Jun 27, 2013 at 12:57 PM, Mare Libero  wrote:
> Hello everybody,
>
> Does anyone have any recommendation regarding the installation of gromacs 4.6 
> on Ubuntu 12.04? I have the nvidia-cuda-toolkit that comes in synaptic 
> (4.0.17-3ubuntu0.1 installed in /usr/lib/nvidia-cuda-toolkit) and the drivers 
> 304.88.
> Apparently, this is not compatible with gcc-4.5 and higher. When I issue:
>
>
> $ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit 
> -DGMX_BUILD_OWN_FFTW=ON
> $ make
>
> the compilation ends with:
>
> In file included from 
> /usr/lib/nvidia-cuda-toolkit/include/cuda_runtime.h:59:0,
>  from :0:
> /usr/include/host_config.h:82:2: error: #error -- unsupported GNU version! 
> gcc 4.5 and up are not supported!
>
> If I downgrade to gcc-4.4 this error disappears, but gromacs compilation 
> fails with a different error:
>
> cc1plus: error: unrecognized command line option "-fexcess-precision=fast"
> CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message):
>   Error generating
>   
> /home/me/Downloads/gromacs-4.6.2/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
>
> make[2]: *** 
> [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o]
>  Error 1
> make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2
> make: *** [all] Error 2

I guess what happens is that you are using gcc 4.5 for the CPU code
and gcc 4.4 as the nvcc host compiler. However, the compiler options
used for gcc (CMAKE_CXX_FLAGS) get propagated to nvcc;
-fexcess-precision=fast is supported by gcc 4.5, but not by 4.4, hence
the error when compiling CUDA code.

>
> Also, I tried the Intel compilers that comes with the non-commercial  Intel 
> c++ composer XE (which I believe are recommended). The compilation produces a 
> number of warnings, and then dies with the following error:
>
>
> $ CC=/opt/intel/bin/icc  cmake .. -DGMX_GPU=ON 
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON
>
> [ 63%] Building C object share/template/CMakeFiles/template.dir/template.c.o
> make[2]: *** No rule to make target `src/gmxlib/libgmx.so.8', needed by 
> `share/template/template'.  Stop.
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2

This should work, but CUDA 4.0 is ancient surely does not support icc
13. I suggest that you get CUDA 5.0 and use gcc 4.7 (or a new icc). If
you really want to stick to CUDA 4.0, try using gcc 4.4 as the general
C++ compiler (CMAKE_CXX_COMPILER) which should avoid the above error.

> Thanks in advance for your help,
>
> Al
>
> --
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[gmx-users] Visualize Protein ligand complex

[Sainitin Donakonda]

Hi,

I simulated protein ligand complex for 20 ns  now i want to visualize this
complex after simulation in pymol.To look ligand interactions with protein
binding site

I tried trjconv to convert .xtc trajectory to .pdb but xtc file is too huge
with solvent molecules so pymol couldnot visualize complex

Can anybody tell me command how to visualize protein ligand complex
trajectory in pymol

Thanks,
Sainitin
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[gmx-users] still dealing with GFP-like chromophore with LINCS warnings

[Anna Marabotti]

Dear gmx-users,
I'm still dealing with the problem of GFP-like chromophore. To be 
honest, with the help of another gmx user, I was able to obtain the 
topology of my chromophore, in protonated and unprotonated form, and I 
started performing the simulations. For the protonated chromophore, all 
worked well, and I obtained my simulations without many problems.


Instead, I'm experimenting problems with the protein containing the 
unprotonated form. In particular, when I started calculating the 
production run, using in the .mdp files exactly the same parameters used 
for the protonated form, I started obtaining a lot of LINCS warnings and 
production of a lot of stepX.pdb files. This happened only during 
the production run, whereas I have no errors during minimization and 
position-restrained dynamics. The minimization step seems to be OK and I 
did not further continue with it (I set emtol=500 and emstep=0.01; the 
result of minimization was:


Steepest Descents converged to Fmax < 500 in 2114 steps

Potential Energy= -6.84833590617959e+05

Maximum force=4.57025361763790e+02 on atom 2129

Norm of force=9.42624640937790e+00

that seems pretty good for me.)

I tried to overcome the problem by using longer PR-MD (100 ps instead of 
10 for NVT; 1 ns instead of 100 ps for NPT) but it doesn't work, despite 
the fact that the energies and all other factors (temperature, pressure) 
are really stable during PR-MD. I also watched the trajectory using VMD 
but, apart from parts of protein crossing periodic boundaries (a thing 
that I see regularly in my simulations), I don't see anything "strange" 
(like system exploding). Apparently, it simply stops, and that's all.


Other things that trouble me are:
1) I checked the atoms with LINCS warning, and I see that not only those 
atoms belonging to chromophore are perturbed, but also other atoms in 
the backbone of the protein (mainly CA-C-N; many of them, but not all, 
are spatially close to chromophore).
2) during these production runs I also experimented many hardware 
problems (power outages) and software problems (bad job schedulation, 
problems in core communications etc) and I don't understand if these 
problems could affect the results of my simulation in this way. I ask 
this because my first production run was stopped because of a power 
outage, and in the .log file I saw a lot of errors very early; when the 
machine turned on, I resent exactly the same dynamics, and the errors 
were far later than before (in the first run, they came across 5 ns; in 
the second run not before 20 ns).
3) Last thing: when I started the production run, I switched the 
pressure coupling from Berendsen to Parrinello-Rahman (obviously not 
giving the .edr file to grompp for the creation of the full.tpr file) 
(on the contrary, the temperature coupling was left V-rescale both in 
PR-Md and production run). Can this switch perturb the system?


My question is: do I have to suppose that the unprotonated form of 
chromophore is badly parametrized, and this can influence all the rest 
of the protein in this way? If yes, why nothing happens when I do PR-MD? 
If not, do I have simply to perform a very very very long stabilization, 
do I have to perform a deeper minimization, do I have to avoid switching 
from Berendsen to Parrinello? What do you suggest me to do?


Thanks a lot
Anna

--
__
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Giovanni Paolo II, 132
84084 Fisciano (SA)
Italy
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: amarabo...@unisa.it
Skype: annam1972
Web page: http://www.unisa.it/docenti/annamarabotti/index

"Indifference is the eighth deadly sin" (don Andrea Gallo)

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Re: [gmx-users] Installation on Ubuntu 12.04LTS

[Mark Abraham]

On Thu, Jun 27, 2013 at 12:57 PM, Mare Libero  wrote:
> Hello everybody,
>
> Does anyone have any recommendation regarding the installation of gromacs 4.6 
> on Ubuntu 12.04? I have the nvidia-cuda-toolkit that comes in synaptic 
> (4.0.17-3ubuntu0.1 installed in /usr/lib/nvidia-cuda-toolkit) and the drivers 
> 304.88.
> Apparently, this is not compatible with gcc-4.5 and higher. When I issue:
>
>
> $ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit 
> -DGMX_BUILD_OWN_FFTW=ON
> $ make
>
> the compilation ends with:
>
> In file included from 
> /usr/lib/nvidia-cuda-toolkit/include/cuda_runtime.h:59:0,
>  from :0:
> /usr/include/host_config.h:82:2: error: #error -- unsupported GNU version! 
> gcc 4.5 and up are not supported!
>
> If I downgrade to gcc-4.4 this error disappears, but gromacs compilation 
> fails with a different error:
>
> cc1plus: error: unrecognized command line option "-fexcess-precision=fast"
> CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message):
>   Error generating
>   
> /home/me/Downloads/gromacs-4.6.2/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
>
> make[2]: *** 
> [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o]
>  Error 1
> make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2
> make: *** [all] Error 2
>

CUDA 4.0 is two years old, so I would(did) get the latest package from
Nvidia rather than rely on synaptic to be up to date with emerging
technologies.

And use a more recent gcc!

> Also, I tried the Intel compilers that comes with the non-commercial  Intel 
> c++ composer XE (which I believe are recommended). The compilation produces a 
> number of warnings, and then dies with the following error:

Yeah CUDA's wrapper compiler does not play perfectly with non-gcc, but
the result should be OK. We have filed bug reports with CUDA.

> $ CC=/opt/intel/bin/icc  cmake .. -DGMX_GPU=ON 
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON
>
> [ 63%] Building C object share/template/CMakeFiles/template.dir/template.c.o
> make[2]: *** No rule to make target `src/gmxlib/libgmx.so.8', needed by 
> `share/template/template'.  Stop.
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2

On the other hand, FFTW development is nearly stopped, so libfftw3-dev
from synaptic is fine, and I suspect the origin of this issue is
either a race condition in the internal FFTW build (which will go away
if you make again), or perhaps icc being evil and conveniently
wrapping an FFTW interface over its MKL. We believe we've fixed the
latter, but there are too many moving targets...

Mark

> Thanks in advance for your help,
>
> Al
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
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Re: [gmx-users] multiple chain restrain problem

[Justin Lemkul]

On 6/27/13 6:27 AM, Albert wrote:

Hello:

  I've got two protein chain in my system. I generate gmx.pdb by pb2gmx, and
gromacs generate toplogy and restrain file for each chain:

gmx.pdb
  topol_chain_A.itp
topol_chain_B.itp
porschain_A.itp
porschain_B.itp

I noticed that the gmx.pdb doesn't contain any chain information. I am going to
equilibrate the system first restrain the heavy atoms which can be specified by
porschain_A.itp and porschain_B.itp. However, in the next step I am going to
restrain only the backbone of chain A, how can we to do this? The chain
information in new generated gmx.pdb lost When I use command:

genrestr -f gmx.pdb -p porsB

it doesn't contains selection for chain



Then select by residue number.  Note that genrestr will only work for the first 
molecule, since position restraint numbering is based on the [moleculetype] 
numbering, not the coordinate file numbering.


-Justin

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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] Dear Sir

[Justin Lemkul]

On 6/27/13 5:59 AM, Sathish Kumar wrote:

Fatal error:
[ file spc.itp, line 32 ]
Atom index (1) in bonds out of bounds (1-0).
This probably means that you have inserted topology
section "settles" in a part belonging to a different
molecule than you intended to. in that case move the
"settles" section to the right molecule


the above error i am getting while running grommp command for membrane
simulation. I made up the correct topology file.Here i used tip3p
water model. But why this error coming i did not understood. Can you
please clarify and suggest how to overcome this error.



http://www.gromacs.org/Documentation/Errors#Atom_index_(1)_in_bonds_out_of_bounds

-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: Re: Re: [gmx-users] GPU-based workstation

[James Starlight]

Back to my question
I want to build gpu-based workstation based onto 2 titans geforces.

My current budget allow me only hight-end  6nodes core i 7-3930  and MB
with 5 PCI-E (like Asus rampage IV series). Would this system be balanced
with two GPUs ? Should I use two 6-8 nodes XEONS instead of i7?

James

2013/5/29 James Starlight 

> Dear Dr. Pall!
>
> Thank you for your suggestions!
>
> Asumming that I have budget of 5000 $ and I want to build gpu-based
> desktop on this money.
>
> Previously I've used single 4 core i5 with GTX 670 and obtain average 10
> ns\day performance for the 70k atoms systems (1.0 cutoffs, no virtual sites
> , sd integrator).
>
> Now I'd like to build system based on 2 hight-end GeForces (e.g like
> TITAN).
> Should that system include 2 cpu's for good balancing? (e.g two 6 nodes
> XEONS with faster clocks for instance could be better for simulations than
> i7, couldnt it?)
>
> What addition properties to the MB should I consider for such system ?
>
> James
>
>
> 2013/5/28 lloyd riggs 
>
>> Dear Dr. Pali,
>>
>> Thank you,
>>
>> Stephan Watkins
>>
>> *Gesendet:* Dienstag, 28. Mai 2013 um 19:50 Uhr
>> *Von:* "Szilárd Páll" 
>>
>> *An:* "Discussion list for GROMACS users" 
>> *Betreff:* Re: Re: [gmx-users] GPU-based workstation
>> Dear all,
>>
>> As far as I understand, the OP is interested in hardware for *running*
>> GROMACS 4.6 rather than developing code. or running LINPACK.
>>
>>
>> To get best performance it is important to use a machine with hardware
>> balanced for GROMACS' workloads. Too little GPU resources will result
>> in CPU idling; too much GPU resources will lead to the runs being CPU
>> or multi-GPU scaling bound and above a certain level GROMACS won't be
>> able to make use of additional GPUs.
>>
>> Of course, the balance will depend both on hardware and simulation
>> settings (mostly the LJ cut-off used).
>>
>> An additional factor to consider is typical system size. To reach near
>> peak pair-force throughput on GPUs you typically need >20k-40k
>> particles/GPU (depends on the architecture) and throughput drops below
>> these values. Hence, in most cases it is preferred to use fewer and
>> faster GPUs rather than more.
>>
>> Without knowing the budgdet and indented use of the machine it is hard
>> to make suggestions, but I would say for a budget desktop box a
>> quad-core Intel Ivy Bridge or the top-end AMD Piledriver CPU with a
>> fast Kepler GTX card (e.g. GTX 680 or GTX 770/780) should work well.
>> If you're considering dual-socket workstations, I suggest you go with
>> the higher core-count and higher frequency Intel CPUs (6+ cores >2.2
>> GHz), otherwise you may not see as much benefit as you would expect
>> based on the insane price tag (especially if you compare to an i7
>> 3939K or its IVB successor).
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>> On Sat, May 25, 2013 at 1:02 PM, lloyd riggs  wrote:
>> > More RAM the better, and the best I have seen is 4 GPU work station. I
>> can
>> > use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is
>> > really 3-4 GPU, except the tyan mentioned (there designed as blades so
>> an 8
>> > or 10 slot board really holds 8 or 10 GPU's). There's cooling problems
>> > though with GPU's, as on a board there packed, so extra cooling things
>> may
>> > help not blow a GPU, but I would look for good ones (ask around), as
>> its a
>> > video game market and they go for looks even though its in casing? The
>> > external RAM (not onboard GPU RAM) helps if you do a larger sim, but I
>> dont
>> > know performance wise, the onboard GPU, the more RAM the marrier...so
>> yes,
>> > normal work stations you can get 4 GPU's for a 300 US$ board, but then
>> the
>> > price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered
>> abroad is
>> > also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests
>> > software, not Gromacs, so would be nice to see performance...for a
>> small 100
>> > atom molecule and 500 solvent, using just the CPU I get it to run 5-10
>> > minutes real for 1 ns sim, but tried simple large 800 amino, 25,000
>> solvent
>> > eq (NVT or NPT) runs and they clock at around 1 hour real for say 50 ps
>> > eq's
>> >
>> > Stephan
>> >
>> > Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
>> > Von: "James Starlight" 
>> > An: "Discussion list for GROMACS users" 
>> > Betreff: Re: [gmx-users] GPU-based workstation
>> > Dear Dr. Watkins!
>> >
>> > Thank you for the suggestions!
>> >
>> > In the local shops I've found only Core i7 with 6 cores (like Core
>> > i7-39xx) and 4 cores. Should I obtain much better performance with 6
>> cores
>> > than with 4 cores in case of i7 cpu (assuming that I run simulation in
>> > cpu+gpu mode )?
>> >
>> > Also you've mentioned about 4 PCeI MD. Does it means that modern
>> > work-station could have 4 GPU's in one home-like desktop ? According to
>> my
>> > current task I suppose that 2 GPU's would be suitable for my simulations
>> > (assuming that I use typical ASUS

[gmx-users] Installation on Ubuntu 12.04LTS

[Mare Libero]

Hello everybody,

Does anyone have any recommendation regarding the installation of gromacs 4.6 
on Ubuntu 12.04? I have the nvidia-cuda-toolkit that comes in synaptic 
(4.0.17-3ubuntu0.1 installed in /usr/lib/nvidia-cuda-toolkit) and the drivers 
304.88.
Apparently, this is not compatible with gcc-4.5 and higher. When I issue: 


$ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit 
-DGMX_BUILD_OWN_FFTW=ON
$ make

the compilation ends with:

In file included from /usr/lib/nvidia-cuda-toolkit/include/cuda_runtime.h:59:0,
 from :0:
/usr/include/host_config.h:82:2: error: #error -- unsupported GNU version! gcc 
4.5 and up are not supported!

If I downgrade to gcc-4.4 this error disappears, but gromacs compilation fails 
with a different error:

cc1plus: error: unrecognized command line option "-fexcess-precision=fast"
CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message):
  Error generating
  
/home/me/Downloads/gromacs-4.6.2/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o

make[2]: *** 
[src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o]
 Error 1
make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2
make: *** [all] Error 2


Also, I tried the Intel compilers that comes with the non-commercial  Intel c++ 
composer XE (which I believe are recommended). The compilation produces a 
number of warnings, and then dies with the following error:


$ CC=/opt/intel/bin/icc  cmake .. -DGMX_GPU=ON 
-DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON

[ 63%] Building C object share/template/CMakeFiles/template.dir/template.c.o
make[2]: *** No rule to make target `src/gmxlib/libgmx.so.8', needed by 
`share/template/template'.  Stop.
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2

Thanks in advance for your help,

Al

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[gmx-users] multiple chain restrain problem

[Albert]

Hello:

 I've got two protein chain in my system. I generate gmx.pdb by pb2gmx, 
and gromacs generate toplogy and restrain file for each chain:


gmx.pdb
 topol_chain_A.itp
topol_chain_B.itp
porschain_A.itp
porschain_B.itp

I noticed that the gmx.pdb doesn't contain any chain information. I am 
going to equilibrate the system first restrain the heavy atoms which can 
be specified by porschain_A.itp and porschain_B.itp. However, in the 
next step I am going to restrain only the backbone of chain A, how can 
we to do this? The chain information in new generated gmx.pdb lost 
When I use command:


genrestr -f gmx.pdb -p porsB

it doesn't contains selection for chain

thank you very much

Albert

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[gmx-users] Dear Sir

[Sathish Kumar]

Fatal error:
[ file spc.itp, line 32 ]
Atom index (1) in bonds out of bounds (1-0).
This probably means that you have inserted topology
section "settles" in a part belonging to a different
molecule than you intended to. in that case move the
"settles" section to the right molecule


the above error i am getting while running grommp command for membrane
simulation. I made up the correct topology file.Here i used tip3p
water model. But why this error coming i did not understood. Can you
please clarify and suggest how to overcome this error.



Regards
M.SathishKumar
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Re: [gmx-users] REMD

[Mark Abraham]

Wrong way around. Decide what you want to observe and how you will
measure it *before* you do a simulation. Now you have a chance of
doing the right simulation.

On point, check out out chapter 8 of the manual.

Mark

On Thu, Jun 27, 2013 at 7:17 AM, Shine A  wrote:
> Hai Sir,
>
> I did an REMD simulation for an intrinsically disordered
> peptide.Then I extracted thousands of conformations(pdb) from trajectory.
> Now I want to compare experimental Chemical Shifts and NOE distance for the
> peptide with all these conformations.How can I do this?
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Re: [gmx-users] Protein RMSD high

[Mark Abraham]

Your call. Is that motion significant to what you are trying to report
by your observation of the RMSD?

Mark

On Thu, Jun 27, 2013 at 9:03 AM, tarak karmakar  wrote:
> Dear All,
>
> While simulating a protein, I see the rmsd fluctuates around a mean of 0.6
> nm. I carefully looked at the trajectory (VMD movie) and saw there are two
> flexible terminii fluctuating with a very high amplitude contributing to
> the high value of RMSD. Is it ok to report this problem with this RMSD
> value?
>
> Thanks
> Tarak
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[gmx-users] Protein RMSD high

[tarak karmakar]

Dear All,

While simulating a protein, I see the rmsd fluctuates around a mean of 0.6
nm. I carefully looked at the trajectory (VMD movie) and saw there are two
flexible terminii fluctuating with a very high amplitude contributing to
the high value of RMSD. Is it ok to report this problem with this RMSD
value?

Thanks
Tarak
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