Yes I tried without pull code. Atleast I ran for 10ns and it works (i.e DPPC bilayer with a butane molecule in the water). I am not sure why it doesnt work with pull code.
Mohan
On 13/04/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]
> wrote:
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Today's Topics:
1. RE: Using Pull code with Coarse grain model (Dallas B. Warren)
2. (error in MD run) (jahanshah ashkani)
3. REMD (Dongsheng Zhang)
4. Re: REMD (Mark Abraham)
5. Re: REMD (Dongsheng Zhang)
6. Re: REMD (David van der Spoel)
7. Re: Using Pull code with Coarse grain model (David van der Spoel)
----------------------------------------------------------------------
Message: 1
Date: Thu, 13 Apr 2006 10:36:04 +1000
From: "Dallas B. Warren" < [EMAIL PROTECTED]>
Subject: RE: [gmx-users] Using Pull code with Coarse grain model
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset=us-ascii
Mohan,
What happens if you run it without using the pull code? i.e. is it a MD
parameter problem or something to do with the pull code specifically.
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
------------------------------
Message: 2
Date: Wed, 12 Apr 2006 21:16:14 -0700 (PDT)
From: jahanshah ashkani <[EMAIL PROTECTED]>
Subject: [gmx-users] (error in MD run)
To: gmx-users@gromacs.org
Message-ID: < [EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I have a problem in md run:
"Fatal error: realloc for nlist->jjnr (160825344 bytes, file ns.c, line 368, nlis t->jjnr=0x0x64960020): No such file or directory"
My .tpr and .top files are including:
[ molecules ]
; Compound #mols
Protein 1
SOL 686247
NA+ 131
And .mdp file is including:
title =
cpp = cpp
include =
define = -DFLEXIBLE
integrator = steep
tinit = 0
dt = 0.001
nsteps = 400
Tcoupl = berendsen
tc_grps = protein sol NA+
tau_t = 0.1 0.1 0.1
Ref_t = 300 300 300
emtol = 0.00001
emstep = 0.1
nstcgsteep = 1000
I would be glad if someone helps me in this case.
Thank you very much.
Best,
Jahanshah Ashkani
---------------------------------
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Message: 3
Date: Thu, 13 Apr 2006 01:06:52 -0400
From: Dongsheng Zhang <[EMAIL PROTECTED]>
Subject: [gmx-users] REMD
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED] >
Content-Type: text/plain
Dear gmx users:
I am trying to run REMD with two replicas (for testing). I used
grompp -f -c -p -o replica0 to get replica0.tpr
grompp -f -c -p -o replica1 to get replica1.tpr
then used
mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica
-v -N 2
to run it.
I got an error message "Segmentation fault" from my script output, but
no error message in both log files. When I tried to run individual tpr
file, it worked fine.
Could someone can comment why I got "Segmentation fault"? Thank you for
your help!
Dongsheng
------------------------------
Message: 4
Date: Thu, 13 Apr 2006 15:17:30 +1000 (EST)
From: "Mark Abraham" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] REMD
To: "Discussion list for GROMACS users" < gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED] >
Content-Type: text/plain;charset=iso-8859-1
> Dear gmx users:
>
> I am trying to run REMD with two replicas (for testing). I used
> grompp -f -c -p -o replica0 to get replica0.tpr
> grompp -f -c -p -o replica1 to get replica1.tpr
>
> then used
> mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica
> -v -N 2
> to run it.
mdrun doesn't take '-N 2' but I'm not sure this is the problem. Otherwise,
looks fine to me.
> I got an error message "Segmentation fault" from my script output, but
> no error message in both log files. When I tried to run individual tpr
> file, it worked fine.
>
> Could someone can comment why I got "Segmentation fault"? Thank you for
> your help!
Your MPI setup might require you use a command like "mpirun -N 2 mdrun_mpi
..." to make it work - the segfault might be a gromacs-MPI interaction
problem. If you can run an MPI process from the command line you may get
more helpful feedback.
Mark
------------------------------
Message: 5
Date: Thu, 13 Apr 2006 02:42:20 -0400
From: Dongsheng Zhang <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] REMD
To: Discussion list for GROMACS users < gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain
dear Mark,
Thank you very much for your prompt reply. I try to use parallel
computing. It works fine.
for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle
to get replica0.tpr
then, mdrun_mpi -np 2 -s replica0.tpr
The error message mentioned in the previous email looks very strange to
me. MPI works fine, and individual tpr runs fine. The error message
comes out before replica exchange. replica0 stops at step 500, replica1
stops at step 400, even the output informatio can't be complted. The
last lines in replica1.log is
Step Time Lambda
400 0.80000 0.00000
Rel. Constraint Deviation: Max between atoms RMS
I hope these further information can help you to figure out what's the
problem.
Best Wishes!
Dongsheng
On Thu, 2006-04-13 at 15:17 +1000, Mark Abraham wrote:
> > Dear gmx users:
> >
> > I am trying to run REMD with two replicas (for testing). I used
> > grompp -f -c -p -o replica0 to get replica0.tpr
> > grompp -f -c -p -o replica1 to get replica1.tpr
> >
> > then used
> > mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica
> > -v -N 2
> > to run it.
>
> mdrun doesn't take '-N 2' but I'm not sure this is the problem. Otherwise,
> looks fine to me.
>
> > I got an error message "Segmentation fault" from my script output, but
> > no error message in both log files. When I tried to run individual tpr
> > file, it worked fine.
> >
> > Could someone can comment why I got "Segmentation fault"? Thank you for
> > your help!
>
> Your MPI setup might require you use a command like "mpirun -N 2 mdrun_mpi
> ..." to make it work - the segfault might be a gromacs-MPI interaction
> problem. If you can run an MPI process from the command line you may get
> more helpful feedback.
>
> Mark
>
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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------------------------------
Message: 6
Date: Thu, 13 Apr 2006 09:52:42 +0200
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] REMD
To: Discussion list for GROMACS users <gmx-users@gromacs.org >
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dongsheng Zhang wrote:
> dear Mark,
>
> Thank you very much for your prompt reply. I try to use parallel
> computing. It works fine.
> for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle
> to get replica0.tpr
> then, mdrun_mpi -np 2 -s replica0.tpr
>
please give EXACT command line and do use mpirun
>
> The error message mentioned in the previous email looks very strange to
> me. MPI works fine, and individual tpr runs fine. The error message
> comes out before replica exchange. replica0 stops at step 500, replica1
> stops at step 400, even the output informatio can't be complted. The
> last lines in replica1.log is
>
> Step Time Lambda
> 400 0.80000 0.00000
>
> Rel. Constraint Deviation: Max between atoms RMS
>
>
> I hope these further information can help you to figure out what's the
> problem.
>
> Best Wishes!
>
> Dongsheng
>
>
> On Thu, 2006-04-13 at 15:17 +1000, Mark Abraham wrote:
>>> Dear gmx users:
>>>
>>> I am trying to run REMD with two replicas (for testing). I used
>>> grompp -f -c -p -o replica0 to get replica0.tpr
>>> grompp -f -c -p -o replica1 to get replica1.tpr
>>>
>>> then used
>>> mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica
>>> -v -N 2
>>> to run it.
>> mdrun doesn't take '-N 2' but I'm not sure this is the problem. Otherwise,
>> looks fine to me.
>>
>>> I got an error message "Segmentation fault" from my script output, but
>>> no error message in both log files. When I tried to run individual tpr
>>> file, it worked fine.
>>>
>>> Could someone can comment why I got "Segmentation fault"? Thank you for
>>> your help!
>> Your MPI setup might require you use a command like "mpirun -N 2 mdrun_mpi
>> ..." to make it work - the segfault might be a gromacs-MPI interaction
>> problem. If you can run an MPI process from the command line you may get
>> more helpful feedback.
>>
>> Mark
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> 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
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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
--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
------------------------------
Message: 7
Date: Thu, 13 Apr 2006 09:53:29 +0200
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Using Pull code with Coarse grain model
To: Discussion list for GROMACS users < gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Mohan Boggara wrote:
> Hi all,
>
> I am trying to use the pull code for constrained force method in a
> coarse grain dppc bilayer model developed by Dr. S.J. Marrink. But I am
> getting error message Warning: pressure scaling > 1% . The problem
> persist even after I changed the tau_p from 1.0 to 1.5.
> Has anyone had any success on similar runs.
>
change it to 20 or 50.
> Mohan
>
> --
> Mohan Boggara
> Department of Chemical Engineering
> University of Houston
> S222 Engineering Bldg 1
> Houston, Texas-77204, USA
> Mobile: 1-713-259-2166
> Office: 1-713-743-4314
> http://polymer.chee.uh.edu/
>
> All human actions have one or more of these seven causes: chance,
> nature, compulsion, habit, reason, passion, and desire.-- Aristotle
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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
--
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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End of gmx-users Digest, Vol 24, Issue 44
*****************************************
--
Mohan Boggara
Department of Chemical Engineering
University of Houston
S222 Engineering Bldg 1
Houston, Texas-77204, USA
Mobile: 1-713-259-2166
Office: 1-713-743-4314
http://polymer.chee.uh.edu/
All human actions have one or more of these seven causes: chance, nature, compulsion, habit, reason, passion, and desire.-- Aristotle
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