[gmx-users] RE : gmx-users Digest, Vol 108, Issue 154
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Thu Apr 25 15:26:32 CEST 2013
Hello Xavier,
Thank you for your response.
>> nstlist = 10 and the rlist = 1.0
My mistake, i did not changes these values when i switched to PME,
I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The average Temp of the system is better than previously but fluctuate around (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations.
I have also visualized my system at the end of the NPT run, the na+, water, surfactant, octane molecules form a slab with void
What's wrong ?
Stephane
------------------------------
Message: 5
Date: Thu, 25 Apr 2013 13:34:21 +0200
From: XAvier Periole <x.periole at rug.nl>
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4632C83B-CD6F-4C92-B887-A1C39DFF4F94 at rug.nl>
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Did you visualise the system? T in function of time? Epot in function of time?
As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if nstlist =10.
On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 <Stephane.ABEL at cea.fr> wrote:
> Hello all,
>
> I am trying to test the martini force field with PME for a charged system that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My system works well, if i use the standard shift parameters (correct temp, and pressure). But for for the simulation with PME , the temp of the system decrease to 290 K. Below my *.mdp parameters for a NPT equil at 298K
>
>
> integrator = md
> dt = 0.020
> nsteps = 10000 ; 200ps
> nstcomm = 10
> comm-grps =
> ;refcoord_scaling = com
>
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstlog = 1000
> nstenergy = 100
> ;nstxtcout = 1000
> xtc_precision = 100
> ;xtc-grps =
> energygrps = AOT W ION OCT
>
> nstlist = 10
> ns_type = grid
> pbc = xyz
> rlist = 1.
>
> ; PME parameters
> coulombtype = PME
> rcoulomb = 1.2
> rvdw = 1.2
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
>
> tcoupl = v-rescale
> tc-grps = AOT_W_ION OCT
> tau_t = 1.0 1.0
> ref_t = 298 298
> Pcoupl = berendsen
> Pcoupltype = isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
>
> ;gen_vel = no
> ;gen_temp = 0
> ;gen_seed = 473529
>
>
> ; MARTINI and CONSTRAINTS
> ; for ring systems and stiff bonds constraints are defined
> ; which are best handled using Lincs.
>
> constraints = none
> constraint_algorithm = Lincs
> unconstrained_start = no
> lincs_order = 4
> lincs_warnangle = 3
>
>
> Results obtained with W/ PME
>
> Statistics over 10001 steps using 1001 frames
>
> Energies (kJ/mol)
> Bond G96Angle LJ (SR) Coulomb (SR) Coul. recip.
> 1.63789e+04 1.25195e+03 -4.02093e+05 -8.22079e+03 -4.86843e+04
> Potential Kinetic En. Total Energy Temperature Pressure (bar)
> -4.41367e+05 7.81801e+04 -3.63187e+05 2.90373e+02 -1.76470e+01
> T-AOT_W_ION T-OCT
> 2.90629e+02 2.90357e+02
>
> Results W:o PME
>
> Energies (kJ/mol)
> Bond G96Angle LJ (SR) Coulomb (SR) Potential
> 1.60482e+04 1.24820e+03 -3.34608e+05 -7.33665e+02 -3.18046e+05
> Kinetic En. Total Energy Temperature Pressure (bar)
> 8.02685e+04 -2.37777e+05 2.98129e+02 -3.07123e+01
>
> Box-X Box-Y Box-Z
> 1.52926e+01 1.52926e+01 1.52926e+01
>
>
> T-AOT_W_ION T-OCT
> 2.98141e+02 2.98129e+02
>
>
> Did I miss something ?
>
>
> Note that for the moment i do not use the polarizable water model.
>
> Thanks for your help
>
> Stephane
>
>
>
>
> --
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------------------------------
Message: 6
Date: Thu, 25 Apr 2013 14:05:51 +0200
From: Berk Hess <gmx3 at hotmail.com>
Subject: RE: [gmx-users] Differences between 4.5.5 and 4.6.2-dev?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <DUB124-W4FD05B41F4EFBF070FDD08EB60 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
Twin-range will lead to extra errors, which could be negligible or not.
But the errors should be the same and have the same effects in different versions.
I think nothing has changed in the twin-range treatment from 4.5 to 4.6, but I am not 100% sure.
Which version with twin-range matches your non twin-range results?
Cheers,
Berk
----------------------------------------
> Subject: Re: [gmx-users] Differences between 4.5.5 and 4.6.2-dev?
> From: kessel at icp.uni-stuttgart.de
> Date: Thu, 25 Apr 2013 10:38:35 +0200
> To: gmx-users at gromacs.org
>
> Dear Berk, der GMXers,
>
> On Apr 23, 2013, at 2:54 PM, Stefan Kesselheim <kessel at icp.uni-stuttgart.de> wrote:
>
> > The temperature is 300.6, target temperature was 300. That should be fine. I did check weaker fields and weaker thermostat coupling. Everything stayed optimally consistent, within 4.5.5, however incompatible with 4.6.2.
> > I'm rerunning with cutoffs=1.4 now. I should get results by tomorrow.
>
> Now results are there and without twin-range I obtain consistent results between the GMX-versions. I'm now switching on twin-range and rerunning to check if the error does reappear.
>
> I don't know what would be better: Either I did something wrong in a very stupid way, or ...
>
> Thanks for your patience
> Stefan
>
> --
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------------------------------
Message: 7
Date: Thu, 25 Apr 2013 14:28:56 +0200
From: Sainitin Donakonda <saigro16 at gmail.com>
Subject: [gmx-users] Problem with gromacs in Cluster
To: gmx-users at gromacs.org
Message-ID:
<CAB1QHmssKoi4s0nWER+NXMdOs-LSZnexW314SSWre+MQA=eb=g at mail.gmail.com>
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Hey all,
I recently ran 20ns simulation of protein ligand complex on cluster i used
following script to run simulation
grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
md_test.tpr
mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8
*I saved this as MD.sh And then submited to cluster using following script*
#!/bin/bash
#BSUB -J testgromacs # the job's name/array job
#BSUB -W 120:00 # max. wall clock time in hh:mm
#BSUB -n 8,8 # number of processors Min,Max
#BSUB -o test/output_%J.log # output file
#BSUB -e test/errors_%J.log # error file
#BSUB -M 8192 #Memory limit in MB
echo "Started at `date`"
echo
cd test
echo "Running gromacs test in `pwd`"
./MD.sh
echo "Finished at `date`"
It gave result but when checked files .xtc and created RMSD plots in that
x-axis of this plot i see only 8ns ...but in MD.MDP file i specified 20ns..
Cluster Output says that "TERM_RUNLIMIT: job killed after reaching LSF run
time limit.
Exited with exit code 140". i gave maximum cluster time 120 hours..still it
is not sufficient ..
Can any body tell me how do it split script i such that i will get all
20ns simulation
Thanks in advance ,
Sainitin
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