Hello
I want to run a simulation in gromacs/4.0.7 because this version
supports v-rescale option for thermostat and I need that.
tcoupl=v-rescale
Do the job properly, and install 4.5.4 for better parallel performance
and more bug fixes.
*in this version the grompp command does not need -np option. please
let me know how I can specify the number of processors for my job.*
See
http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp#Parallel_calculations
I use a *.ll* file to submit my job. in this file the command line is:
*mpiexec mdrun_mpi -v -s topol.tpr -np 8*
(this is a coomand line which I used previously in my .ii file for
gromacs/3.3
is this command line suitable for version 4/0/7 as well or I should
change something?
It will work in 4.0.7 and 4.5.4 using all the processors available to
mpiexec, and the "-np 8" is ignored.
Mark
Thanks in advance
D.Aghaie
--- On *Fri, 4/8/11, Justin A. Lemkul /<[email protected]>/* wrote:
From: Justin A. Lemkul <[email protected]>
Subject: Re: [gmx-users] unable to equilibrate protein in membrane
with NPT
To: "Discussion list for GROMACS users" <[email protected]>
Date: Friday, April 8, 2011, 5:32 PM
Peter C. Lai wrote:
> Hello again
>
> In my protein-membrane-water-ion system (inserted via g_membed)
I have run a 1ns NVT equilibration with the protein restrained and
now I am trying to equilibrate with NPT and LINCS/mdrun is
crashing after about 5000 iterations.
>
> Here is my NPT mdp file:
>
> define =-DPOSRES
> integrator = md
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.002
> nsteps = 500000
> init_step = 0
> comm-mode = Linear
> nstcomm = 1
> comm-grps = Protein_POPC SOL_CL
> nstxout = 100 ; save coordinates every 0.2 ps
> nstvout = 100 ; save velocities every 0.2 ps
> nstenergy = 100 ; save energies every 0.2 ps
> nstlog = 100 ; update log file every 0.2 ps
> continuation = yes
> constraint_algorithm = lincs ; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H
bonds)
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ns_type = grid ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> rlist = 1.2 ; short-range neighborlist
cutoff (in nm)
> rlistlong = 1.4
> rcoulomb = 1.2 ; short-range electrostatic
cutoff (in nm)
> rvdw = 1.2 ; short-range van der Waals
cutoff (in nm)
> vdwtype = switch
> rvdw_switch = 0.8
> coulombtype = PME
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> tcoupl = Nose-Hoover
> tc-grps = Protein POPC SOL_CL
> tau-t = 0.5 0.5 0.5
> ref-t = 300 300 300
> gen-vel = no
> pcoupl = Parrinello-Rahman ; Pressure coupling
on in NPT
> pcoupltype = semiisotropic ;
> tau_p = 5.0 ; time constant,
in ps
> ref_p = 1.01325 1.01325
> compressibility = 4.5e-5 4.5e-5
>
> Any suggestions?
Try using the Berendsen barostat. P-R allows for wider
oscillations that can lead to instability in incompletely
equilibrated systems.
-Justin
-- ========================================
Justin A. Lemkul
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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