[gmx-users] problem with mpiexec, mdrun in gromacs/4.0.7

[delara aghaie]

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
 
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.
 
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?
 
Thanks in advance
D.Aghaie

--- On Fri, 4/8/11, Justin A. Lemkul <jalemkul at vt.edu> wrote:


From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] unable to equilibrate protein in membrane with NPT
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
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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