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

[Mark Abraham]

> 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 /<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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