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<div>Hello</div>
<div>I want to run a simulation in gromacs/4.0.7 because
this version supports v-rescale option for thermostat
and I need that.</div>
<div>tcoupl=v-rescale</div>
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<br>
Do the job properly, and install 4.5.4 for better parallel
performance and more bug fixes. <br>
<br>
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<div><strong>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.</strong></div>
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<br>
See
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp#Parallel_calculations">http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp#Parallel_calculations</a><br>
<br>
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<div> </div>
<div>I use a <strong>.ll</strong> file to submit my job.
in this file the command line is:</div>
<div><strong><font color="#7f007f">mpiexec mdrun_mpi -v -s
topol.tpr -np 8</font></strong></div>
<div>(this is a coomand line which I used previously in my
.ii file for gromacs/3.3</div>
<div>is this command line suitable for version 4/0/7 as
well or I should change something?</div>
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<br>
It will work in 4.0.7 and 4.5.4 using all the processors available
to mpiexec, and the "-np 8" is ignored.<br>
<br>
Mark<br>
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<div> </div>
<div>Thanks in advance</div>
<div>D.Aghaie<br>
<br>
--- On <b>Fri, 4/8/11, Justin A. Lemkul <i><a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a></i></b>
wrote:<br>
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From: Justin A. Lemkul <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a><br>
Subject: Re: [gmx-users] unable to equilibrate protein
in membrane with NPT<br>
To: "Discussion list for GROMACS users"
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
Date: Friday, April 8, 2011, 5:32 PM<br>
<br>
<div class="plainMail"><br>
<br>
Peter C. Lai wrote:<br>
> Hello again<br>
> <br>
> 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.<br>
> <br>
> Here is my NPT mdp file:<br>
> <br>
> define =-DPOSRES<br>
> integrator = md<br>
> ; Start time and timestep in ps<br>
> tinit = 0<br>
> dt = 0.002<br>
> nsteps = 500000<br>
> init_step = 0<br>
> comm-mode = Linear<br>
> nstcomm = 1<br>
> comm-grps = Protein_POPC SOL_CL<br>
> nstxout = 100 ; save
coordinates every 0.2 ps<br>
> nstvout = 100 ; save velocities
every 0.2 ps<br>
> nstenergy = 100 ; save energies
every 0.2 ps<br>
> nstlog = 100 ; update log file
every 0.2 ps<br>
> continuation = yes<br>
> constraint_algorithm = lincs ; holonomic
constraints<br>
> constraints = all-bonds ; all bonds (even
heavy atom-H bonds)<br>
> lincs_iter = 1 ; accuracy of
LINCS<br>
> lincs_order = 4 ; also related to
accuracy<br>
> ns_type = grid ; search
neighboring grid cells<br>
> nstlist = 5 ; 10 fs<br>
> rlist = 1.2 ; short-range
neighborlist cutoff (in nm)<br>
> rlistlong = 1.4<br>
> rcoulomb = 1.2 ; short-range
electrostatic cutoff (in nm)<br>
> rvdw = 1.2 ; short-range van
der Waals cutoff (in nm)<br>
> vdwtype = switch<br>
> rvdw_switch = 0.8<br>
> coulombtype = PME<br>
> pme_order = 4 ; cubic
interpolation<br>
> fourierspacing = 0.16 ; grid spacing
for FFT<br>
> tcoupl = Nose-Hoover<br>
> tc-grps = Protein POPC SOL_CL<br>
> tau-t = 0.5 0.5 0.5<br>
> ref-t = 300 300 300<br>
> gen-vel = no<br>
> pcoupl = Parrinello-Rahman ;
Pressure coupling on in NPT<br>
> pcoupltype = semiisotropic ;<br>
> tau_p = 5.0 ;
time constant, in ps<br>
> ref_p = 1.01325 1.01325<br>
> compressibility = 4.5e-5 4.5e-5<br>
> <br>
> Any suggestions?<br>
<br>
Try using the Berendsen barostat. P-R allows for
wider oscillations that can lead to instability in
incompletely equilibrated systems.<br>
<br>
-Justin<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]vt.edu | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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