<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><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>
<DIV> </DIV>
<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>
<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>
<DIV> </DIV>
<DIV>Thanks in advance</DIV>
<DIV>D.Aghaie<BR><BR>--- On <B>Fri, 4/8/11, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: Justin A. Lemkul <jalemkul@vt.edu><BR>Subject: Re: [gmx-users] unable to equilibrate protein in membrane with NPT<BR>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><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
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>-- gmx-users mailing list <A href="http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=_blank>http://www.gromacs.org/Support/Mailing_Lists/Search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <A href="http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read
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