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 <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] unable to equilibrate protein in membrane with NPT To: "Discussion list for GROMACS users" <gmx-users@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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
