Hi justin, thanks for your response..... following is the .mdp file pasted..
_____ title = trp_drg warnings = 10 cpp = /lib/cpp ; location of cpp on SGI define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 2500000 ; total 5000.0 ps. nstcomm = 1 nstxout = 25000 ; output coordinates every 0.5 ps nstvout = 100000 ; output velocities every 2.0 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 energygrps_excl = freeze freeze freeze SOL ! To remove computation of interactions between the frozen groups with surroundings (i.e. the solvent, SOL) fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc_grps = protein sol NDP ref_t = 300 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ; Non-equilibrium MD stuff freezegrps = freeze freezedim = Y Y Y ____ With Thanks, Vivek 2008/10/17 Justin A. Lemkul <[EMAIL PROTECTED]> > > > vivek sharma wrote: > >> Hi Tehre, >> i am running a job by keeping a part of molecule freeze ....by using the >> .mdp option.... >> > > What is your entire .mdp file? > > -Justin > > ______________ >> > ________ > >> energygrps_excl = Terminal Terminal Terminal SOL ! To remove >> computation of nonbonding interactions between the frozen groups with each >> other >> and surroundings (i.e. the solvent, SOL) >> freezegrps = Terminal ! Index group to freeze >> freezedim = Y Y Y ! Freeze this group in all >> directions, x, >> y, and z >> ___________________________________________________ >> >> >> where frreze is a group mentioned in the index file... >> During the run the job is being terminated with the following error >> . >> __________________________________________________________ >> Step 1 Warning: pressure scaling more than 1%, mu: -3.51079e+22 >> -3.51079e+22 -3.51079e+22 >> >> ------------------------------------------------------- >> Program mdrun_d, VERSION 3.3.3 >> Source code file: ns.c, line: 258 >> >> Fatal error: >> Box was shifted at least 10 times. Please see log-file. >> ------------------------------------------------------- >> >> Error on node 0, will try to stop all the nodes >> Halting parallel program mdrun_d on CPU 0 out of 24 >> >> srun: error: n216: task0: Aborted >> srun: Terminating job >> __________________________________________________________________ >> >> Can somebody give an insight in the problem for figuring out the probable >> cause of the error. >> >> PS::Before the run I mentioned the boxsize in editconf as "-box 7.5 5 6 ", >> to keep the size of box and number of solvent optimum. >> Does it have anything to do with the mentioned error ? >> >> >> Looking for suggestions.. >> with thanks, >> Vivek >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > 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 [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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