hi, did u specify an index file in your command line for the 2 groups (protein and SOl?
> Dhananjay, > > Consider searching the list archive... All possible solutions are in > there. > > Cheers, > > Tsjerk > > On 7/27/07, Dhananjay <[EMAIL PROTECTED]> wrote: >> Hello all, >> >> I am getting error in pr dynamics when I run mdrun for a protein consist >> of >> two chains with 326 residues each. >> >> The error is as follows: >> >> Program grompp, VERSION 3.3 >> Source code file: readir.c, line: 1131 >> >> Fatal error: >> Not enough ref_t and tau_t values! >> ------------------------------------------------------- >> >> >> >> I want to perform simulation at 300 K. But how much tau_t value can I >> vary ? >> >> The mdp file used for the simulation is as follows: >> Can anybody tell me whats wrong here ? >> >> >> Thanking you in advance ........................ >> >> >> >> title = none >> cpp = /usr/bin/cpp >> define = -DPOSRES >> constraints = all-bonds >> integrator = md >> dt = 0.001 ; ps ! >> nsteps = 500000 ; total 500 ps. >> nstcomm = 1 >> nstxout = 250 >> nstvout = 1000 >> nstfout = 0 >> nstlog = 10 >> nstenergy = 10 >> nstlist = 10 >> ns_type = grid >> rlist = 0.9 ;nm >> coulombtype = PME >> rcoulomb = 0.9 ;nm >> rvdw = 1.4 >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4 >> ewald_rtol = 1e-5 >> optimize_fft = yes >> ; Berendsen temperature coupling is on in three groups >> Tcoupl = berendsen >> tau_t = 0.5 0.5 >> tc_grps = protein sol >> ref_t = 300 300 >> ; Pressure coupling is on >> Pcoupl = berendsen >> pcoupltype = isotropic >> tau_p = 1.0 >> 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 >> >> >> >> -- Dhananjay >> >> >> _______________________________________________ >> 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 >> > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > _______________________________________________ > 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 > > > _______________________________________________ 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
