Hi, On Friday, 15. February 2008 14:51, Anamika Awasthi wrote: > Dear all, > > I am working on a biological dimer of 330 residues. > I dont think that I got any error message when I did grompp. > Please find pr.mdp filesbelow and RMSD as attachment. > Please tell me why it happened? > > pr.mdp > ; > ; User spoel (236) > ; Wed Nov 3 17:12:44 1993 > ; Input file > title = CM_2ao2_A > cpp = /usr/bin/cpp > define = -DPOSRES > constraints = all-bonds > integrator = md > dt = 0.001 > nsteps = 100000 > nstcomm = 1 > nstxout = 250 > nstvout = 1000 > nstfout = 0 > nstlog = 10 > nstlist = 10 > ns_type = grid > rlist = 1 > coulombtype = PME > rcoulomb = 1.0 > rvdw = 1.0 > 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 > Tcoupl = berendsen > tau_t = 0.01 0.01 > tc_grps = protein non-protein > ref_t = 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 > > > Thanking you > > With best regards > Anamika
you are using PBC and your system is sometimes jumping out of the box, so you have to mirror it back to its normal box trjconv -f yourtraj.trr -o yourtraj_fit.trr -s topol.tpr -pbc nojump should fix it again. Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ 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
