Quoting Anamika Awasthi <[EMAIL PROTECTED]>: > 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.
Don't think, or don't know? These types of things are important. > Please find pr.mdp filesbelow and RMSD as attachment. > Please tell me why it happened? Well, look at your trajectory - what's happening when the RMSD graph spikes? That should provide you with some ideas. My guess would be your protein is jumping across the simulation box, but you have not described your setup - box size/distance from protein to the box edge, and whether or not you observed any periodic jumping. -Justin > > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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
