Re: [gmx-users] simulation of long chains in vacuum
Rongliang Wu wrote: > Hello, gmx-users， > i generated a chain of 1000 units and intended to simulate in vacuum, > but the system exploded and the mdp file is as follows: Please tell us you have done normal things like energy minimization and or position-restrained MD, and checked visually that things look OK else we might suspect the problem is that you haven't done these basic things and not bother wasting our time telling you to do them. > are there any obvious errors? Looks OK to me. > and my system is quite large, about 49.90900 70.12100 231.85800 ns > is there any upper limits for gromacs systems? I don't believe so. You could look in the manual... Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] simulation of long chains in vacuum
Hello, gmx-users， i generated a chain of 1000 units and intended to simulate in vacuum, but the system exploded and the mdp file is as follows: title= PE cpp = /usr/bin/cpp include = define = integrator = md dt = 0.002 nsteps = 10 nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy= 500 nstxtcout= 2000 xtc_grps = energygrps = comm_mode= angular nstlist = 0 ns_type = simple rlist= 0 rvdw = 0 rcoulomb = 0 pbc = no tcoupl = Berendsen tc-grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no ;Pcoupltype = isotropic ;tau_p= 1.0 ;compressibility = 4.5e-4 ;ref_p= 1.0 ;annealing = single ;annealing_npoints = 15 ;annealing_time = 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 ;annealing_temp = 370 365 360 355 350 345 340 335 330 325 320 315 310 305 300 gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds optimize_fft = yes are there any obvious errors? and my system is quite large, about 49.90900 70.12100 231.85800 ns is there any upper limits for gromacs systems? Regards Thanks Rongliang Wu [EMAIL PROTECTED] 2006-05-10 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
