Thank you. I will do so. kind regards, Andrea
2008/11/11 Justin A. Lemkul <[EMAIL PROTECTED]>: > > > Andrea Muntean wrote: >> >> I am simulating one chain of PS. The box is produced by pdb2gmx. If I >> run simulations with timestep 0.1 fs up to 0.4 fs everything seem to >> be ok. With 1 fs (which should be a normal time for my system) I would >> get the following warning: >> >> Warning: 1-4 interaction between 290 and 299 at distance 108.224 which >> is larger than the 1-4 table size 1.000 nm >> These are ignored for the rest of the simulation >> This usually means your system is exploding, >> if not, you should increase table-extension in your mdp file >> >> The parameters I use are the following: >> >> title = PS >> cpp = /lib/cpp >> integrator = md >> dt = 0.0001 ; ps ! >> nsteps = 10000 ; total 10 ps >> nstlist = 10 >> nstxout = 100 >> nstvout = 100 >> nstenergy = 100 >> unconstrained-start = yes >> nstxtcout = 50 >> nstlog = 50 >> constraints = none >> ns_type = grid >> vdwtype = Cut-off >> fourierspacing = 0.055 ; Lbox/0.055 ~ 50 >> rlist = 0.9 >> rvdw = 1.2 >> tc_grps = system >> tcoupl = berendsen >> tau_t = 0.1 >> ref_t = 540 >> Pcoupl = no >> optimize_fft = yes >> >> the rest is set default >> >> Did I miss something? What goes wrong? >> > > You are running a very high temperature with no bond constraints. I would > expect you would need a very small timestep (like 0.1 fs) to get reasonable > dynamics. Try using constraints. > > -Justin > >> Any help and/or comments are really appreciated. >> >> Thank you! >> >> Andrea >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users@gromacs.org > 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 gmx-users@gromacs.org 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