Dear Justin: Thanks for your response.
The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Yanmei Song wrote: > >> Dear Users: >> >> I was running a system by non-equilibrium MD using a plain Cut-off for the >> electrostatics: >> >> title = water >> cpp = /lib/cpp >> constraints = all_bonds >> integrator = md >> dt = 0.004 ; ps ! >> nsteps = 500000 ; total 8ns. >> nstcomm = 1 >> nstxout = 50000 >> nstvout = 50000 >> nstfout = 0 >> nstlog = 5000 >> nstenergy = 5000 >> nstxtcout = 25000 >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> coulombtype = Cut-off >> rlist = 0.8 >> rcoulomb = 0.9 >> rvdw = 0.8 >> fourierspacing = 0.12 >> ewald_rtol = 1e-5 >> ;nemd >> cos_acceleration = 0.005 >> ; Berendsen temperature coupling is on in two groups >> Tcoupl = berendsen >> tc_grps = SOL >> tau_t = 0.1 >> ref_t = 300 >> ; Energy monitoring >> energygrps = SOL >> ; Isotropic pressure coupling is now on >> Pcoupl = berendsen >> pcoupltype = isotropic >> ;pc-grps = SOL >> tau_p = 1.0 >> ref_p = 1.0 >> compressibility = 4.5e-5 >> >> ; Generate velocites is off at 300 K. >> gen_vel = yes >> gen_temp = 300.0 >> gen_seed = 100000 >> >> I can not figure out where I did wrong, the temperature of the system is >> 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for >> the help in advance! >> > > Why are you using cutoff for coulombtype? It is the reason for the heating > you are seeing: > > http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html > > -Justin > > -- >> Yanmei Song >> Ph.D. Candidate >> Department of Chemical Engineering >> Arizona State University >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php