Thank you for your hints. I'll give it a try right now. Regards, Andrea
2010/3/1 Berk Hess <[email protected]> > Hi, > > Shake is not relevant for water and also a time step of 2 fs should be > fine. > The cut-off's are the problem. You have a buffer size of 0.1 nm, > which is already smaller than 2 times the distance from the center of > geometry > of a water molecule to a hydrogen. You need some additional distance > for water diffusion. I would use a buffer of 0.25 to 0.3 nm. > You don't list you coulombtype setting. Use pme (or if you want perfect > energy > conservation: pme-switch), you can also use reaction-field-zero if you > really don't > want to use PME. > Then use nstlist=-1, run a short simulation and check in at the end of your > log file > that the neighbor list lifetime is somewhere between 5 and 20 steps. > > We should have a wiki entry for such details. Maybe there is one, but I was > too lazy > to check or make one. > > Berk > > > Date: Mon, 1 Mar 2010 09:16:36 +0100 > > From: [email protected] > > To: [email protected] > > Subject: Re: [gmx-users] NVE of water > > > > > Hi Andrea, > > Did you use double precision? Also, I'd try a lower dt (say 1fs) and > > shake tolerance (maybe 1E-8). > > Good luck, > > Ran > > > > Andrea wrote: > > > Dear users, > > > > > > for test purposes in order to set up a bigger system, I try to run NVE > > > simulations of SPC water, but the energy increases very rapidely. My > > > guess is that the cutoffs I use are not good for water. I that the > > > case ( I would be grateful for a good reference for suitable SPC water > > > parameters) or do I miss something else? > > > My parameter file for the NVE is: > > > > > > title = NVE > > > cpp = /lib/cpp > > > integrator = md > > > dt = 0.002 ; ps ! = 2 fs > > > nsteps = 50000 ; total 100 ps > > > nstxout = 5000 > > > nstvout = 5000 > > > nstxtcout = 0 > > > nstlog = 5000 > > > nstenergy = 5000 > > > nstlist = 10 > > > ns_type = grid > > > rlist = 1.1 > > > > > > unconstrained-start = yes > > > constraints = all-bonds > > > constraint_algorithm = shake > > > shake_tol = 0.0001 > > > ;VdW > > > vdwtype = Switch > > > rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist > > > rvdw_switch = 0.9 > > > gen_vel = no ; yes > > > gen_temp = 300 > > > gen_seed = -1 > > > ;Temperature coupling > > > tc_grps = system > > > tcoupl = no ;nose-hoover > > > tau_t = 0.1 > > > ref_t = 300 > > > ;Pressure coupling > > > pcoupl = no > > > optimize_fft = yes > > > > > > Any suggesions are really welcome. > > > > > > Thank you. > > > > > > Regards, > > > Andrea Muntean > > > > > > -- > > ------------------------------------------------------ > > Ran Friedman > > Postdoctoral Fellow > > Computational Structural Biology Group (A. Caflisch) > > Department of Biochemistry > > University of Zurich > > Winterthurerstrasse 190 > > CH-8057 Zurich, Switzerland > > Tel. +41-44-6355559 > > Email: [email protected] > > Skype: ran.friedman > > ------------------------------------------------------ > > > > -- > > gmx-users mailing list [email protected] > > 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 [email protected]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ------------------------------ > New Windows 7: Find the right PC for you. Learn > more.<http://windows.microsoft.com/shop> > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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