On Mon, Jul 15, 2013 at 3:00 AM, <gmx-users-requ...@gromacs.org> wrote:
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: How to calculate enthalpy (Dr. Vitaly Chaban) > 2. enery conserving problem in NVE simulations with SMW4-NPD > polarizable force field (Ding Yun) > > > ------------------------------ > > Message: 2 > Date: Mon, 15 Jul 2013 09:43:38 +0000 > From: "Ding Yun" <yun.d...@phys.chem.ethz.ch> > Subject: [gmx-users] enery conserving problem in NVE simulations with > SMW4-NPD polarizable force field > To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > Message-ID: <e82f84d319900f4ca5fcf4b9bb98716c16242...@mbx23.d.ethz.ch> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > I'm trying to simulate liquid water (512 water molecules) with SMW4-NPD > polarizable force field. The NVT simulation looks fine, but when I restart > it with NVE runs, the total energy of the system keeps drifting down. > > The time step I'm using now is 0.5 fs and emtol=0.01 kJ/mol/nm. Gromacs > is also compiled with double precision. Does anyone have any suggestions > for this kind of problem? Thanks a lot. > > Regards, > Yun > > > My .mdp file: > > ; RUN CONTROL PARAMETERS > integrator = md > tinit = 800 > init_step =0 > dt = 0.0005 ; time step (ps) > nsteps = 400000 ; number of steps > > ; OUTPUT CONTROL OPTIONS > nstenergy = 100 > nstxout =100 > > > ; NEIGHBORSEARCHING PARAMETERS > nstlist = -1 > ns_type = grid > pbc = xyz > rlist = 1.24 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > coulombtype = PME-Switch > rcoulomb = 1.05 > rcoulomb_switch = 0.85 > vdw-type = shift > rvdw = 1.05 > ewald_rtol =1e-4 > > > ; OPTIONS FOR BONDS > constraints = h-bonds > ; Type of constraint algorithm > constraint-algorithm = Lincs > > > ; Polarizable model parameters > emtol = 0.01 > niter = 20 > > ; Temperature coupling > tcoupl = no > > ; pressure coupling > > pcoupl = no > > ; GENERATE VELOCITIES FOR STARTUP RUN > gen_vel = no > > > ------------------------------ > > -- > 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/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 111, Issue 69 > ****************************************** > Try the following for "options for bonds". constraint-algorithm = shake shake-tol = 1e-10 I hope this helps. -- *S. Alireza Bagherzadeh, M.A.Sc. <https://circle.ubc.ca/handle/2429/26269> * * * *PhD Candidate * * * *Dept. of Chem. & Bio. Eng. <http://www.chbe.ubc.ca/>* * * *University of BC <http://www.ubc.ca/> * *T: *604.827.3194* | C: *778.990.1383* | F: *604.822.6003* * ** * * *6.03 - 2360 East Mall* * * *Vancouver BC V6T1Z3* *"**Success is not final, failure is not fatal: it is the courage to continue that counts." --W. S. Churchill* -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists