Hello, My apollogies, the drift is present whether I use tabulated potentials or not. The email's title I chose is misleading. If I am not mistaken I am using a buffer when I put rcut= 1.0 and rlist=1.3 , but this was not entirely clear to me using with the manual.
Sergio El 05/09/2017 12:29, Mark Abraham escribió: > Hi, > > Your earlier email implied that the drift was present when you used the > group cutoff-scheme, whether or not you used tabulated interactions. But > just now you implied something different. Unbuffered cutoffs with the group > scheme are not comparable with e.g. the default buffering used with the > Verket scheme. > > Mark > > On Mon, Sep 4, 2017 at 10:56 AM <serper...@alum.us.es> wrote: > > Hello, > > Thank you very much for your thoughtfull response. The structural > properties seem to be represented correctly so I guess it should work. I > know that drifts are something we must live with but since it appeared > when changing the system to a tabulated potential+a group cutoff I was > not sure if I was making some mistake. > > Sergio > > El 01/09/2017 12:48, Mark Abraham escribió: > > Hi, > > There's not easy answers to such questions. A practical implementation of > MD that can actually do most relevant kinds of science in relevant time > frames can't have bitwise conservation. Drift accumulates from multiple > aspects of the implementation, too, including the system size, and > constraint algorithm, which can dominate over the effects of missing > interactions over the lifetime of pair lists. See the discussion in the > GROMACS reference manual, e.g. figure 3.5. > > One proper question to ask is at what point your protocol correctly models > whatever relevant physical data exists that is relevant to what you want to > observe. Drift that is too large is likely to affect observables, but will > affect different ones differently. > > Mark > > On Fri, Sep 1, 2017 at 12:12 PM <serper...@alum.us.es> wrote: > > Dear GROMACS Community, > > I am trying to do a simulation using a tabulated potential which forces > me to use the group cut-off. I get a drift in the conserved quantity of > -600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules > and a Na+ ion. I imagine that eventhough it will soon be deprecated the > group cutoff scheme still works correctly. I have tryed to change the > parameters without success and in any case the ones I use seem > reasonable (in my experience using other programs). The rdfs of the > system look normal so I ruled out topology problems. > > It seems that the problem is in the group cut-off since > when I change the tabulated potential for a regular vdw the problem > persists. I have followed the instructions of: > > http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf > > to implement the tabulated potentials. > > Is this the kind of energy drift acceptable? I have pasted a copy .mdp > > Thanks for your help, > > Sergio Perez-Conesa > > integrator = md > dt = 0.001 > nsteps = 100000 > init-step = 0 > cutoff-scheme = group > nst-list = 1 > verlet-buffer-tolerance = 0.0005 > ns-type = grid > rlist = 1.3 > pbc = xyz > coulombtype = PME-switch > rcoulomb = 1. > rcoulomb-switch = 0.95 > pme-order = 4 > fourierspacing = 0.1 > ewald-rtol = 1.e-5 > vdwtype = user > rvdw = 1.0 > DispCorr = No > tcoupl = v-rescale > tc-grps = System > ;nsttcouple = 1 > tau-t = ref-t = 300.0 > constraints = all-angles > constraint-algorithm = LINCS > lincs_iter = 1 > lincs_order = 4 > energygrps = NA OW > energygrp_table = NA OW > comm-mode = linear > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
