[gmx-users] Energy drift combining tabulated potentials and group cut-off.

[Mark Abraham]

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 <serpercon at 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
> --
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