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

[serpercon at alum.us.es]

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 <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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