[gmx-users] (Don't know if mail worked last time)Drift with groups+tabulated potential.

sperez14 at us.es sperez14 at us.es
Tue Aug 15 14:25:52 CEST 2017

Dear GROMACS Community, 

First of all, if someone got this email twice, I am sorry. It is my
first post and I was not sure if it worked.  

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: 


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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