[gmx-users] About coulmb & Vanderrwalls cutoff

[Justin Lemkul]

On 6/4/13 11:25 AM, vidhya sankar wrote:
> Dear Justin Thank you for yoyr Previuos reply
>                                                                  I am using  Gromos96 53a6
>
> so i am using  the following parameters
> ns_type     = grid
> nstlist     = 5
> rlist       = 0.9
> rcoulomb    = 0.9
> rvdw        = 1.4
>
> is this value is reasonable   ?

Yes.

> But when i run the grommp i got warnings as follows
> nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>    nstcomm to nstcalcenergy
>
> NOTE 2 [file CNTPEPnvt.mdp]:
>    You are using a cut-off for VdW interactions with NVE, for good energy
>    conservation use vdwtype = Shift (possibly with DispCorr)
>
> NOTE 3 [file CNTPEPnvt.mdp]:
>    You are using a cut-off for electrostatics with NVE, for good energy
>    conservation use coulombtype = PME-Switch or Reaction-Field-zero
>
>   if Chnge vdwtupe=shift with   disspCorr  =  DispCorr    = EnerPres
>
> I have got the  error as follows
> WARNING 2 [file CNTPEPnvt.mdp]:
>    The sum of the two largest charge group radii (0.498722) is larger than
>    rlist (0.900000) - rvdw (1.400000)
> How to to Avoid this error? (Due to warning grompp_d terminated )
>

The notes and warnings arise from settings that are still incorrect.  Gromos96 
force fields do not use shifted potentials for vdW interactions; they are simply 
truncated at rvdw using a plain cutoff.  The plain cutoff for Coulombic 
interactions is also wrong.  The original Gromos96 development was done with a 
reaction field term, but more recent work has shown PME to be superior.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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