[gmx-users] Semiisotropic pressure coupling

[Justin Lemkul]

On 2/12/15 10:34 PM, shivangi nangia wrote:
>>
>> Dear Justin,
>>
>
> Thanks for the reply.
>
> The link you have mentioned says the parameters are for GROMACS 5.0
>
> I am using an older version, 4.6.1
>
> Is there another link/suggestions for that version.
>
> Sorry, I forgot to mention.
>
> On trying to use those parameters with my version of GROMACS, I get the
> error:
>
> ERROR 1 [file md.mdp, line 78]:
>    Invalid enum 'force-switch' for variable vdw-modifier, using
>    'Potential-shift-Verlet'
>    Next time use one of: 'Potential-shift-Verlet' 'Potential-shift' 'None'
>    'Potential-switch' 'Exact-cutoff'
>
>
> The mdp options manual says:
>
> *Force-switch*Smoothly switches the forces to zero between *rvdw-switch*
>   and *rvdw*. This shifts the potential shift over the whole range and
> switches it to zero at the cut-off. Note that this is more expensive to
> calculate than a plain cut-off and it is not required for energy
> conservation, since *Potential-shift* conserves energy just as well
>
> Can I use Potential-shift instead of my version?

No.  Read the description of Potential-shift: "Note that this does not affect 
the forces or the sampling."  Force-switching is required for proper use of the 
lipid force field.  The old "vdwtype = shift" with the group cutoff scheme 
should do the same thing as force-switch, but we haven't tested it explicitly. 
What i know for sure is that CHARMM's vfswitch and GROMACS' "vdw-modifier = 
force-switch" produce identical forces, hence the strong recommendation.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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