[gmx-users] Calculating Dielectric constant

[Life Sciences Inc]

Dear Justin


I tried to run the simulation by changing cutoff scheme from verlet to
group, but its giving error of too many LINCS warnings (1001), Any idea how
to fix this issue I have already minimized and equiliberated my structure
with nvt for few ps and npt for 5ns.

Thanks

On Mon, May 30, 2016 at 2:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/30/16 8:33 AM, Life Sciences Inc wrote:
>
>> Dear ALL Gromacs users
>>
>> I am trying to calculate Dielectric constant using the option in my
>> simulation file as epsilon-surface = 70 . whenever I try to run the
>> simulaton I get this warning message
>>
>> "Since molecules/charge groups are broken using the Verlet scheme, you can
>> not use a dipole correction to the PME electrostatics."
>>
>> I am ignoring this warning by using maxwarn but after few ns simulation is
>> crashing, kindly someone tell me the solution to this problem?
>>
>>
> Warnings like that should be a pretty clear indicator of "what you are
> doing should not be done," so of course if you override the warning, you
> should expect problems :)  Not all features are compatible yet with Verlet;
> try with the group cutoff scheme to see if it works there.
>
> -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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