[gmx-users] Calculating Dielectric constant

[David van der Spoel]

On 31/05/16 15:26, Life Sciences Inc wrote:
> 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.
run trjconv -pbc whole on your input coords. I bet one of your molecules 
is broken over the PBC.
>
> 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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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se