[gmx-users] Solvating in a solvent other than water

[Jarvist Moore Frost]

Possible the molecules are broken, but I've also seen this occur where the
replica box (in this example evidently a 3x3x3 expansion) had slight gaps
at the edge of the replicas, so when you minimise the energy, the clumps of
matter pull themselves together.

Try equilibrating under MD with a barostat. If the molecules have been
chopped, the simulation will explode. If it's merely gappy, it will melt
itself together.

Best,

Jarv

On 21 September 2015 at 13:19, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/21/15 12:13 AM, Pallavi Banerjee wrote:
>
>> Yes, I should have put up the images.
>> I have uploaded two images, one of the expanded box before energy
>> minimization and the other after, which shows the formation of blocks. I
>> performed an NVT equilibration with this bad, 'block'ed box, and too many
>> LINCS warning show up.
>>
>>
>> 1. Before minimization:
>>
>> https://drive.google.com/file/d/0B0oti29Tm3S2VFhheVJ5SFBKQ1E/view?usp=sharing
>>
>> 2. After minimization:
>>
>> https://drive.google.com/file/d/0B0oti29Tm3S2VGd5SnpZTDVhYUE/view?usp=sharing
>>
>>
> Looks like you probably didn't make the molecules whole before replicating
> the box; the molecules at the edges look distorted, but it's a bit hard to
> tell.
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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