[gmx-users] Energy minimization problem in Choline Chloride+Urea mixture in Gromacs

[Justin Lemkul]

On 1/2/15 11:21 AM, Suman Das wrote:
> Hi,
>   I am trying to simulate a mixture of Choline Chloride+Urea mixture with
> 33:67 ratio at 298 K. I have taken the force field of choline from this
> paper :http://pubs.acs.org/doi/full/10.1021/jp404619x
> <https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp404619x>,
> chloride from http://pubs.acs.org/doi/full/10.1021/jp063901o
> <https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp063901o>
> and urea from http://pubs.acs.org/doi/full/10.1021/jp030534x
> <https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp030534x>.
> During the minimization process Fmax < 200 but potential energy was quite
> high~5.4465270e+04. And finally the simulation crushes.  I have used this
> force field of urea previously which matches well with experimental data.
> So I have tried with another force field of choline (
> http://pubs.acs.org/doi/full/10.1021/jp301270y
> <https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp301270y>)
> but exactly the same thing happens. I have also tried the freeze group
> option. But the result is same. I built the box using packmol. I took the
> initial box length 5nm.
>

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

-- 
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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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