[gmx-users] TFE-water homogeneous system -NPT

[Justin Lemkul]

On 2/10/14, 12:12 PM, Archana Sonawani-Jagtap wrote:
> Hello,
>
> I am trying to perform peptide simulation using TFE-water system. I did lot
> of literature search and according carried out NVT for 32ns followed by NPT
> 10ns simulation for TFE-water system.
>
> I found that the TFE get accumulated in the center of the box and water
> molecules surround them. The system is no more homogeneous.
>
> Is this normal or something is going wrong? Any help regarding this is
> appreciated.
>

It sounds to me like either the force field parameters are bad (i.e. the TFE is 
too hydrophobic and just aggregates) or there could be problems with the .mdp 
file.  Without more information, there's nothing definitive to suggest.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

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

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