[gmx-users] TFE-water simulation

[Justin Lemkul]

On 7/17/13 1:03 AM, Archana Sonawani-Jagtap wrote:
> HI,
>
> I want to simulate helical peptide in TFE-water (1:1 vol) solvent.
>
> 1. From previous searches, I got to know that tfe.itp is present in
> gmx.ff folder. Can I use this itp file by including it in my top file
> generated during pdb2gmx.
>

Since that file requires the use of the deprecated (i.e. don't use it) gmx.ff 
force field, I wouldn't.

> 2. I also got TFE-water (1:1 vol) pdb and gro pre-equilibrated system
> from ATB site. I dont know if I can use either this pdb or gro file
> during genbox step for -cs flag
>

Sure, if it suits your purpose.  See also 
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents.

-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
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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