[gmx-users] TFE-water simulation
jalemkul at vt.edu
Wed Jul 17 13:02:43 CEST 2013
On 7/17/13 6:26 AM, Archana Sonawani-Jagtap wrote:
> Hi Justin,
> Thanks...it was really helpful. I saw the
> http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents site.
> Now I don't know how to calculate the number of cosolvents (in my case
> TFE for TFE-water in 1:1 vol). Is there any formula to carry out this
> calculation. I can follow other mentioned steps.
Sure, based on density and the volume of your unit cell, calculating the number
of molecules that occupy that space is quite simple.
> Thanks in advance.
> On Wed, Jul 17, 2013 at 2:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 7/17/13 1:03 AM, Archana Sonawani-Jagtap wrote:
>>> 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
>> 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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Justin A. Lemkul, Ph.D.
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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