[gmx-users] TFE-water simulation

[Archana Sonawani-Jagtap]

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.

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:
>>
>> 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
>
> --
> ==================================================
>
> 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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-- 
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339