[gmx-users] TFE-water simulation

[Justin Lemkul]

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.

-Justin

> 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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>
>

-- 
==================================================

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

==================================================