[gmx-users] watrebox with osmolites

[niyaz.sabir]

Hello, Justin,

you are always so helpful,

Regards,

NS


----- Original Message ----- 
From: "Justin Lemkul" <jalemkul at vt.edu>
To: <gmx-users at gromacs.org>; "niyaz.sabir" <niyaz.sabir at gmail.com>
Sent: Wednesday, October 01, 2014 12:33 AM
Subject: Re: [gmx-users] watrebox with osmolites


>
>
> On 9/30/14 3:31 PM, niyaz.sabir wrote:
>> Dear Gromacs users,
>> Is there any tutorial to simulate a protein in water solution containing 
>> neutral zwitterionic osmolite such as trimethylglycine? Evaluating 
>> effects of the compound on protein stability/secondary structure 
>> flexibility is to be considered.
>
> http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
>
> Add your osmolyte with genbox (gmx insert-molecules in 5.0) -ci -nmol, 
> update the topology, and solvate as usual with water.
>
> -Justin
>
> -- 
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================