[gmx-users] TFE-water simulation

Archana Sonawani-Jagtap ask.archana at gmail.com
Thu Oct 24 19:13:43 CEST 2013

Dear Justin,

I have not constructed the system but I have downloaded it from ATB
website. To maintain the number of TFE and water molecules(1:1 v/v) in the
system (I don't want to add extra water molecules) I tried many options in
genbox but still it adds 678 water molecules. Can you provide me some hint?

Is their need to remove periodicity of this pre-equilibrated system as in
case of lipids?


On Wed, Oct 23, 2013 at 5:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 10/23/13 7:20 AM, Archana Sonawani-Jagtap wrote:
>> Hi all,
>> I have never performed TFE-water simulation therfore I want to know after
>> inserting the peptide in the pre-equilibrated TFE-water mixture, do we
>> need
>> to adjust the number of TFE or water molecules ?
> That depends on how you constructed the system.  genbox will not
> automatically update the number of TFE, but it can update the number of
> water molecules if you chose the proper command-line option.  Regardless,
> the [molecules] section of the .top must accurately reflect the contents of
> the configuration in terms of order and number of molecules.  Simple grep
> statements will let you count how many of each are present.
> -Justin
> --
> ==============================**====================
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> ==============================**====================
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Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
Mumbai, India.

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