[gmx-users] TFE-water simulation

[Archana Sonawani-Jagtap]

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?

Regards,
Archana




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