[gmx-users] TFE-water homogeneous system -NPT

[João Henriques]

Hello again Archana,

Glad to see you managed to build the system and simulate it since we last
exchanged e-mails.

In my simulations TFE is never 100% miscible but doesn't also display such
hydrophobic behavior as you report here. However it's hard to answer your
questions without more information about the system, settings and
parameters (especially which force field and TFE parameters did you use, etc).


P.S.: By the way, what is the rationale behind the 32 ns NVT + 10 ns NPT
scheme?

Best regards,
João



On Mon, Feb 10, 2014 at 6:12 PM, Archana Sonawani-Jagtap <
ask.archana at gmail.com> wrote:

> Hello,
>
> I am trying to perform peptide simulation using TFE-water system. I did lot
> of literature search and according carried out NVT for 32ns followed by NPT
> 10ns simulation for TFE-water system.
>
> I found that the TFE get accumulated in the center of the box and water
> molecules surround them. The system is no more homogeneous.
>
> Is this normal or something is going wrong? Any help regarding this is
> appreciated.
>
> --
> Archana Sonawani-Jagtap
> Senior Research Fellow,
> Biomedical Informatics Centre,
> NIRRH (ICMR), Parel
> Mumbai, India.
> 9960791339
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