[gmx-users] changing the viscosity of water in a simulation

[Christoph Junghans]

> Date: Tue, 2 Sep 2014 20:02:01 +0200
> From: "Dr. Vitaly Chaban" <vvchaban at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] changing the viscosity of water in a
>         simulation
> Message-ID:
>         <CAPXdD+ZBQiUfCZrKQgFenNG7_7iQv0SfoO9GeS=M_aFV28jM+w at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Tue, Sep 2, 2014 at 10:59 AM, soumadwip ghosh
> <soumadwipghosh at gmail.com> wrote:
>> Hello,
>>
>>       I am a newbie to MD simulation. We are working in the direction of
>> finding the molecular origin of internal friction of protein folding. For
>> this we have to run folding simulations at different solvent viscosity and
>> plot protein reconfiguration time against solvent viscosity. Currently, we
>> have been using TIP3P water molecules for simulations run on GROMACS 4.5.6.
>> I wwill be highly grateful if someone tells me how to change the viscosity
>> of water.
>
>
> To change water viscosity, you must be assigned as God.
That is not 100% correct, there are thermostats, which allow to change
the transport properties (incl. the viscosity):
<http://dx.doi.org/10.1016/j.cpc.2008.01.018>
Unfortunately the DPD thermostat isn't implemented in Gromacs, so you
will have to use another MD package like OpenMM,  ESPResSo++ or
ESPResSo.

Cheers,

Christoph
>
> Pick up another FFM.
>
>
> Dr. Vitaly V. Chaban
>
> ??????? ?????????? ?????
>
>
>>
>> Best,
>> Soumadwip.
>> --
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-- 
Christoph Junghans
Web: http://www.compphys.de