Re: [gmx-users] regarding tha langevin thermostat (integrator sd)

[Mark Abraham]

Hi,

On Thu, May 11, 2017 at 11:45 PM Felix Y Yang  wrote:

> Hello,
>
> I am trying to use a Langevin Thermostat to only heat up a specific group
> of atoms in my molecule specified by an index file, while not doing
> anything to the rest of the system (grouped as another group in the index
> file). Is there any way I can achieve this effect?
>

Either the sd integrator or the v-rescale stochastic thermostat support
temperature coupling groups, which in effect functions as a langevin
thermostat. You can disable coupling to any group by choosing the
appropriate time constant...
http://manual.gromacs.org/documentation/2016.3/user-guide/mdp-options.html#temperature-coupling

Can I set up temperature annealing and set ref_t for the rest of the
> system as constant 300K over the run period (which is the temperature
> achieved for the system prior via v-rescale thermostat), while heating up
> the specific group to a higher temperature over the same time? Would this
> have the same effect as not affecting the rest of my system?
>

Yes, that kind of approach will be useful if you want gradual heating. But
I'm not sure whether you're correctly describing "not affecting the rest of
the system" if you actually mean leaving a normal coupling group on it ;-)

Mark


> Any feedback would be greatly appreciated. Thanks.
>
> Felix Yang
> Graduate Master's Student
> Department of Chemistry & Biochemistry
> University of California, San Diego
>
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[gmx-users] regarding tha langevin thermostat (integrator sd)

[Felix Y Yang]

Hello,

I am trying to use a Langevin Thermostat to only heat up a specific group
of atoms in my molecule specified by an index file, while not doing
anything to the rest of the system (grouped as another group in the index
file). Is there any way I can achieve this effect?

Can I set up temperature annealing and set ref_t for the rest of the
system as constant 300K over the run period (which is the temperature
achieved for the system prior via v-rescale thermostat), while heating up
the specific group to a higher temperature over the same time? Would this
have the same effect as not affecting the rest of my system?

Any feedback would be greatly appreciated. Thanks.

Felix Yang
Graduate Master's Student
Department of Chemistry & Biochemistry
University of California, San Diego

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