[gmx-users] how many groups shall I use to control the temperature?

[Dr. Vitaly Chaban]

There is no rule regarding how many thermostats per system one needs.

Often people choose separate thermostats for parts of system, which
exhibit different mobility. I do not see any connection to functional
forms of the interactions and, therefore, to force fields.


Dr. Vitaly V. Chaban


On Thu, Jun 12, 2014 at 2:33 PM, 陈功 <gchen511 at gmail.com> wrote:
> Thanks a lot, Justin. I do CG simulation using Martini force field. So maybe I can find some useful infomation on the forum of martini.
> Thanks :)
>
>
>
>
>
> From: Justin Lemkul
> Date: 2014-06-12 17:44
> To: gmx-users
> Subject: Re: [gmx-users] how many groups shall I use to control the temperature?
>
>
> On 6/12/14, 2:37 AM, 陈功 wrote:
>> Dear justin,
>>       I have doubts that whether I should use two groups to control the temperature or just one since there are just 604 hundred Protein beads and 60000+ solvent beads. It is said that two groups are more accurate but when when i split them into two groups "Protein nonProtein", I found that fluctulation of temperature in group "Protein" are obvious, Im afraid that would have an effect on accuracy on my simulation results. So how many groups shall I use to control the temperature?
>
> What protocol is used in published studies similar to what you're doing?  Small
> groups will have larger fluctuations in temperature, that's a given.  I don't do
> CG simulations, so I don't know how such groups are commonly treated.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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