Re: [AMBER] Thermostat question

From: Daniel Roe <>
Date: Wed, 8 May 2019 08:55:08 -0400


You can use the ‘temperature’ command in cpptraj along with masks selecting
protein/solvent to determine the temperature of each region. See the manual
for full details.


On Wed, May 8, 2019 at 2:52 AM Karolina Mitusińska (Markowska) <> wrote:

> Dear Amber Users,
> I'm curious how is pmemd or sander dealing with the thermostat of the whole
> system.
> I've recently read about the hot solvent, cold solute problem and would
> like to ask, if it is possible in either sander or pmemd to check the
> temperature separately for the protein and the solvent?
> And is it possible to set the thermostat separately for the protein and the
> solvent?
> How can I be sure that I'm not having a cold protein surrounded by hot
> water?
> I'm looking forward for some more knowledge!
> Best regards,
> Karolina Mitusińska
> PhD student
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Wed May 08 2019 - 06:00:04 PDT
Custom Search