[gmx-users] Re: reliability of NOTES

Vitaly V. Chaban vvchaban at gmail.com
Wed Jul 22 00:53:24 CEST 2009

> Hello,
> I am trying to prepare the input files for an MD run. After running grompp,
> I received the following note:
> NOTE 1 [file npt.mdp, line unknown]:
>  The Berendsen thermostat does not generate the correct kinetic energy
>  distribution. You might want to consider using the V-rescale thermostat.
> How reliable this note is?

It's true.

> And how can I implement V-rescale thermostat in y
> input file (I found nothing in the manual).

Substitute "berendsen" with "V-rescale" in the mdp file.

> Also, when I changed the thermostat to nose-hoover, it said that it can not
> be used with Berendsen barostat. Why?
> C'est la vie...

Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua,vvchaban at gmail.com
skype: vvchaban, mob.: +38-097-8259698
!!! Looking for a postdoctoral position !!!
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