[gmx-users] Nose-hoover T-coupling in REMD

[David van der Spoel]

On 2010-12-24 13.15, ms wrote:
> On 24/12/10 10:36, David van der Spoel wrote:
>> On 2010-12-24 11.04, Mark Abraham wrote:
>>> On 22/12/2010 5:44 PM, Qin Qiao wrote:
>>>> Dear all,
>>>>
>>>> I posted yesterday but didn't get answer..I guess it's due to my wrong
>>>> approach to ask. I would like to explain more and hope I would get
>>>> your help.
>>>>
>>>> I'm doing an REMD, and want to have a strong temperature coupling to
>>>> make sure every replica is at its target temperature. I guess I could
>>>> do it by setting tau_t small in the Nose-hoover T coupling, but there
>>>> will come the warning in Gromacs.
>>>>
>>>> I maxwarned the warning to proceed, and find the temperature is ok,
>>>> but I am not sure whether it will introduce some artifacts in the
>>>> simulation and what kind of artifacts. Could you tell me? Thanks a lot.
>>>
>>> The temperature coupling algorithms are discussed in the literature,
>>> when they were derived (citations in GROMACS manual) and subsequently. I
>>> suggest you do your own homework there. The use of REMD is more or less
>>> irrelevant to the trade-offs when deciding what temperature coupling
>>> scheme to use.
>>>
>> That is correct, but do not use Berendsen! There is a recent paper from
>> the Garcia group (IIRC) about the effect of Berendsen coupling on REMD
>> sampling. Not good.
>>> Mark
>
> I'm not an expert, but isn't Berendsen usually not used because it
> doesn't give a correct ensemble? I may be partial because I personally
> know Giovanni Bussi, but it seems from what I've heard that v-rescale is
> the best choice usually.
>
V-rescale is a good choice. Berendsen not only gives you the wrong 
ensemble but it also biases the energy distribution to lower energies.


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se