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

[David van der Spoel]

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
>
>>
>> Best,
>>
>> Qin
>>
>> 2010/12/21 Qin Qiao <qiaoqin47 at gmail.com <mailto:qiaoqin47 at gmail.com>>
>>
>>     Dear all,
>>
>>     I wonder what will happen in Nose-hoover coupling when tau_t = dt
>>     * nsttcouple, while nsttcouple = nstlist. (I used -maxwarn 1 to
>>     ignore the Gromacs warning)
>>
>>     I tried this setting, to 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 in advance.
>>
>>     Best,
>>
>>     Qin
>>
>>
>>
>


-- 
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