[gmx-users] Exchange interval in REMD

[David van der Spoel]

On 2012-01-26 06:37, Gianluca Interlandi wrote:
> Hi Mark,
>
> Thanks for the answer. Just to be clear: you think that a too short
> interval might introduce artefacts? I agree with this. So, do you think
> that an interval between 1 and 10 ps could be a good value?
It also depends whether or not you use constant pressure, in which case 
it makes sense to increase the time to long enough to let the volume relax.
I still do not understand why people do NVT REMD, because it makes all 
but one replica have a pressure that is not the ambient pressure.

>
> Gianluca
>
>
> On Thu, 26 Jan 2012, Mark Abraham wrote:
>
>> On 26/01/2012 11:38 AM, Gianluca Interlandi wrote:
>>> Hi,
>>>
>>> I have been going through the How-to for REMD in gromacs:
>>>
>>> http://www.gromacs.org/Documentation/How-tos/REMD
>>>
>>> Is there a recommended value for the exchange interval and does it
>>> depend on system size? For example, is an interval of 100 ps
>>> appropriate for a sytem with 60,000 atoms? Is a too long interval
>>> simply a waste of time or can it actually introduce artefacts?
>>
>> There's literature by Sindhikara (sp?) and Roitberg that says you
>> should have a short an interval as possible, and other literature that
>> says you shouldn't go shorter than around the autocorrelation time of
>> PE, ~1ps. I don't buy the former, and think some of their data support
>> the latter, and have some of my own not-ready-for-publication data
>> that I think suggests artefacts from the former. Work from Hansmann et
>> al suggests that achieving steady-state replica flow is rather tricky
>> even for seemingly trivial peptides, so increasing the number of
>> exchange attempts might help a little. I'm not aware of any good case
>> for a long interval between attempts.
>>
>> Mark
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>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca at u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------


-- 
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