[gmx-users] Exchange interval in REMD

[Gianluca Interlandi]

Hi David,

I am actually performing Simulated Tempering which is the same as RE 
except that it is in series. But I guess that the same thinking concerning 
exchange interval still applies.

Gianluca

On Thu, 26 Jan 2012, David van der Spoel wrote:

> 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
> -- 
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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.
-----------------------------------------------------