AMBER Archive (2008)

Subject: Re: AMBER: REMD temperature profile

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Jul 09 2008 - 10:28:59 CDT

this program was just a simple test to generate some
temperatures for example REMD and other simple cases.
it was NOT meant to be a comprehensive program to
optimize temperature selection for replicas. Please
look into the recent literature if you are interested in
how to optimize spacing and exchange ratios, as it is
more of a research topic than a code issue.

On Wed, Jul 9, 2008 at 9:47 AM, <guardiani_at_fi.infn.it> wrote:
> Dear Amber experts,
>
> I have read with great interest the new REMD Tutorial
> which I found extremely useful.
>
> I also took a look at the program tslop3.f that is
> distributed for the computation of the optimal temperature
> schedule in REMD. As far as I understood temperatures are
> chosen in geometric progression, but I don't understand how
> the temperature ratio T_{i+1}/T_i can be chosen to exactly
> correspond to the exchange rate set by the user.
>
> Could you tell me where I can find an explanation of the
> algorithm upon which the tslop3.f program is based ?
> Could you refer me to the appropriate literature ?
>
> I have another question about REMD temperatures. I am
> currently performing REMD simulations with implicit solvent
> on a peptide with 135 atoms. I use sqrt(135) =~ 12 replicas
> and the temperatures are chosen in geometric progression
> from Tmin = 310 K to Tmax = 652 K. More precisely my
> temperatures are: 310, 332, 355, 380, 406, 435, 465, 498,
> 533, 570, 610, 652. The exchange ratio that I attain in this
> way is about 50%:
>
> # exchange 4000
> 1 1.03 321.09 -550.21 310.00 332.00 0.46
> 2 0.97 488.78 -461.72 498.00 465.00 0.42
> 3 -1.00 507.12 -404.89 533.00 533.00 0.46
> 4 -1.00 390.59 -485.06 406.00 406.00 0.44
> 5 1.03 433.58 -446.13 465.00 498.00 0.44
> 6 0.97 397.22 -504.53 380.00 355.00 0.46
> 7 -1.00 599.28 -386.71 570.00 570.00 0.45
> 8 -1.00 441.25 -464.09 435.00 435.00 0.47
> 9 0.97 335.21 -547.63 332.00 310.00 0.45
> 10 0.97 644.75 -392.44 652.00 610.00 0.00
> 11 1.03 593.48 -399.11 610.00 652.00 0.47
> 12 1.03 322.63 -519.08 355.00 380.00 0.45
>
> At first I thought this exchange ratio was pretty good, but I then
> noticed that in the REMD literature the exchange ratio is usually
> around 30-35%. Is there any scientific reason for this particular
> value ? Is there any influence of the exchange ratio on the structural
> distribution produced by a REMD simulation ? Do you think I should
> decrease the number of temperatures and thus reduce the exchange ratio?
>
> Thank you very much for your help.
>
> Best regards,
>
> Carlo Guardiani
>
>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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