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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Received on Sun Jul 13 2008 - 06:07:09 PDT
