sarbani chattopadhyay wrote:
Hi everyone, I will like to do Replica exchange simulation on a peptide. We have a single
machine with 4 cpus and the gromacs3.3.2 is installed.
Thus I will be able to select only 4 temperature values. I came across the "T-REMD" caculator for temperature distributions . However over a high range of temperature there are more than 4, values given in the optimal tempearture distribution as obtained as an output from the "T- REMD" calculator. How to choose the best possible 4 temperature values.

Using explicit solvent with a low number of replicas will severely limit the temperature space you can span while achieving exchanges in accessible simulation times. See http://dx.doi.org/10.1021/ct800016r and references therein.

Mark
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