On 10/02/2012 1:20 PM, bharat gupta wrote:
Hi,
I am planning to carry out a REMD study on a 12 residue beta-hairpin
peptide. I have read the gromacs tutorial for that . I have certain
doubts regarding the tutorial :-
1. Step. 4 says that "run short simulations to have an estimate of the
exchange rate (can get a good estimate within ~100 ps) and modify the
temperatures if it does not correspond to the wished exchange." Do I
have to run short MD of 100 ps for each replica . I am not able to
understand this step ??
You want to obtain an real estimate of the exchange acceptance frequency
before you commit large resources. So do a short REMD simulation to see
what that frequency is.
2. I have currently 24 processors available for REMD. The temperature
range that I have obtained from tgenerator server has 69 different
values (300K-600K). I want to know how to calculate the no. of
processors required for carrying out REMD for a certain temperature
range ??
Your system size, number of replicas, temperature range and exchange
acceptance frequency are interlinked. You can only choose three of them
independently.
Mark
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
