sreelakshmi ramesh wrote:
dear all ,
I am new to ReMD simulations.And i done a trial run of 100 ps for 7
replicas . if i view the log file for output i get something like this
for every replica
for one of the replica the log file looks like this
Replica exchange at step 1000 time 2
Repl 0 <-> 1 dE = 6.793e+02 dpV = 0.000e+00 d = 6.793e+02
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00
Replica exchange at step 2000 time 4
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00
Replica exchange at step 3000 time 6
Repl 0 <-> 1 dE = 6.790e+02 dpV = 0.000e+00 d = 6.790e+02
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00
Replica exchange at step 4000 time 8
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00
Replica exchange at step 5000 time 10
Repl 0 <-> 1 dE = 6.874e+02 dpV = 0.000e+00 d = 6.874e+02
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00
Replica exchange at step 6000 time 12
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00
Replica exchange at step 7000 time 14
Repl 0 <-> 1 dE = 6.535e+02 dpV = 0.000e+00 d = 6.535e+02
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00
i had attached only few lines of log file.can any one tel me how to
understand the output.
I assume you've seen the following?
http://www.gromacs.org/Documentation/How-tos/REMD#Understanding_REMD-related_Output
Listed are the exchange probabilities between neighboring replicas. Your
results indicate that your systems are not exchanging (e.g. probability is zero).
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
