[gmx-users] Related to REMD

ISHRAT JAHAN jishrat17 at gmail.com
Tue Jan 2 11:44:21 CET 2018

Dear all,
I am trying to do REMD simulation. I had equillbrated the system for 5ns
and extracted the seed conformation at 3ns using the command-
gmx trjconv -f traj.trr -o 3ns.gro -s topol.tpr -dump 3000 -pbc mol
I had used temperature generator for REMD simulation from
folding.bmc.uu.se/remd with transition probability of 0.25 in temperature
range of 290-400K.it gives too many replica and i want only 10 replica.
will anyone tell me what criteria should be taken for taking 10 replicas
and also tell how to extract the one seed conformation from multiple seed
conformation which i had generated using above command.
Thanks in advance

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