From: Miguel Ángel Mompeán García (mig.mompean_at_gmail.com)
Date: Tue Jun 12 2012 - 06:02:17 CDT
Dear NAMD users,
I am very new with this program and I want to know how to properly set my
conf file for a TMD work.
I have minimized, and NVT and NPT-equilibrated both the two structures to
Let say that I want to go from stateA.pdb to stateB.pdb Should I just
indicate in the conf file
## EXTRA PARAMETERS
Or should I continue the simulation doing a restart from the NPT
equilibration at the last point and include binCoordinates, binVelocities
If so, I guess I should set up the TMDFile not just as the initial
"stateB.pdb", but as the pdb resulting from the NPT equilibration. How can
I extract those coordinates from the simulation?
Thanks for your help.
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