Targeted Molecular Dynamics

From: Miguel Ángel Mompeán García (
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
be studied.

Let say that I want to go from stateA.pdb to stateB.pdb Should I just
indicate in the conf file


structure $WORKING_DIRECTORY/stateA.psf
coordinates $WORKING_DIRECTORY/stateA.pdb
firsttimestep 0

And then:


TMD on
TMDFirststep 0

Or should I continue the simulation doing a restart from the NPT
equilibration at the last point and include binCoordinates, binVelocities
and binExtendedSystem?

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.

Best regards,

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