[gmx-users] Umberella sampling

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Wed Apr 6 16:56:34 CEST 2011

Dear Dr.Justin

I had asked this question before but unfortunately I didn't answered good!

Instead of Pulling and separating some structures in definite distances,
I located my drug in definite distances along z axis (as my initial
structures for doing umbrella sampling).
Am I right?

The main problem underlying this question is :

Do we need to know the velocity of drug in every structure we choose for
doing umbrella sampling?(do they need to include the velocities too?)
if no,which criteria assures with this K our molecule can cover the length
of it's windows?

Because I have chosen windows with different lingthes,And I want now to
choose K so that it can sweep the lengthes.

Thanks in advance for your reply
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