[gmx-users] Force constant - Umbrella Sampling

lloyd riggs lloyd.riggs at gmx.ch
Mon Mar 19 11:43:49 CET 2012

>From liturature it ranges around 1K for unravling proteins, and protein-protein dissociations range around 2-3k (kj/mol that is).  For small molecules I have no clue.  Id like to know if somone finds out ranges for any of these though....

Stephan Watkins 

-------- Original-Nachricht --------
> Datum: Mon, 19 Mar 2012 08:48:15 +0000
> Von: Steven Neumann <s.neumann08 at gmail.com>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>, jalemkul at vt.edu
> Betreff: [gmx-users] Force constant - Umbrella Sampling

> Dear Gmx Users, Dear Justin,
> As I saw in your tutorial you used the force of 1000 kJ/mol nm2 for the
> harmonic potential. You pulled the whole chain which is quite heavy. Would
> you decrease the force constant for a small molecule (app. 500 Da) during
> the umbrella sampling (e.g. 500 kJ/mol nm2) ? Is it a guess or I should
> check calculations for e.g. 3 force constants and see the influence on the
> final binding free energy?
> Thank you,
> Steven

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