**From:** *steve.kaminski_at_mail.tu-berlin.de*

**Date:** Tue Nov 11 2008 - 13:43:51 CST

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Dear all.

My aim is to calculate a PMF of a certain molecule as a function of a

dihedral angle. Therefore, I use the adaptive biasing force method. As

long as I scan the complete dihedral space (xiMin=-180 / xiMax=180)

the calculations run without problems. But in my case I just want to

scan a reduced space, so if I change the values e.g. of xiMin to -100

or any other value, I get immediately the following error message from

NAMD:

Warning: Constraint failure in RATTLE algorithm for atom 19

Warning: Constraint failure in RATTLE algorithm for atom 22

If I turn off rigidBonds in the NAMD config-file I receive the

following error:

ERROR: Atom 20 velocity is 1050.76 -3548.3 -5428.46 (limit is 5000)

ERROR: Atoms moving too fast; simulation has become unstable.

ERROR: Exiting prematurely.

Thank you very much in advance for your suggestions.

Steve

**Next message:**Jerome Henin: "Re: failure in RATTLE algorithm using the adaptive biasing force method"**Previous message:**Peter Freddolino: "Re: solvate using Helmut Grubmuller's SOLVATE and then VMD, then how to minimize properly!"**Next in thread:**Jerome Henin: "Re: failure in RATTLE algorithm using the adaptive biasing force method"**Reply:**Jerome Henin: "Re: failure in RATTLE algorithm using the adaptive biasing force method"**Reply:**Giacomo Fiorin: "Re: failure in RATTLE algorithm using the adaptive biasing force method"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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