[EMAIL PROTECTED] wrote:
I use constraints on the c-alpha atoms, so the helix should be stable.
I of course optimized the starting geometry, I tried to use the output
geometry of a 600 K run as input file, and I tried the simulation with a
larger box, but none of this worked. What else can I try ? What could be
going wrong ?
Constraints can make your simulation unstable, especially if there are
many and/or they are very tight. The problem is that tight (or many)
constraints are prone to high-frequency oscillations, which may be too
fast for the integration timestep that you are using. (But, that does
not explain why your 600K simulations do not crash...)
Have you tried slowly (e.g. over several 100 ps) decreasing the
temperature, e.g. using the simulated annealing option?
--
Groetjes,
Anton
* NOTE: New Affiliation, Phone & Fax numbers (below) *
_____________ _______________________________________________________
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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
| | [EMAIL PROTECTED] - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
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