[gmx-users] Simulated Annealing
feenstra at chem.vu.nl
Wed Jan 21 09:45:06 CET 2004
>>4) How would I encode the gradual release of the [TM_C-alpha] group at
>>the last stage of the protocol?
> Not implemented, you'd want the force constant of the restraint to go to
> zero slowly, but there is no way currently. You can however just use a
> lower force constant (by rerunning genpr).
Also, you could consider releasing different groups of atoms in several
steps, i.e. define a 'core' region, then first releas the non-core side
chains only, then the non-core backbone as well, then the core sidechains
and finally all. I've done something similar in the final stages of
optimizing a homology model.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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