[gmx-users] Re: gmx-users digest, Vol 1 #937 - 8 msgs

[Anton Feenstra]

Tanos wrote:
>    Dear Anton,
>    I am afraid I didn't understood properly the LD. My system runs well 
> the EM but how could I perform a PR LD if LD is done only in vacuum ????

Put on position restraints, then run LD.

>    I am trying to change tmeperature and friction coefficient values but 
> it didn't workout yet. My substrates are jump out the box.

Check messages by Berk Hess on this list, he suggested some good starting
values for the friction coefficient. Temperature normally should be around
300K, and timesteps at 2 fs (0.002ps).

Is your substrate jumping out of the box not simply a PBC issue?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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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