[gmx-users] Lagevin dynamics

[Anton Feenstra]

Tanos wrote:
>     Hi Folks,
>     I am trying to perform a LD in a protein with 608 residues but the 
> energy is raising too much and the system is halting. I am not sure of 
> using the correct procedure. Could someone send me right sequence of 
> comands to prepare a system to a LD dynamics ?????

Generally, it would be similar to MD setup procedures, like EM and
position restrained (PR) equilibration. Does your system minimize well in
EM? Can you run a short bit of PR MD, or PR LD?

The behaviour of LD depends on the LD temperature and the friction coefficient.
If you have the friction wrong, your timescale is off and you might have an
effective timestep that is too large.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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