[gmx-users] Lagevin dynamics
feenstra at chem.vu.nl
Mon Aug 18 10:02:03 CEST 2003
> 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.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
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