[gmx-users] problem with MD
feenstra at chem.vu.nl
Mon Nov 3 10:37:00 CET 2003
> Dear Anton
>>Did you first do (in this order): EM and MD with position restraints?
> Yes, that was the order, but I am not sure about the position restraints
> bit. I followed exactly the tutorial.
>>Where there any problems/errors/warnings/strange things during that?
> AS the expected files were generated, I didn't really pay close attention to
> this. However I attach the log file and will appreciate if you could kindly
> let me there is something wrong with the EM.
Hmm, it seems as thouhh the EM was not very effective. Did you use constraints?
Did you use 'flex_spc'? (sorry, I'm too lazy to chech what the tutorial says...)
Did you EM your protein and/or ligand first without solvent?
My default equilibration setup is:
1) EM protein + ligand in vacuum (include possible crystal waters,
optionally with position restraints on prot+lig(+water) )
2) add water (genbox, do not remove crystal waters)
3) EM prot+lig+water, with posres on prot+lig
4) MD prot+lig+water, with posres on prot+lig
5) 'production MD' (normally without posres).
| | |
| _ _ ___,| 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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