[gmx-users] problem with MD

[Anton Feenstra]

Dastmalchi wrote:

> 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).


-- 
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/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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