[gmx-users] Re: gmx-users digest, Vol 1 #1248 - 7 msgs

[Anton Feenstra]

Jorge Hernanez Fernandez wrote:

> Dear GMXers!:
> 
>       Im using GMX for a year, and actually interested in the free energy
> evaluation in a Enzyme-inhibitor system. My protein is a metallo (Zn) and
> inhibitor is a small peptide. 
>       The central problem is that pdb2gmx read my system as a one whole
> protein, and am not able to create a working index to obtain my peptide as a
> separate Ener-group. Make_ndx is working find (I think….):
[...]

For temperature coupling, all atoms must be in *one* group only. I'm not
sure from your descxription what your system looks like, exactly, but I'd
suggest you couple enzyme-zn-inhibitor to one, and solvent (water and
sodium) to another bath. For that, you will only need to combine groups
1 and 12 (protein + Zn), and 13 and 14 (Sol and Na). and chenge the t-coupl
line in your mdp file accordingly.


-- 
Groetjes,

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