[gmx-users] MD on a protein region

[Anton Feenstra]

deepa rajamani wrote:

> Hi,
> 
> I am trying to run MD on a region of protein. I tried the following things
[...]
> What would be the best way to do a quick run on a part of the protein

IMHO, there is no 'best' way to do that - all options will introduce 
artefacts. At any rate, freezegroups can give problems (as you saw) so 
you could try position restraints in stead. Be aware that any form of 
fixed boundary will introduce artificially high ordering in the system, 
possibly 'freezing' most large scale motions of your protein as well.

And, what do you mean by 'quick'? Gromacs isn't fast enough for you? ;-)


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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