[gmx-users] how to set the MD parameters?

[Anton Feenstra]

Nguyen Hoang Phuong wrote:

>>Hi everybody,
>>I've just started using Gromacs (so far I did the tutorial and been playing
>>around a little); the purpose of my project is to study a protein from a
>>mechanical point of view. So I guess I'll have to perform elongations
>>(constraining distances) and take care of the energy variations. However,
>>firstly an optimization of the molecule is needed (by the way, I'm working
>>with the PDB 1QUU). Got a (likely silly) question about MD parameters. The
>>gmx manual says:
>>
>>"A sample .mdp file is available. This should be appropriate to start a
>>normal simulation. Edit it to suit your specific needs and desires."
>>
>>How can you do that? I mean, practically, how to create or modify a .mdp
>>file?
> 
> 
> practically, you go to :
> 
> http://www.gromacs.org/documentation/reference_3.2/online/mdp_opt.html
> 
> then you will see  "sample .mdp file is available", click at that
> sentence, you will see how the sample.mdp file look like.
> 
> If you want to modify it, you should look at the "mdp opion-table of
> contents" (same page) to see the meaning of parameters.

Very practically, you'll need a text editor to do the actual modifications. ;-)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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