[gmx-users] a question

[Anton Feenstra]

yangkun at dlut.edu.cn wrote:

> 
> I am performing GROMACS simulations and I only want to do energy minimization. 
> So if I don't add box and water in protein in vacuum, I want to know whether I 
> need to neutralise charge (using command 'genion'). If I ignore charge and 
> then do MD, the result of MD is correct or wrong. 

For the Gromos (ffG43a) there is a version with reduced charges that may
work reasonably well in vacuum.

Generally, for EM it may not be so bad to exclude solvent and leave the
charges as they are.

What do you mean by 'ignore charge'? Leave them out (no charges) or leave
them as they are? In both cases, MD in vacuum is quite senseless, in my opinion.
Whether they are 'correct' or 'wrong', can depend on your objectives, but
at least it will be very hard to convince other people of them being 'correct'.

You may, however, try (one of?) the contunuum solvent model(s?) that have
recently been implemented. But I don't know if they are already in a released
version...


-- 
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 few.vu.nl - www.few.vu.nl/~feenstra/         |
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