[gmx-users] trivial question?

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue Feb 24 23:54:01 CET 2004


>I am interested in simulating proteins under different solvent densities. 
>What I would like to do is generate a box of solvent and adjust the system 
>density to that desired, place the protein into the box and remove all 
>solvent molecules

What comes to mind here is changing the reference pressure in the pressure 
coupling to change the solvent's density, if you don't want to change the 
actual solvent molecules.  Could be a better way or doing it.

>whose atoms are within ~1.4Å of any protein atom. This is easy in 
>insight/discover but I've yet to figure it out for GROMACS (no I haven't 
>cracked my head against it yet, will if necessary, but was wondering what 
>sort of resource I had here).

trjorder might be of help there.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.

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