[gmx-users] Two doubts about GMX!

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 6 04:33:24 CEST 2006

Samuel Silva Pita wrote:
> Hi, GMXers,
> i've some doubts about the use of GMX and implicit solvent models.
>  I have an huge system ( moreless 10 000 protein atoms) and trying to do MD using explicit solvents but my computer limitations doesn't work very well.
> 1) someone could help me giving some light in how can i simulate my system in vacuum? I tried and my protein colapses using PME and GMX FF number 4 in GMX3.2.1;

Find a force field parameterized for vacuum simulations, or just use a 
random number generator.

> 2) and so, if someone have tried to incorporate implicit solvents in simulations like GB, SASA, or others . This would be useful for me if give me some instructions.
> sincerely,

Not in GROMACS. Try AMBER, or doubtless others.


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