On 4/04/2011 6:11 PM, battis...@libero.it wrote:
Dear all,
I got some question about the implicit solvent.
1) In gromacs, is it possible simulate a protein in a layer of
explicit water, and put this system (protein + SOL) into a big box and
make the MD simulation with implicit solvent?
How I have to set the md.mdp parameter (; IMPLICIT SOLVENT ALGORITHM)
in this case?
Do you know some tutorial about this method?
It can't work as simply as that, because the waters on the edge will fly
off into the implicit solvent region. People have tried various things -
check out the literature.
2) I'd like to put into my box a definied number of explicit number of
molecule of water eg. 100, so
I used
genbox -cp conf.gro -cs -maxsol 100 -p topol.top -o out.gro
but the water molecule is not in the random position in the box, but
is in clustered conformation.
Is it possible tell to genbox to put in a random way, in all space the
defined number of molecule?
What do you actually want - a uniform gas of a given density?
3) For that system (100 explicit solvent molecule + implicit solvent)
I generated the topol.tpr using the following set up into the mdp file:
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = GBSA
;GENERALIZED BORN ELECTROSTATICS;
;Algorithm for calculating Born radii
gb_algorithm = Still
grompp do not give problem at all, but mdrun give problem:
segmantation fault or
Norm of force = nan
I think that the problem is the use of explicit water molecule and the
implcit water together.
Maybe. We haven't got enough information to know.
Mark
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