R: [gmx-users] implicit water and a layer of explicit water molecule
battistia at libero.it
battistia at libero.it
Mon Apr 4 11:12:54 CEST 2011
Dear Mark,
about point 2, yes I need to have
a uniform distribution of a defined numberof water molecule (eg. 100 water molecule ) into my box.
Is it possible with genbox?
After, I'll have to make the md simulation for my
system in implicit solvent
(I'll have "protein + 100 molecule SOL + implicit solvent")
So my next problem is to set the parameter into mdp file, for this mixed type of kind of water.
Thanks for your reply
Anna
>>> 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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