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


>>> 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         = GBSA
> ;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.

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