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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