[gmx-users] implicit water and a layer of explicit water molecule

battistia at libero.it battistia at libero.it
Mon Apr 4 10:11:10 CEST 2011

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?

2) I'd like to put into my box a definied number of explicit number of molecule of water eg. 100, soI usedgenbox -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?
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     =            nanI think that the problem is the use of explicit water molecule and the implcit water together.
Can you help me?
All the best
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