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 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 = nanI think that the problem is the use of explicit water molecule and the implcit water together. Can you help me? All the best Anna
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