R: [gmx-users] implicit water and a layer of explicit water molecule
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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: R: [gmx-users] implicit water and a layer of explicit water molecule
On 4/04/2011 7:12 PM, battis...@libero.it wrote: Dear Mark, about point 2, yes I need to have a uniform distribution of a defined number of water molecule (eg. 100 water molecule ) into my box. Is it possible with genbox? Yes, but not by starting with a uniform distribution of a condensed-phase density. You need one of the right density to start with. A better approach is to decide how large a box of what density you want. Work out how much volume that gives to each molecule. Take a single molecule and put it in a box of that size with editconf. Move the molecule a bit off-center. Then use genconf -rot to replicate that box into a large one. Then equilibrate that thoroughly to get rid of the residual ordering. If, later on, you want a different size, genbox with the box you've equilibrated here will be a good approach. 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. You have more problems than that. The force fields probably don't have implicit solvation parameters for water atom types. You'll need to source them somehow. And like I told you last time, your solvent molecules are not going to stay happily around your solvent like you hope. I'm going to stop repeating myself :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
R: [gmx-users] implicit water and a layer of explicit water molecule
Thank you very much for your suggestions! Anna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
