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

2011-04-04 Thread battis...@libero.it
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 li

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

2011-04-04 Thread Mark Abraham
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-pha

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

2011-04-04 Thread battis...@libero.it
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 + impl

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

2011-04-04 Thread Mark Abraham
On 4/04/2011 6:11 PM, battis...@libero.it wrote: 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?

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

2011-04-04 Thread battis...@libero.it
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 SOLVE