Easiest solution can think of, make box that is of sufficient size the when filled contains 846 waters, fill with waters, use editconf to scale the box size to that which you require, run EM to get the waters back to the dimensions they should be.
Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of cuong nguyen Sent: Tuesday, 1 May 2012 12:21 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Box of water Thanks, I tried to add -maxsol 846 to the command and got the box with 846 water molecules. However, when I use VMD to visualize the box, these molecules concentrate on 1/3 the box space. I do need the molecules to spread out whole box. Cheers, Cuong 2012/5/1 Justin A. Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu>> On 4/30/12 10:02 PM, cuong nguyen wrote: Dear Gromacs Users, I used the command "genbox -cs spc216.gro -o box1.g96 -p topol.top -box 3 3 10" to create box of 3010 water molecules. However, now I need to create a same size box with only 846 water molecules. Please help me to do this. Use the -maxsol option when invoking genbox. -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080<tel:%28540%29%20231-9080> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org<mailto:gmx-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<mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981
-- gmx-users mailing list gmx-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
