Thanks Justin,
Here is the steps that I followed: pdb2gmx -f eth.pdb -o eth.gro -p eth.top pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5 genbox -cp box.gro -cs spc216.gro -ci eth.gro -nmol 1000 -o solvated.gro I got the box with ionomer in ethanol and water solution. However, I only have 400 of eth and 423 water molecule. The box wasn't large enough? What should I do with .top file? I have the .top file for ionomer and .top file for one eth molecule. Kind regards, Ehsan ----- Original Message ----- From: "Justin Lemkul" <jalem...@vt.edu> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Sent: Thursday, October 31, 2013 1:18:07 PM Subject: Re: [gmx-users] problem vwith ethanol-water solution On 10/31/13 2:25 PM, Ehsan Sadeghi wrote: > Hi gmx users, > > I want to solvate nafion molecules in a 3:1 ethanol water solution. I used > genbox with -ci option to add ethanol to water when generating the box, but > it did not work. Then, first I solvated the ethanol in water, and then added What "did not work?" In the absence of exact commands and description of the undesirable output, there's little to suggest from such statements. > the nafion to the system, but these 3 molecules each sit a part from each > other in the box in the pdb file. Any suggestion? > http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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 -- 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
