[gmx-users] problem vwith ethanol-water solution
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 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? Kind regards, Ehsan -- 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: [gmx-users] problem vwith ethanol-water solution
Dear Ehsan, Did you try to pack your box with packmol? I have a similar system and packmol pack my system quite well and in a random way. Regards, Riccardo -Original Message- From: Ehsan Sadeghi Sent: Thursday, October 31, 2013 7:25 PM To: Discussion list for GROMACS users Subject: [gmx-users] problem vwith ethanol-water solution 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 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? Kind regards, Ehsan -- 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 -- 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: [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 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: [gmx-users] problem vwith ethanol-water solution
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 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 -- 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: [gmx-users] problem vwith ethanol-water solution
On 10/31/13 7:03 PM, Ehsan Sadeghi wrote: 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? Follow the advice at the link I posted before. Trying to add ethanol while simultaneously solvating is a bad idea. If genbox cannot add 1000 ethanol molecules without trying to do anything else, then yes, the box is simply too small. At this point, we can't say because it could simply be that simultaneous solvation might have been competing for available box volume. What should I do with .top file? I have the .top file for ionomer and .top file for one eth molecule. It is simple to covert between .top and .itp and #include them however you see fit. Probably the conceptually easiest methhod is to consider ethanol just like any other solvent (i.e. water) and #include it within the .top for the ionomer, which is just like any other solute. -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 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
