[gmx-users] Neutralizing the total charge of the system in vacuum
Hi all, I am performing a simulation in vacuum. The peptide has nonzero charge, so I attempted to neutralize the total charge via genion;however as it is known, it asks for a continuous group for replacing, but I have no solvent molecules for the replacement. How can I neutralize the total charge while performing simulations in vacuum? Thanks in advance Oz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Neutralizing the total charge of the system in vacuum
Ran Friedman, Biochemisches Inst. wrote: Hello, You can add a few ions manually or use genbox. However, it's probably better to use a vacuum force field and have your peptide uncharged for vacuum simulations. Any ions you add will have a very strong interaction with the peptide. I assume you have a good reason to simulate in vacuo - the mailing list archives give many reasons why it's not advised. It is not advised as a model for peptides in solution, but if you want to model something in vacuo then it is fine. In that case you may want to look for evidence of the charge of the peptide in vacuo from mass spec experiments. Ran. On Sat, 24 Nov 2007 19:47:43 +0200 OZGE ENGIN [EMAIL PROTECTED] wrote: Hi all, I am performing a simulation in vacuum. The peptide has nonzero charge, so I attempted to neutralize the total charge via genion;however as it is known, it asks for a continuous group for replacing, but I have no solvent molecules for the replacement. How can I neutralize the total charge while performing simulations in vacuum? Thanks in advance Oz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6354493 Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Neutralizing the total charge of the system in vacuum
Hello, You can add a few ions manually or use genbox. However, it's probably better to use a vacuum force field and have your peptide uncharged for vacuum simulations. Any ions you add will have a very strong interaction with the peptide. I assume you have a good reason to simulate in vacuo - the mailing list archives give many reasons why it's not advised. Ran. On Sat, 24 Nov 2007 19:47:43 +0200 OZGE ENGIN [EMAIL PROTECTED] wrote: Hi all, I am performing a simulation in vacuum. The peptide has nonzero charge, so I attempted to neutralize the total charge via genion;however as it is known, it asks for a continuous group for replacing, but I have no solvent molecules for the replacement. How can I neutralize the total charge while performing simulations in vacuum? Thanks in advance Oz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6354493 Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
