Re: [gmx-users] Does GROMACS write charges?
On 2/4/18 4:48 AM, dgfd dgdfg wrote: Does GROMACS write atomic charges in "trr" or "edr" files during trajectory calculation? No, because that would be a waste of disk space. Charges are a fixed aspect of the topology, so there's no point writing the same information repeatedly. You'll find charges in .itp, .top, and .tpr files. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Does GROMACS write charges?
> >No, because that would be a waste of disk space. Charges are a fixed Then "gmx dipoles" will be incorrect in the analisys of the simulation with variable charges. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Does GROMACS write charges?
On 2/4/18 9:39 AM, dgfd dgdfg wrote: No, because that would be a waste of disk space. Charges are a fixed Then "gmx dipoles" will be incorrect in the analisys of the simulation with variable charges. GROMACS doesn't natively support fluctuating charge models. How can charges be variable? gmx dipoles reads the charges in the .tpr file when doing its analysis, and computes dipole properties based on the changes in coordinates of the selected molecules. You can only ever have one set of charges being analyzed. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
