[gmx-users] gmx dens charge
Dear users, I need to know for charge density calculation specially for water, should we use -center /-symm option or not and if not why? Since I tried the option (-center/-symm) for charge density calculation of water and gmx dens module was not reading frame. I used the gromacs version 5.1.4 for the analysis. I will be highly thankful if any one can suggest me regarding this. -- 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.
[gmx-users] Extracting trajectory
Dear users, I want to extract the trajectory of water molecules near the protein surface within 5 angstorm region. I was able to do that in using gmx select and gmx trjcat, but it is for only one time frame and than the water molecules diffuses away for the next time frame. I want to extract the trajectory of only those water molecules that are near protein surface within 5 angstorm region for each individual time frame so that i can get the complete trajectory of water molecules that are near the protein surface excluding the water molecules that diffuses away in each next frame.. I will be thankful for help. Thanks and regards, Anupama -- 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.
[gmx-users] Selection of water molecules
Dear users, I have to calculate the Pair Distribution Function of water present in my system near protein surface at 5 angstorm region for which I already did the indexing using gmx select (dynamic indexing). But when I tried to calculate the Pair Distribution Function using gmx rdf, I am getting option as to select the reference "the atoms present in one frame", not the atom/molecule for the system within a defined region and hence, I am unable to calculate the RDF of water molecule within a defined region for the whole trajectory which I want to do. Is there any possibility in gromacs to do so. I'll highly greatful if any one can help. Thanks in advance With regards, Anupama -- 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.
[gmx-users] Selection of Water Molecules for Individual Frames
Dear users, Currently, I have explored gmx select to identify the water molecules present within 5 angstrom distance window from protein alpha carbon atom. However, I am unable to select water molecules for individual frames within the defined region. Here, I am requesting your suggestions to move forward. Thank in advance, With regards, Anupama -- 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.
[gmx-users] Trans-Gauche fraction for surfactant chain
Dear users, I need help regarding the calculation of gauche fraction for surfactant chain and the way to do that. -- 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.
[gmx-users] Tilt angle distribution
Dear users, I am working on ctab/water surfactant system and got stuck with the calculation of tilt angle distribution of hydrocarbon chain. Is there any tool to calculate the tilt angle distribution in gromacs. Please specify the way to do that... -- 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.
[gmx-users] Tilt- angle Distribution
dear users, Is there any module in gromacs to calculate the tilt angle distribution? -- 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.
[gmx-users] Help for using Lincs along with constraint
Dear user's I need help for using lincs along with constraint. I am doing water (tip4p/2005) and carbon nanotube simulation and since I am using tip4p/2005, I had used exclusion for rigid body dynamics and for that I kept lincs off. But after nvt simulation bonds in carbon nanotube is getting broken. What I can do for that. Anupama -- 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.
[gmx-users] Help regarding applying constraint on individual molecule in a system
Dear user's, I need help regarding constraint. I am doing simulation of water ( tip4p/2005) and carbon nanotube and want to put constraint only on carbon nanotube as after nvt simulation I had observed that carbon nanotube is getting deformed. -- 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.
