Re: [gmx-users] pdb2gmx gives topol.top without values for bonds angles and dihedrals.
Thank you very much Justin for your quick answer. Greetings -- View this message in context: http://gromacs.5086.x6.nabble.com/pdb2gmx-gives-topol-top-without-values-for-bonds-angles-and-dihedrals-tp5013521p5013524.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] pdb2gmx gives topol.top without values for bonds angles and dihedrals.
On 12/24/13, 6:04 PM, David Saez wrote: Dear all, I want to create a topology for S-adenosylmethionine using AMBER99SB force field. I had to create some new atomtypes and, accordingly, I have modified all the necessary files (atomtypes.atp, ffbonded, ffnonbonded, etc). When I make pdb2gmx -f sam.pdb I obtain a topol.top describing correctly the charges, and the atoms forming the bonds, angles, etc. generated from the data I introduced in the rtp entry. My problem is that file doesn't show the values of the force constants, bond lengths, etc. It looks like pdb2gmx were succesfully reading rtp entry but were not looking into ffbonded.itp: I wonder if the problem is because this a standalone residue, (not forming part of a chain). Below you can see what th eTerminal shows when I type pdb2gmx -f sam.pdb If some one can tell me what I am doing wrong I am going to be very grateful. There is nothing wrong. For the AMBER, CHARMM, and OPLS force fields, there are no values explicitly printed to the .top file. They are looked up in ffbonded.itp when grompp is executed; if something is missing (i.e. not found in the force field), it triggers a fatal error. -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 == -- 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] pdb2gmx gives topol.top without values for bonds angles and dihedrals.
Dear all, I want to create a topology for S-adenosylmethionine using AMBER99SB force field. I had to create some new atomtypes and, accordingly, I have modified all the necessary files (atomtypes.atp, ffbonded, ffnonbonded, etc). When I make pdb2gmx -f sam.pdb I obtain a topol.top describing correctly the charges, and the atoms forming the bonds, angles, etc. generated from the data I introduced in the rtp entry. My problem is that file doesn't show the values of the force constants, bond lengths, etc. It looks like pdb2gmx were succesfully reading rtp entry but were not looking into ffbonded.itp: I wonder if the problem is because this a standalone residue, (not forming part of a chain). Below you can see what th eTerminal shows when I type pdb2gmx -f sam.pdb If some one can tell me what I am doing wrong I am going to be very grateful. I wish you a merry christmas. David Saez S. -- View this message in context: http://gromacs.5086.x6.nabble.com/pdb2gmx-gives-topol-top-without-values-for-bonds-angles-and-dihedrals-tp5013521.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] bug in aminoacids.c.tdb (gromos 54a7) ?
Hi Facundo, This is intended. The actual dihedral is a combination of two simpler types. Cheers, Tsjerk On Tue, Dec 24, 2013 at 8:07 PM, fciocco wrote: > Hi, > > I'm not sure if this is a bug, but I have noted that in aminoacids.c.tdb > (gromos 54a7 FF) two different dihedrals are defined for the same set of > atoms: > > for [ COO- ] C-termini: > > [ dihedrals ] > N CA C O2 gd_45 > N CA C O2 gd_42 > > and for [ COOH ]: > > [ dihedrals ] > N CA C O gd_45 > N CA C O gd_42 > CA C O HO gd_12 > > regards, > Facundo > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/bug-in-aminoacids-c-tdb-gromos-54a7-tp5013519.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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] bug in aminoacids.c.tdb (gromos 54a7) ?
Hi, I'm not sure if this is a bug, but I have noted that in aminoacids.c.tdb (gromos 54a7 FF) two different dihedrals are defined for the same set of atoms: for [ COO- ] C-termini: [ dihedrals ] N CA C O2 gd_45 N CA C O2 gd_42 and for [ COOH ]: [ dihedrals ] N CA C O gd_45 N CA C O gd_42 CA C O HO gd_12 regards, Facundo -- View this message in context: http://gromacs.5086.x6.nabble.com/bug-in-aminoacids-c-tdb-gromos-54a7-tp5013519.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Calculating the displacement of an atom QUERY
On 12/24/13, 2:38 AM, rbbioinfo wrote: Hi, I want to plot the total displacement of an atom/ion along Z axis with respect to time. Anybody kindly help me regarding how to calculate the movement of any atom using gromacs. An early response will be highly appreciated. Sounds like a job for g_traj. -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 == -- 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] GridMAT-MD & gnuplot
On 12/24/13, 9:59 AM, shahab shariati wrote: Dear gromacs users I used GridMAT-MD to obtain area per lipid and bilayer thickness. I used vector for output_format in param_example file. Based on the user guide for GridMAT-MD, when I used gnuplot: perl convert_to_gnuplot.pl output.frame1.20x20.average_thickness.dat 20 20 I encountered with invalid command. What is problem about that? If you are using our latest version, the conversion script is no longer necessary as the output format is controlled when running GridMAT-MD. If you have further questions about GridMAT-MD, you can contact me directly rather than posting to this list. -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 == -- 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] GridMAT-MD & gnuplot
Dear gromacs users I used GridMAT-MD to obtain area per lipid and bilayer thickness. I used vector for output_format in param_example file. Based on the user guide for GridMAT-MD, when I used gnuplot: perl convert_to_gnuplot.pl output.frame1.20x20.average_thickness.dat 20 20 I encountered with invalid command. What is problem about that? Best wishes -- 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] Potential energy calculations
Justin Lemkul wrote > Gromacs reports energies in kJ per mole of equivalent systems. If you're > looking for a value like configurational energy, use g_energy -nmol as > needed to divide by the number of molecules in the system. > > -Justin > > > On Mon, Dec 23, 2013 at 8:49 PM, virk < > virkblitz@ > > wrote: > >> I am trying to simulate mixture of DMSO and water at different mole >> fractionbut this value is for 100% DMSO. >> >> -- >> View this message in context: >> http://gromacs.5086.x6.nabble.com/Potential-energy-calculations-tp5013495p5013499.html >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >> -- >> 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-request@ > . >> > > > > -- > > == > > 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 > jalemkul@.umaryland > | (410) 706-7441 > > > == > -- > 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-request@ > . Justin Lemkul wrote > Gromacs reports energies in kJ per mole of equivalent systems. If you're > looking for a value like configurational energy, use g_energy -nmol as > needed to divide by the number of molecules in the system. > > -Justin > > > On Mon, Dec 23, 2013 at 8:49 PM, virk < > virkblitz@ > > wrote: > >> I am trying to simulate mixture of DMSO and water at different mole >> fractionbut this value is for 100% DMSO. >> >> -- >> View this message in context: >> http://gromacs.5086.x6.nabble.com/Potential-energy-calculations-tp5013495p5013499.html >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >> -- >> 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-request@ > . >> > > > > -- > > == > > 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 > jalemkul@.umaryland > | (410) 706-7441 > > > == > -- > 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-request@ > . Justin Lemkul wrote > Gromacs reports energies in kJ per mole of equivalent systems. If you're > looking for a value like configurational energy, use g_energy -nmol as > needed to divide by the number of molecules in the system. > > -Justin > > > On Mon, Dec 23, 2013 at 8:49 PM, virk < > virkblitz@ > > wrote: > >> I am trying to simulate mixture of DMSO and water at different mole >> fractionbut this value is for 100% DMSO. >> >> -- >> View this message in context: >> http://gromacs.5086.x6.nabble.com/Potential-energy-calculations-tp5013495p5013499.html >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >> -- >> 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-request@ > . >> > > > > -- > > == > > 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 > jalemkul@.umaryland > | (410) 706-7441 > > > =
Re: [gmx-users] Gromos DPPC bilayer: different results for 4.0.7 and 4.6.5
Just wondering, has anybody done a comparison with the Verlet scheme? It could be useful to know whether it produces results consistent with the 4.6 group scheme implementation or exhibits different behavior. Cheers, -- Szilárd On Sun, Dec 22, 2013 at 1:08 AM, Lutz Maibaum wrote: > On Dec 20, 2013, at 3:17 PM, Patrick Fuchs > wrote: >> to follow up on this, the simulation with "Reaction-Field-nec" under 4.5.3 >> has completed. The final area is 0.60 nm^2 (see >> http://redmine.gromacs.org/issues/1400 for the plot). Lutz, you mentionned >> you tried a simulation with nstlist=1, could you give feedback on red mine? > > > I uploaded another comparison to redmine: > > http://redmine.gromacs.org/attachments/download/1114/comparison.png > > It indeed looks like setting nstlist=1 allows one to recover the results form > Gromacs 4.0.7 with nstlist=5 (but it is computationally not really feasible). > > Best, > > Lutz > > -- > 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. -- 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.
