[gmx-users] Genion command not working
Dear Gmxers, I want to simulate 5M nabr aqueous solution.To add the ions I use genion command and add 22 na and br ions respectively to the system of pure 108 water molecules.But on running the command genion I get error message Processing topology Back Off! I just backed up topol.top to ./#topol.top.9# Replacing solvent molecule 12 (atom 36) with NA Replacing solvent molecule 52 (atom 156) with CL Replacing solvent molecule 35 (atom 105) with NA Replacing solvent molecule 17 (atom 51) with CL Replacing solvent molecule 41 (atom 123) with NA Replacing solvent molecule 70 (atom 210) with CL Replacing solvent molecule 44 (atom 132) with NA Replacing solvent molecule 66 (atom 198) with CL Replacing solvent molecule 34 (atom 102) with NA Replacing solvent molecule 29 (atom 87) with CL --- Program genion, VERSION 4.0.7 Source code file: ../../../../src/tools/gmx_genion.c, line: 85 Fatal error: No more replaceable solvent! --- How should I add ions in the system.I have tried doing it but could not get it please if someone may point my error. -- DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live -- 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] Genion command not working
Hi Deepak, You have to set the minimal distance between ions lower. Check the help of genion. Cheers, Tsjerk On Aug 28, 2013 8:04 AM, Deepak Ojha alwaysinthem...@gmail.com wrote: Dear Gmxers, I want to simulate 5M nabr aqueous solution.To add the ions I use genion command and add 22 na and br ions respectively to the system of pure 108 water molecules.But on running the command genion I get error message Processing topology Back Off! I just backed up topol.top to ./#topol.top.9# Replacing solvent molecule 12 (atom 36) with NA Replacing solvent molecule 52 (atom 156) with CL Replacing solvent molecule 35 (atom 105) with NA Replacing solvent molecule 17 (atom 51) with CL Replacing solvent molecule 41 (atom 123) with NA Replacing solvent molecule 70 (atom 210) with CL Replacing solvent molecule 44 (atom 132) with NA Replacing solvent molecule 66 (atom 198) with CL Replacing solvent molecule 34 (atom 102) with NA Replacing solvent molecule 29 (atom 87) with CL --- Program genion, VERSION 4.0.7 Source code file: ../../../../src/tools/gmx_genion.c, line: 85 Fatal error: No more replaceable solvent! --- How should I add ions in the system.I have tried doing it but could not get it please if someone may point my error. -- DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live -- 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
[gmx-users] Long range Lennard Jones
Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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] Long range Lennard Jones
DispCorr might be what you are looking for, correction for LJ beyond the cut-off. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Gianluca Interlandi Sent: Wednesday, 28 August 2013 4:36 PM To: gmx-users@gromacs.org Subject: [gmx-users] Long range Lennard Jones Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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] Long range Lennard Jones
Lennard-Jones PME is planned for 5.0 Mark On Aug 28, 2013 8:36 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org --**--- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Gentle heating with implicit solvent
It can be. Lack of explicit degrees of freedom of solvent can make achieving equipartition tricky. With CHARMM27 and virtual sites in implicit solvent, I have sometimes found it necessary to use a sub-femtosecond time step at the start of equilibration, even where there were no atomic clashes. Maybe the system was just unlucky with generating velocities, though :-) Mark On Aug 28, 2013 7:16 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: How important is it to do gentle heating (using simulated annealing) with GBSA? Often with explicit water it is enough to perform some equilibration with positional restraints. Would it be enough to do the same with implicit solvent? Thanks, Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org --**--- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Long range Lennard Jones
Hi, What is LJ PME? I googled it and got this publication? http://pubs.acs.org/doi/abs/10.1021/ct400146w So, LJ will not be cut off at some r, but you will have a real+fourier part similar to electrostatics. Is that LJ PME? What are the advantages? On Wed, Aug 28, 2013 at 12:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Lennard-Jones PME is planned for 5.0 Mark On Aug 28, 2013 8:36 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/ http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org --**--- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Long range Lennard Jones
On 2013-08-28 09:31, rajat desikan wrote: Hi, What is LJ PME? I googled it and got this publication? http://pubs.acs.org/doi/abs/10.1021/ct400146w So, LJ will not be cut off at some r, but you will have a real+fourier part similar to electrostatics. Is that LJ PME? What are the advantages? http://pubs.acs.org/doi/abs/10.1021/ct400140n On Wed, Aug 28, 2013 at 12:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Lennard-Jones PME is planned for 5.0 Mark On Aug 28, 2013 8:36 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/ http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org --**--- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Long range Lennard Jones
Secondarily, one could use the same cut-off for LJ and electrostatics, and treat their respective lattice components however you like. This simplifies implementations for computing short-ranged interactions, while facilitating iso-accuracy load balancing across heterogeneous compute units. Mark On Wed, Aug 28, 2013 at 10:08 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2013-08-28 09:31, rajat desikan wrote: Hi, What is LJ PME? I googled it and got this publication? http://pubs.acs.org/doi/abs/10.1021/ct400146w So, LJ will not be cut off at some r, but you will have a real+fourier part similar to electrostatics. Is that LJ PME? What are the advantages? http://pubs.acs.org/doi/abs/10.1021/ct400140n On Wed, Aug 28, 2013 at 12:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Lennard-Jones PME is planned for 5.0 Mark On Aug 28, 2013 8:36 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/ http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org --**--- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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
[gmx-users] total charge
Hi Dear Gromacs users, I have a question about the total charge of a system. I executed pdb2gmx command which the result is quited below: Keeping all generated dihedrals Making cmap torsions...There are 7808 dihedrals, 591 impropers, 5298 angles 7596 pairs, 2922 bonds and 0 virtual sites Total mass 20072.826 a.m.u. Total charge -3.000 e Writing topology Including chain 1 in system: 2869 atoms 180 residues Including chain 2 in system: 2869 atoms 180 residues Including chain 3 in system: 2869 atoms 180 residues Now there are 8607 atoms and 540 residues Total mass in system 60218.478 a.m.u. Total charge in system -9.000 e If I want to neutralize the system with Na atoms, how many atoms should I add? 3 or 9? I think I need 9 atoms, but I am not sure about that. Best Regards. S. Faraji -- 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] total charge
If you're not sure what charge your chains should have had, then you should go back and think about the titratable residues and what you're trying to model. Don't assume some code's defaults are what you want! The earlier mention of total charge -3 refers to one of the chains, but pdb2gmx is not completely clear with its output. Mark On Wed, Aug 28, 2013 at 1:25 PM, Group Gro group...@yahoo.com wrote: Hi Dear Gromacs users, I have a question about the total charge of a system. I executed pdb2gmx command which the result is quited below: Keeping all generated dihedrals Making cmap torsions...There are 7808 dihedrals, 591 impropers, 5298 angles 7596 pairs, 2922 bonds and 0 virtual sites Total mass 20072.826 a.m.u. Total charge -3.000 e Writing topology Including chain 1 in system: 2869 atoms 180 residues Including chain 2 in system: 2869 atoms 180 residues Including chain 3 in system: 2869 atoms 180 residues Now there are 8607 atoms and 540 residues Total mass in system 60218.478 a.m.u. Total charge in system -9.000 e If I want to neutralize the system with Na atoms, how many atoms should I add? 3 or 9? I think I need 9 atoms, but I am not sure about that. Best Regards. S. Faraji -- 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
[gmx-users] DMPC Bilayer
Hello, At NPT stage the two leaflets in DMPC bilayer is separated a while and comes closer. Is this common in this stage or any thing goes wrong in equillibration. Thanks --Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/DMPC-Bilayer-tp5010783.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] DMPC Bilayer
On 8/28/13 11:12 AM, Rama wrote: Hello, At NPT stage the two leaflets in DMPC bilayer is separated a while and comes closer. Is this common in this stage or any thing goes wrong in equillibration. Depending on what the previous preparation steps were, this can certainly occur. -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] work in 4.5.5 but failed in 4.6.1
Hello: I am constraining one part of the protein and trying to generate md.tpr with command: grompp -f md.mdp -c npt4.gro -n -o md.tpr it works fine in 4.6.3, but it failed in 4.5.5 with following warning messages: WARNING 1 [file md.mdp, line 65]: Unknown left-hand 'cutoff-scheme' in parameter file WARNING 2 [file helix.itp, line 1]: Too few parameters on line (source file toppush.c, line 1501) WARNING 3 [file md.mdp]: The sum of the two largest charge group radii (13.715767) is larger than rlist (1.00) There were 3 notes There were 3 warnings --- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 1584 Does anybody have any idea? thx Albert -- 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] problem of submitting job in HPC
Hello: I am trying to use following command to run 4.6.3 in a HPC cluster: mpiexec -n 32 /opt/gromacs/4.6.3/bin/mdrun_mpi -dlb yes -v -s md.tpr -x md.xtc -o md.trr -g md.log -e md.edr md.info the 4.5.5 works fine in this machine with command: mpiexec -n 32 mdrun -nosum -dlb yes -v -s md.tpr -x md.xtc -o md.trr -g md.log -e md.edr md.info the difference is that the option -nosum is not available in 4.6.3 but 4.6.3 always failed. It generate a lot of similar files and log informations. It looks like use mpiexec evoke serial mdrun. Does anybody have any idea? thank you very much. best Albert -- 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 of submitting job in HPC
On 8/28/13 12:39 PM, Albert wrote: Hello: I am trying to use following command to run 4.6.3 in a HPC cluster: mpiexec -n 32 /opt/gromacs/4.6.3/bin/mdrun_mpi -dlb yes -v -s md.tpr -x md.xtc -o md.trr -g md.log -e md.edr md.info the 4.5.5 works fine in this machine with command: mpiexec -n 32 mdrun -nosum -dlb yes -v -s md.tpr -x md.xtc -o md.trr -g md.log -e md.edr md.info the difference is that the option -nosum is not available in 4.6.3 but 4.6.3 always failed. It generate a lot of similar files and log informations. It looks like use mpiexec evoke serial mdrun. Does anybody have any idea? Have you verified that the 4.6.3 mdrun was correctly installed such that it can make use of MPI? -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] work in 4.5.5 but failed in 4.6.1
On 8/28/13 11:48 AM, Albert wrote: Hello: I am constraining one part of the protein and trying to generate md.tpr with command: grompp -f md.mdp -c npt4.gro -n -o md.tpr it works fine in 4.6.3, but it failed in 4.5.5 with following warning messages: WARNING 1 [file md.mdp, line 65]: Unknown left-hand 'cutoff-scheme' in parameter file Makes sense; this option did not exist before version 4.6. WARNING 2 [file helix.itp, line 1]: Too few parameters on line (source file toppush.c, line 1501) Looks concerning - what's line 1? WARNING 3 [file md.mdp]: The sum of the two largest charge group radii (13.715767) is larger than rlist (1.00) How big is your box? This may very well be a simple periodicity issue. http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb -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] work in 4.5.5 but failed in 4.6.1
On 08/28/2013 07:07 PM, Justin Lemkul wrote: WARNING 2 [file helix.itp, line 1]: Too few parameters on line (source file toppush.c, line 1501) Looks concerning - what's line 1? here is the initial lines: ; position restraints for part of C-alpha of Protein [ position_restraints ] ; i funct fcxfcyfcz 51300300300 241300300300 WARNING 3 [file md.mdp]: The sum of the two largest charge group radii (13.715767) is larger than rlist (1.00) How big is your box? This may very well be a simple periodicity issue. http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb -Justin I've see this informations from gromacs website. my box is: 6.96418 6.96418 9.77176 in the last line of my input .gro file. I don't understand, why this warning not appear in 4.6.3, but failed in 4.5.5 thank you very much Albert -- 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] work in 4.5.5 but failed in 4.6.1
On 8/28/13 1:21 PM, Albert wrote: On 08/28/2013 07:07 PM, Justin Lemkul wrote: WARNING 2 [file helix.itp, line 1]: Too few parameters on line (source file toppush.c, line 1501) Looks concerning - what's line 1? here is the initial lines: ; position restraints for part of C-alpha of Protein [ position_restraints ] ; i funct fcxfcyfcz 51300300300 241300300300 Looks normal, so without context of how it is #included, there's not much to diagnose here. WARNING 3 [file md.mdp]: The sum of the two largest charge group radii (13.715767) is larger than rlist (1.00) How big is your box? This may very well be a simple periodicity issue. http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb -Justin I've see this informations from gromacs website. my box is: 6.96418 6.96418 9.77176 in the last line of my input .gro file. I don't understand, why this warning not appear in 4.6.3, but failed in 4.5.5 The misinterpretation of periodicity in warning 3 was a bug that was fixed at some point, so the fact that it doesn't show up in 4.6.3 makes sense. -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] work in 4.5.5 but failed in 4.6.1
On 08/28/2013 07:25 PM, Justin Lemkul wrote: Looks normal, so without context of how it is #included, there's not much to diagnose here. here is my #include in topol.top file: ; Include Position restraint file #ifdef POSRES #include restrain.itp #endif I first generate restrain for all the protein CA by genrest command, after that I delete the atoms which I don't want to restrain from output restrain.itp. Probably that's the problem? Maybe I should set the unwanted restrain atoms into 0 force constant instead of delete them from restrain.itp file? thx a lot Albert -- 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] work in 4.5.5 but failed in 4.6.1
On 8/28/13 1:36 PM, Albert wrote: On 08/28/2013 07:25 PM, Justin Lemkul wrote: Looks normal, so without context of how it is #included, there's not much to diagnose here. here is my #include in topol.top file: ; Include Position restraint file #ifdef POSRES #include restrain.itp #endif I first generate restrain for all the protein CA by genrest command, after that I delete the atoms which I don't want to restrain from output restrain.itp. Probably that's the problem? Maybe I should set the unwanted restrain atoms into 0 force constant instead of delete them from restrain.itp file? That's not the problem. It's complaining about whatever is on line 1 (not clear from the previous message if the comment line is #1 or a blank line), so assuming that the #ifdef is in the right place (probably is, or the error would be different), it's possible that there's some weird hidden character that is causing the 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 == -- 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] work in 4.5.5 but failed in 4.6.1
On 08/28/2013 07:38 PM, Justin Lemkul wrote: That's not the problem. It's complaining about whatever is on line 1 (not clear from the previous message if the comment line is #1 or a blank line), so assuming that the #ifdef is in the right place (probably is, or the error would be different), it's possible that there's some weird hidden character that is causing the error. -Justin IC. the problem solved when I run command dos2unix. thank you very much. Albert -- 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 of submitting job in HPC
On Wed, Aug 28, 2013 at 7:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/28/13 12:39 PM, Albert wrote: Hello: I am trying to use following command to run 4.6.3 in a HPC cluster: mpiexec -n 32 /opt/gromacs/4.6.3/bin/mdrun_mpi -dlb yes -v -s md.tpr -x md.xtc -o md.trr -g md.log -e md.edr md.info the 4.5.5 works fine in this machine with command: mpiexec -n 32 mdrun -nosum -dlb yes -v -s md.tpr -x md.xtc -o md.trr -g md.log -e md.edr md.info the difference is that the option -nosum is not available in 4.6.3 but 4.6.3 always failed. It generate a lot of similar files and log informations. It looks like use mpiexec evoke serial mdrun. Does anybody have any idea? Have you verified that the 4.6.3 mdrun was correctly installed such that it can make use of MPI? i.e. by inspecting the top of the .log file, or the output of mdrun -version? Mark -- 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] Long range Lennard Jones
Thanks for your replies, Mark. What do you think about the current DispCorr option in gromacs? Is it worth it trying it? Also, I wonder whether using DispCorr for LJ + PME for Cb justifies reducing the cutoff for non-bonded to 1 nm with the CHARMM force field, where 1.2 nm is usually recommended. Gianluca On Wed, 28 Aug 2013, Mark Abraham wrote: Secondarily, one could use the same cut-off for LJ and electrostatics, and treat their respective lattice components however you like. This simplifies implementations for computing short-ranged interactions, while facilitating iso-accuracy load balancing across heterogeneous compute units. Mark On Wed, Aug 28, 2013 at 10:08 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2013-08-28 09:31, rajat desikan wrote: Hi, What is LJ PME? I googled it and got this publication? http://pubs.acs.org/doi/abs/10.1021/ct400146w So, LJ will not be cut off at some r, but you will have a real+fourier part similar to electrostatics. Is that LJ PME? What are the advantages? http://pubs.acs.org/doi/abs/10.1021/ct400140n On Wed, Aug 28, 2013 at 12:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Lennard-Jones PME is planned for 5.0 Mark On Aug 28, 2013 8:36 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/ http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org --**--- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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] Long range Lennard Jones
On 8/28/13 7:28 PM, Gianluca Interlandi wrote: Thanks for your replies, Mark. What do you think about the current DispCorr option in gromacs? Is it worth it trying it? Also, I wonder whether using DispCorr for LJ + PME for Cb justifies reducing the cutoff for non-bonded to 1 nm with the CHARMM force field, where 1.2 nm is usually recommended. This is risky. Current CHARMM development relies on a 1.2-nm cutoff for LJ, so that's how we balance all of the forces during parameterization. To me, ad hoc changes like these are not worth the tiny (potential) increase in performance. As I recently told someone else on this topic, if you're intent on fiddling with the typical workings of a force field, especially if you're making changes to something so fundamental, be prepared to undertake a demonstration that you can recapitulate all of the expected outcomes of the force field or improve upon them. My gut feeling, in this case and others, is that you won't be able to. You're messing with something that is fairly critical to obtaining sensible results. As for dispersion correction, it is generally helpful, but it assumes a homogeneous environment. If you simulate with a membrane, for instance, this assumption breaks down, though some literature suggests that use of dispersion correction in these cases is still better than nothing. -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] CGennFF in gromacs
Hello everyone, I want to use CGennFF force field in GROMACS. I downloaded the Cgenffbon.itp and Cgenffnb.itp files and I put them in charmm36.ff directory. - I replaced the lines in the forcefield.itp to #include Cgenffbon.itp and #include Cgenffnb.itp - I modified the rtp file and I inserted the corresponding atom, bond, dihedral terms as in charmm rtf file for paracetamol in the rtp file in gromacs - I inserted the new atomtypes at the end of the atomtype.atp file ... I took the atom types from prm file of charmm - I introduced the new residue name to the residuetype file - with pdb2gmx ... I could generate the topol.top file without any error However, when I am using grompp, it give me the following error: Fatal error: Atomtype CG331 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I already have this atomtype inside the atomtype file ... and when I was pdb2gmx ... it did not complain ! Can you help me to figure out what is going on? Thanks G. -- 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] CGennFF in gromacs
On 8/28/13 8:23 PM, Golshan Hejazi wrote: Hello everyone, I want to use CGennFF force field in GROMACS. I downloaded the Cgenffbon.itp and Cgenffnb.itp files and I put them in charmm36.ff directory. - I replaced the lines in the forcefield.itp to #include Cgenffbon.itp and #include Cgenffnb.itp - I modified the rtp file and I inserted the corresponding atom, bond, dihedral terms as in charmm rtf file for paracetamol in the rtp file in gromacs - I inserted the new atomtypes at the end of the atomtype.atp file ... I took the atom types from prm file of charmm - I introduced the new residue name to the residuetype file - with pdb2gmx ... I could generate the topol.top file without any error However, when I am using grompp, it give me the following error: Fatal error: Atomtype CG331 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I already have this atomtype inside the atomtype file ... and when I was pdb2gmx ... it did not complain ! Can you help me to figure out what is going on? That is the only time atomtypes.atp is used. The error from grompp comes because it can't find CG331 in CGenffnb.itp, so check that file carefully. -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] Long range Lennard Jones
Current CHARMM development relies on a 1.2-nm cutoff for LJ, so that's how we balance all of the forces during parameterization. Ok, I agree. What about the use of PME for Coulomb? The CHARMM PARAM22 force field was parametrized using SHIFT on electrostatic forces making it zero after 12 A (please note that SHIFT and FSHIFT in CHARMM greatly differ from the gromacs-style Shift). Also, the CHARMM switch function is different from gromacs Switch (at least from what I can tell reading pages 71-72 of the gromacs manual 4.6.3). Thanks, Gianluca ad hoc changes like these are not worth the tiny (potential) increase in performance. As I recently told someone else on this topic, if you're intent on fiddling with the typical workings of a force field, especially if you're making changes to something so fundamental, be prepared to undertake a demonstration that you can recapitulate all of the expected outcomes of the force field or improve upon them. My gut feeling, in this case and others, is that you won't be able to. You're messing with something that is fairly critical to obtaining sensible results. As for dispersion correction, it is generally helpful, but it assumes a homogeneous environment. If you simulate with a membrane, for instance, this assumption breaks down, though some literature suggests that use of dispersion correction in these cases is still better than nothing. -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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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] Long range Lennard Jones
On 8/28/13 9:09 PM, Gianluca Interlandi wrote: Current CHARMM development relies on a 1.2-nm cutoff for LJ, so that's how we balance all of the forces during parameterization. Ok, I agree. What about the use of PME for Coulomb? The CHARMM PARAM22 force field was parametrized using SHIFT on electrostatic forces making it zero after 12 A (please note that SHIFT and FSHIFT in CHARMM greatly differ from the gromacs-style Shift). Also, the CHARMM switch function is different from gromacs Switch (at least from what I can tell reading pages 71-72 of the gromacs manual 4.6.3). PME is generally vastly better than switched or shifted electrostatics. This has been demonstrated in the literature consistently over many years. -Justin Thanks, Gianluca ad hoc changes like these are not worth the tiny (potential) increase in performance. As I recently told someone else on this topic, if you're intent on fiddling with the typical workings of a force field, especially if you're making changes to something so fundamental, be prepared to undertake a demonstration that you can recapitulate all of the expected outcomes of the force field or improve upon them. My gut feeling, in this case and others, is that you won't be able to. You're messing with something that is fairly critical to obtaining sensible results. As for dispersion correction, it is generally helpful, but it assumes a homogeneous environment. If you simulate with a membrane, for instance, this assumption breaks down, though some literature suggests that use of dispersion correction in these cases is still better than nothing. -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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- == 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] Long range Lennard Jones
Justin, I respect your opinion on this. However, in the paper indicated below by BR Brooks they used a cutoff of 10 A on LJ when testing IPS in CHARMM: Title: Pressure-based long-range correction for Lennard-Jones interactions in molecular dynamics simulations: Application to alkanes and interfaces Author(s): Lague, P; Pastor, RW; Brooks, BR Source: JOURNAL OF PHYSICAL CHEMISTRY B Volume: 108 Issue: 1 Pages: 363-368 Published: JAN 8 2004 There is also a paper by Piana and Shaw where different cutoffs for non-bonded are tested with CHARMM22 on Anton: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039918 They found some subtle differences, in particular for cutoffs shorter than 9 A. However, Anton uses abrupt truncation (no switching) and I believe that the differences they found at cutoffs 9 A would be much smaller if they had used a finer mesh (as they show at the 8 A cutoff). I always use fourierspacing=1.0 I agree though that it strongly depends on the system and I have always run control simulations but never found significant differences in the case of just proteins. Finally, I have not tested it in gromacs, but in NAMD there is a performance gain of 25% when using the shorter cutoff. This is a factor to consider. When I asked for Teragrid supercomputing allocations back in 2006 and 2007 and I suggested 10/12/14 cutoff, the reviewers always complained and cut my requested time of 20% with the justification that I must use a shorter cutoff. Gianluca On Wed, 28 Aug 2013, Justin Lemkul wrote: On 8/28/13 7:28 PM, Gianluca Interlandi wrote: Thanks for your replies, Mark. What do you think about the current DispCorr option in gromacs? Is it worth it trying it? Also, I wonder whether using DispCorr for LJ + PME for Cb justifies reducing the cutoff for non-bonded to 1 nm with the CHARMM force field, where 1.2 nm is usually recommended. This is risky. Current CHARMM development relies on a 1.2-nm cutoff for LJ, so that's how we balance all of the forces during parameterization. To me, ad hoc changes like these are not worth the tiny (potential) increase in performance. As I recently told someone else on this topic, if you're intent on fiddling with the typical workings of a force field, especially if you're making changes to something so fundamental, be prepared to undertake a demonstration that you can recapitulate all of the expected outcomes of the force field or improve upon them. My gut feeling, in this case and others, is that you won't be able to. You're messing with something that is fairly critical to obtaining sensible results. As for dispersion correction, it is generally helpful, but it assumes a homogeneous environment. If you simulate with a membrane, for instance, this assumption breaks down, though some literature suggests that use of dispersion correction in these cases is still better than nothing. -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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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
