Re: [gmx-users] Gromacs Error
Hi Manoj, The error is clear. Check the settings referred to in your .mdp file and modify them accordingly. Cheers, Tsjerk On May 19, 2015 07:35, manoj damale manojaurangabad...@yahoo.co.in wrote: Dear All, i'm geting below error while subjecting my system (Protein-ligand) for equlibriation in nvt.mdp file mgmibt@mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -fnvt.mdp Inputgrompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c em.gro InputStructure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt! Index file -p topol.top InputTopology file -pp processed.top Output, Opt. Topology file -onvt.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -[no]v bool no Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18# ERROR 1 [file nvt.mdp]: With coulombtype = PME-Switch, rcoulomb must be = rlist Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'UNT' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Setting gen_seed to 3507 Velocities were taken from a Maxwell distribution at 300 K --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1356 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Yeah, a Wuzz, Or a Jerk (F. Black) With Best Regards. Mr.Manoj Damale, M.S. Pharma (Pharmacoinformatics) NIPER, Kolkata, West Bengal State, India. -- 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! *
Re: [gmx-users] RDF
Thanks Justin! I cant find so much details in the manual; there are only general facts. does g_density give partial density? On Mon, May 18, 2015 at 11:25 AM, mah maz mahma...@gmail.com wrote: Hi Justin The fact is I want to calculate water density in the system. If I select group1: oxygen and group2: oxygen, g_rdf command gives me very large numbers. Is it the number of atoms that should be changed to g/cm3? Besides, what does it calculate, each O is a reference atom during calculation? Thanks a lot! On Sun, May 17, 2015 at 2:17 PM, mah maz mahma...@gmail.com wrote: Dear all, I want to calculate the radial distribution function of water molecules in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which is not logical I suppose. Is it meaningful if I separate oxygen and hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is reference atom necessary to get RDF? Thanks! -- 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] Gromacs Error
ERROR 1 [file nvt.mdp]: With coulombtype = PME-Switch, rcoulomb must be = rlist On Tue, May 19, 2015 at 10:25 AM, manoj damale manojaurangabad...@yahoo.co.in wrote: what exactly i should modify With Best Regards. Mr.Manoj Damale, M.S. Pharma (Pharmacoinformatics) NIPER, Kolkata, West Bengal State, India. On Tuesday, 19 May 2015 11:32 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Manoj, The error is clear. Check the settings referred to in your .mdp file and modify them accordingly. Cheers, Tsjerk On May 19, 2015 07:35, manoj damale manojaurangabad...@yahoo.co.in wrote: Dear All, i'm geting below error while subjecting my system (Protein-ligand) for equlibriation in nvt.mdp file mgmibt@mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -fnvt.mdp Inputgrompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c em.gro InputStructure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt! Index file -p topol.top InputTopology file -pp processed.top Output, Opt. Topology file -onvt.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -[no]v bool no Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18# ERROR 1 [file nvt.mdp]: With coulombtype = PME-Switch, rcoulomb must be = rlist Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'UNT' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Setting gen_seed to 3507 Velocities were taken from a Maxwell distribution at 300 K --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1356 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Yeah, a Wuzz, Or a Jerk (F. Black) With Best Regards. Mr.Manoj Damale, M.S. Pharma (Pharmacoinformatics) NIPER, Kolkata, West Bengal State, India. -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7
Hi Chris, As far as I understand it, before GROMACS 5 the potential rather than the force was switched off. Since GROMACS 5 you can choose between the two. As for the settings to use with the CHARMM force field, the CHARMM package itself (as Justin has said) uses force switching. However, in NAMD vdw force switching has only implemented from versions 2.7b3 onwards. For proteins, I cannot see this choice having a large impact as the paper implementing the CHARMM force field in GROMACS (Bjelkmar et al.) will have used the potential switch and all the simulation in NAMD prior to version 2.7b3 will have also used this approach. The one case in which I saw this choice having a large impact was for CHARMM36 membranes and when a combination of normal TIP3P and potential switch was used. When combining these two, this resulted in DPPC membranes transitioning to a gel phase at 323K. If either of these was changed (i.e. if either CHARMM TIP3P/TIPS3P was used or the forces were switched off) the membranes behaved well. So I would say that if you are using GROMACS prior to version 5 it should be fine (with the CHARMM TIP3P water, especially if using CHARMM36 DPPC membranes) but it is worth bearing in mind that this is slightly different to how it is done in the CHARMM package. Once again, this is just my understanding of the way it has worked in GROMACS versions. One of the developers who implemented the switch cut-offs (Berk?) should be able to confirm (or deny!) this. Cheers Tom From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Christopher Neale [chris.ne...@alum.utoronto.ca] Sent: 19 May 2015 04:20 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7 Dear Justin: Thank you for the suggestion. I don't use gromacs 5 because of things like this: http://redmine.gromacs.org/issues/1603 that tend to pop up early in a release series. Until I needed to run charmm simulations, I use 4.6.7 because it works and I am confident in it. But your suggestion is really good... use gmx 5 to get energies to test against gmx 4 and see if I can find valid settings. Thank you, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: 18 May 2015 20:29 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7 On 5/18/15 2:21 PM, Christopher Neale wrote: Dear Users: I would like to use the charmm27 force field in gromacs version 4.6.7 and I would like to know if it is possible to get the proper treatment of vdw interactions. Information for gromacs 5 is here: http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM However, Gromacs 4.6.7 does not contain the option for vdw-modifier = force-switch Invalid enum 'force-switch' for variable vdw-modifier, using 'Potential-shift-Verlet' Next time use one of: 'Potential-shift-Verlet' 'Potential-shift' 'None' 'Potential-switch' 'Exact-cutoff' Is a potential-shift the same as a force-switch and therefore the following options are correct for charmm27 in gromacs 4.6.7? ns_type = grid cutoff-scheme = verlet vdwtype = cut-off rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 vdw-modifier = Potential-shift-Verlet coulombtype = PME I know this has been discussed before on the list, but I can't find anything that seems authoritative for gromacs versions prior to v5. I cannot personally attest to anything aside from what's on the wiki. We have verified the forces are equivalent between CHARMM's vfswitch and GROMACS' force-switch modifier. This is how we do all our simulations, so for posterity, what I wrote on the wiki is what I must emphasize is known to be correct. From the manual, it seems that the group scheme + vdwtype = shift is equivalent to the modern force-switch modifier. The language of potential-shift does not sound as if it is the same as force-switch, and I don't know why such redundancy would be present anyway; perhaps legacy naming reasons. Any reason why you can't use 5.0 with the known correct settings? The check I would do is a single-point energy with the settings you think are equivalent and want to test and print out the forces with gmx traj. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list
[gmx-users] The octahedron problem
Dear Gromacs Users, I have the problem with generating the octahedron box. I always get the rectangular box (using VMD) When I searched on the gmx maillist, I saw some people met same problem. Is problem is normal in gromacs? After run simulation, I can display the trajectory on VMD by using the command trjconv -pbc mol -ur compact for converting the system. But I can not display the octahedron box after solvated system. Could someone help me ? Tuong Vy -- 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] The octahedron problem
Hi Tuong Vy, An octahedral or dodecahedral box is pretty tricky. I have a Pymol script for generating them, but it will probably require some more work... Cheers, Tsjerk On May 19, 2015 13:18, Vy Phan phanvy120...@gmail.com wrote: Dear Gromacs Users, I have the problem with generating the octahedron box. I always get the rectangular box (using VMD) When I searched on the gmx maillist, I saw some people met same problem. Is problem is normal in gromacs? After run simulation, I can display the trajectory on VMD by using the command trjconv -pbc mol -ur compact for converting the system. But I can not display the octahedron box after solvated system. Could someone help me ? Tuong Vy -- 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.
[gmx-users] Query
Dear all, While generating RMSD plots of protein in presence of ligand, i am getting a RMSD of around 4.5 Angstrom around 10 ns after which the system is almost stable. Is it an acceptable RMSD? What is the acceptable range for RMSD for structures? -- *Let us all join hands to save our Mother Earth* Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala -- 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] Fwd: Re: Gromacs Error
Please keep conversations on the mailing list. And please read the manual. And note that the error is completely different this time. Tsjerk -- Forwarded message -- From: manoj damale manojaurangabad...@yahoo.co.in Date: May 19, 2015 12:19 Subject: Re: [gmx-users] Gromacs Error To: Tsjerk Wassenaar tsje...@gmail.com Cc: Dear, Sorry to distrub you, when i have replace rcoulomb= 1.4 ; short-range electrostatic cutoff (in nm) with rcoulomb must be = rlist ; short-range electrostatic cutoff (in nm) it again giving error as WARNING 1 [file nvt.mdp, line 44]: Unknown left-hand 'rcoulomb' in parameter file Program grompp, VERSION 4.5.3 Source code file: futil.c, line: 491 File input/output error: index.ndx With Best Regards. Mr.Manoj Damale, M.S. Pharma (Pharmacoinformatics) NIPER, Kolkata, West Bengal State, India. On Tuesday, 19 May 2015 2:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: ERROR 1 [file nvt.mdp]: With coulombtype = PME-Switch, rcoulomb must be = rlist On Tue, May 19, 2015 at 10:25 AM, manoj damale manojaurangabad...@yahoo.co.in wrote: what exactly i should modify With Best Regards. Mr.Manoj Damale, M.S. Pharma (Pharmacoinformatics) NIPER, Kolkata, West Bengal State, India. On Tuesday, 19 May 2015 11:32 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Manoj, The error is clear. Check the settings referred to in your .mdp file and modify them accordingly. Cheers, Tsjerk On May 19, 2015 07:35, manoj damale manojaurangabad...@yahoo.co.in wrote: Dear All, i'm geting below error while subjecting my system (Protein-ligand) for equlibriation in nvt.mdp file mgmibt@mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -fnvt.mdp Inputgrompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c em.gro InputStructure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt! Index file -p topol.top InputTopology file -pp processed.top Output, Opt. Topology file -onvt.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -[no]v bool no Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18# ERROR 1 [file nvt.mdp]: With coulombtype = PME-Switch, rcoulomb must be = rlist Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'UNT' turning all bonds into constraints...
Re: [gmx-users] RDF
On 5/19/15 4:12 AM, mah maz wrote: Thanks Justin! I cant find so much details in the manual; there are only general facts. does g_density give partial density? Read the first sentence of the help description :) -Justin On Mon, May 18, 2015 at 11:25 AM, mah maz mahma...@gmail.com wrote: Hi Justin The fact is I want to calculate water density in the system. If I select group1: oxygen and group2: oxygen, g_rdf command gives me very large numbers. Is it the number of atoms that should be changed to g/cm3? Besides, what does it calculate, each O is a reference atom during calculation? Thanks a lot! On Sun, May 17, 2015 at 2:17 PM, mah maz mahma...@gmail.com wrote: Dear all, I want to calculate the radial distribution function of water molecules in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which is not logical I suppose. Is it meaningful if I separate oxygen and hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is reference atom necessary to get RDF? Thanks! -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Query
On 5/19/15 6:29 AM, Priya Das wrote: Dear all, While generating RMSD plots of protein in presence of ligand, i am getting a RMSD of around 4.5 Angstrom around 10 ns after which the system is almost stable. Is it an acceptable RMSD? What is the acceptable range for RMSD for structures? There is no general rule, and a number without context is meaningless. How did you calculate the RMSD - backbone? heavy atoms? all atoms? Does your protein have a lot of variable loops, and did you consider these? Or did you just consider structured parts of the protein? Did you include termini? Did you watch the trajectory to see what's happening? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] mdp options for charmm27 force field in gromacs version 4.6.7
Ah, cool. I had misread that Chris was saying shift rather than switch in parts of his previous email. Good to know that force switching can also be achieved in GROMACS versions prior to 5. Cheers Tom From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 19 May 2015 12:39 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7 On 5/19/15 5:37 AM, Piggot T. wrote: Hi Chris, As far as I understand it, before GROMACS 5 the potential rather than the force was switched off. Since GROMACS 5 you can choose between the two. As for the settings to use with the CHARMM force field, the CHARMM package itself (as Justin has said) uses force switching. However, in NAMD vdw force switching has only implemented from versions 2.7b3 onwards. For proteins, I cannot see this choice having a large impact as the paper implementing the CHARMM force field in GROMACS (Bjelkmar et al.) will have used the potential switch and all the simulation in NAMD prior to version 2.7b3 will have also used this approach. The one case in which I saw this choice having a large impact was for CHARMM36 membranes and when a combination of normal TIP3P and potential switch was used. When combining these two, this resulted in DPPC membranes transitioning to a gel phase at 323K. If either of these was changed (i.e. if either CHARMM TIP3P/TIPS3P was used or the forces were switched off) the membranes behaved well. So I would say that if you are using GROMACS prior to version 5 it should be fine (with the CHARMM TIP3P water, especially if using CHARMM36 DPPC membranes) but it is worth bearing in mind that this is slightly different to how it is done in the CHARMM package. Once again, this is just my understanding of the way it has worked in GROMACS versions. One of the developers who implemented the switch cut-offs (Berk?) should be able to confirm (or deny!) this. While it is reasonably safe to say that we know of no problems for protein and nucleic acid force fields with potential switching in homogeneous media, that's as far as I can say. Those force fields are a bit more robust in their response to nonbonded treatment. The lipid force field in general (not just DPPC) is very sensitive, and as you note, and needs to be used exactly as prescribed. Note, though, that force-switching has in fact been in GROMACS for quite some time, with vdwtype = shift. NAMD introduced force-switching around the time that the CHARMM default became vfswitch (2010); old versions of the (additive) force field defaulted to vswitch (potential-switching) but vfswitch is the standard now for CHARMM36. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
[gmx-users] query regarding itp file
Hi all, I have some general doubts about the use of an itp file built by some software. I am studying the dynamics of a DNA in presence of a graphene sheet. I am using now the CHARMM27 force field and have obtained a graphene.itp file from PARAMCHEM where the atom types of the sp2 carbon atoms and the terminal hydrogen atoms of the graphene sheet have been taken into account according to the standard CHARMM directory. Now, do I need to modify my aminoacids.rtp file in order to account for the atoms in the PDB file? I have not done any pdb2gmx so do I really need to do that step? The atom types in the .itp file provided by the PARAMCHEM has CA and HP atoms which describe the graphene framework in addition to other non-bonded parameters. The equilibration steps are running without any hitches but I am not getting whether the proper interaction (atomistic) would arise between graphene and DNA atoms. As suggested by Justin i've switched over to CHARMM27 force field and am looking at atlest 200 ns of production run. Another question is, since I have not performed pdb2gmx on graphene, I dont have a posre_graphene file. Is it gonna create some problem later during mdrun? I will be grateful if someone clarifies my doubts. Can I get a posre file for graphene by some other method without doing pdb2gmx if this file is mandatory? Hope I'm not asking for much. Regards, Soumadwip Research Fellow IIT Bombay India -- 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] Lincs all-bonds causing instability in otherwise stable system
Hi everyone, I never got a reply to my message but I figured out the problem by myself. Just in case anyone else runs into a similar problem I thought I should explain what was wrong and share the solution. I was using a DMSO topology from the ATB that uses extra bonds to fix the geometry instead of angle or dihedral terms: [ moleculetype ] ; Name nrexcl DMSO 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 SDmso1DMSO S10.128 32.0600 2 ODmso1DMSO O1 -0.448 15.9994 3 CDmso1DMSO C10.160 15.0350 4 CDmso1DMSO C10.160 15.0350 ; 0.000 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 122 0.1530 8.0400e+06 132 0.1938 4.9500e+06 142 0.1938 4.9500e+06 232 0.2794 2.3900e+06 242 0.2794 2.3900e+06 342 0.2912 2.1900e+06 This topology is fine to use with SHAKE but LINCS doesn't seem to be able to handle it. When I removed the extra bonds my simulations were able to run with all bonds constrained by LINCS. Then I found appropriate angle and dihedral parameters in the GROMOS ffbonded.itp file to control the geometry again. My topology file now looks like this: [ moleculetype ] ; Name nrexcl DMSO 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 SDmso1DMSO S10.128 32.0600 2 ODmso1DMSO O1 -0.448 15.9994 3 CDmso1DMSO C10.160 15.0350 4 CDmso1DMSO C10.160 15.0350 ; 0.000 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 122 0.1530 8.0400e+06 132 0.1938 4.9500e+06 142 0.1938 4.9500e+06 [ angles ] ; ai aj ak funct angle fc 314297.40 469.00 3122 106.75 503.00 4122 106.75 503.00 [ dihedrals ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc 13422 35.26439 334.84617 ; tetrahedral centre I ran an energy minimisation of a single molecule with the new topology and its geometry overlapped the old one perfectly. So the problem was difficult to diagnose but easy to fix. Especially since I was able to energy minimise the individual molecules with all bonds constrained but the constraints went haywire when everything was combined in the full system. Hopefully I can at least save someone else from wasting 3 weeks trying to get a similar topology to work with LINCS. Cara From: cara.kr...@student.curtin.edu.au To: gromacs.org_gmx-users@maillist.sys.kth.se Date: Fri, 15 May 2015 14:31:16 +0800 Subject: [gmx-users] Lincs all-bonds causing instability in otherwise stable system I forgot to include an example of my mdp files. I've tried varying the timestep, running with and without pressure coupling, and obviously changing the constraints as outlined in the previous message: integrator = md dt = 0.001 ; 1fs nsteps = 10 ; 100ps comm_grps= DOPC !DOPC nstxout = 1000 nstvout = 0 nstlog = 1000 nstenergy= 1000 energygrps = DOPC !DOPC nstcalcenergy= 5 nstlist = 5 ns_type = grid pbc = xyz rlist= 0.8 coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 62 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = DOPC !DOPC tau_t= 0.1 0.1 ref_t= 303 303 ;Pcoupl = berendsen ;pcoupltype = semiisotropic ;tau_p= 1.0 1.0 ;compressibility = 4.6e-5 4.6e-5 ;ref_p= 1.0 1.0 gen_vel = no constraints = all-bonds constraint_algorithm = shake continuation = yes From: cara.kr...@student.curtin.edu.au To: gromacs.org_gmx-users@maillist.sys.kth.se Date: Fri, 15 May 2015 14:17:28 +0800 Subject: [gmx-users] FW: Lincs all-bonds causing instability in otherwise stable system Hi, I am having trouble constraining all-bonds with lincs in a system that is stable using shake all-bonds or lincs h-bonds in gromacs 4.6.7. The previous step using lincs h-bonds gave these energies: Step Time Lambda 20 200.00.0 Energies (kJ/mol) G96Bond G96AngleProper Dih. Improper Dih. LJ-14 1.76317e+042.43132e+041.39308e+04
[gmx-users] SOL LJ and Coul energies
Dear all, I am trying to compute the interaction energy between a small peptide and water from a short MD simulation (54a7, reaction-field, Verlet, GPU, gmx 5.04, 1 peptide, 3200 SOL molecules). I have specified SOL and Protein as energy groups. Contrary to my expectations, LJ and Coul energies outputed by 'gmx energy' for SOL-SOL and Protein-SOL are all zero. Is that normal or is it a known bug ? Best wishes Quentin http://cybase.org.au/ PS: The LJ and Coul energies of Protein-Protein are not zero. Simulation ran fine and was stable (rms and total energy) -- 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] query regarding itp file
Hi, You can easily generate position restraints files yourself - have a look at one and learn about the column format from chapter 5. There is also gmx genrestr to help with this - but read the documentation first. Mark On Tue, May 19, 2015 at 2:10 PM soumadwip ghosh soumadwipgh...@gmail.com wrote: Hi all, I have some general doubts about the use of an itp file built by some software. I am studying the dynamics of a DNA in presence of a graphene sheet. I am using now the CHARMM27 force field and have obtained a graphene.itp file from PARAMCHEM where the atom types of the sp2 carbon atoms and the terminal hydrogen atoms of the graphene sheet have been taken into account according to the standard CHARMM directory. Now, do I need to modify my aminoacids.rtp file in order to account for the atoms in the PDB file? I have not done any pdb2gmx so do I really need to do that step? The atom types in the .itp file provided by the PARAMCHEM has CA and HP atoms which describe the graphene framework in addition to other non-bonded parameters. The equilibration steps are running without any hitches but I am not getting whether the proper interaction (atomistic) would arise between graphene and DNA atoms. As suggested by Justin i've switched over to CHARMM27 force field and am looking at atlest 200 ns of production run. Another question is, since I have not performed pdb2gmx on graphene, I dont have a posre_graphene file. Is it gonna create some problem later during mdrun? I will be grateful if someone clarifies my doubts. Can I get a posre file for graphene by some other method without doing pdb2gmx if this file is mandatory? Hope I'm not asking for much. Regards, Soumadwip Research Fellow IIT Bombay India -- 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.
Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7
Hi On Tue, May 19, 2015 at 5:35 AM Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Justin: Thank you for the suggestion. I don't use gromacs 5 because of things like this: http://redmine.gromacs.org/issues/1603 that tend to pop up early in a release series. Until I needed to run charmm simulations, I use 4.6.7 because it works and I am confident in it. Naturally, that's your decision :-) But I hope that people in general adopting that strategy at least try out and compare newer versions of the code for their simulations, even if they don't plan to publish with those versions. The combinatorics of MD validation make centralized testing prohibitively expensive (though there are some plans that might get funded some time...), so if there's a problem that only shows up for an individual user, then it could stay unnoticed for a long time, and that's clearly not in your long term interests. (And you might decide the improved performance enhances your sampling enough to accept what may be higher bug risk...) Hardware and software enhancements will eventually force people to use newer software versions, and both kinds of enhancements are happening exponentially fast at the moment... But your suggestion is really good... use gmx 5 to get energies to test against gmx 4 and see if I can find valid settings. I would strongly encourage that kind of testing - use mdrun -rerun to compare forces and energies to complement reading docs and asking people. Code doesn't lie (much) Mark Thank you, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: 18 May 2015 20:29 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7 On 5/18/15 2:21 PM, Christopher Neale wrote: Dear Users: I would like to use the charmm27 force field in gromacs version 4.6.7 and I would like to know if it is possible to get the proper treatment of vdw interactions. Information for gromacs 5 is here: http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM However, Gromacs 4.6.7 does not contain the option for vdw-modifier = force-switch Invalid enum 'force-switch' for variable vdw-modifier, using 'Potential-shift-Verlet' Next time use one of: 'Potential-shift-Verlet' 'Potential-shift' 'None' 'Potential-switch' 'Exact-cutoff' Is a potential-shift the same as a force-switch and therefore the following options are correct for charmm27 in gromacs 4.6.7? ns_type = grid cutoff-scheme = verlet vdwtype = cut-off rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 vdw-modifier = Potential-shift-Verlet coulombtype = PME I know this has been discussed before on the list, but I can't find anything that seems authoritative for gromacs versions prior to v5. I cannot personally attest to anything aside from what's on the wiki. We have verified the forces are equivalent between CHARMM's vfswitch and GROMACS' force-switch modifier. This is how we do all our simulations, so for posterity, what I wrote on the wiki is what I must emphasize is known to be correct. From the manual, it seems that the group scheme + vdwtype = shift is equivalent to the modern force-switch modifier. The language of potential-shift does not sound as if it is the same as force-switch, and I don't know why such redundancy would be present anyway; perhaps legacy naming reasons. Any reason why you can't use 5.0 with the known correct settings? The check I would do is a single-point energy with the settings you think are equivalent and want to test and print out the forces with gmx traj. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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
Re: [gmx-users] The octahedron problem
Hi Tuong Vy, No, it uses Pymol CGO to draw the cell. I think that won't work in VMD. Cheers, Tsjerk On May 19, 2015 15:28, Vy Phan phanvy120...@gmail.com wrote: Dear Tsjerk Wassenaar Can I display it on the VMD ? Thank a lot Tuong Vy 2015-05-19 20:22 GMT+09:00 Tsjerk Wassenaar tsje...@gmail.com: Hi Tuong Vy, An octahedral or dodecahedral box is pretty tricky. I have a Pymol script for generating them, but it will probably require some more work... Cheers, Tsjerk On May 19, 2015 13:18, Vy Phan phanvy120...@gmail.com wrote: Dear Gromacs Users, I have the problem with generating the octahedron box. I always get the rectangular box (using VMD) When I searched on the gmx maillist, I saw some people met same problem. Is problem is normal in gromacs? After run simulation, I can display the trajectory on VMD by using the command trjconv -pbc mol -ur compact for converting the system. But I can not display the octahedron box after solvated system. Could someone help me ? Tuong Vy -- 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. -- 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.
Re: [gmx-users] query regarding itp file
On 5/19/15 10:15 AM, soumadwip ghosh wrote: Thanks Mark for the prompt reply. I can probably make the posre files if required now. But I would be relieved if someone sheds light on the first question that if I already have an .itp file is is necessary to make an entry for the atoms in the aminoacid.rtp file of the corresponding force field? I did not do pdb2gmx to generate the topology of the graphene No. The .rtp entries are only used by pdb2gmx; if you've obtained the topology by other means the .rtp is totally irrelevant. molecule since I obtained the same from PARAMCHEM and the atom types used for graphene are CA and HP which are consistent with some literature. Do I need to modify my aminoacid.rtp file or can I be assured that proper interactions would arise since I am using A BETTER FORCE FIELD (CHARMM 27) for a longer MD simulation (200ns) as per the suggestion by Justin. As far I am concerned the outputs of PARAMCHEM are reliable. I am confused whether I have provided the correct .itp file and whether the expected interaction would arise or not. The parameters of a graphene sheet or a CNT should be very straightforward for an additive model. Whether or not you'll be able to observe the desired outcome depends on whether or not *any* force field can capture that behavior. Materials like graphene and CNT have interesting electronic properties that may play a role here, none of which would be captured by any additive MM model. Use the literature as a guide. If anyone has attempted something similar, use that as inspiration. The CHARMM force fields for nucleic acids (I would recommend CHARMM36 over CHARMM27) are quite good in terms of modeling subtle behavior of nucleic acids. It should be about as good of a model as you'll find. Whether or not the DNA-graphene interaction is described well, that I don't know. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Problem control output for checkpoint file
Thank you so much for the suggestion. Tuong Vy 2015-05-19 23:15 GMT+09:00 Mark Abraham mark.j.abra...@gmail.com: Hi, EM is implemented separately from MD, and since people rarely write enough trajectory-frame coordinates from EM for I/O to be a serious issue, there's no good reason to support XTC writing. You can always use trjconv to post-process out the groups or steps you want, etc. Mark On Tue, May 19, 2015 at 4:13 PM Justin Lemkul jalem...@vt.edu wrote: On 5/19/15 10:10 AM, Vy Phan wrote: Dear Justin Lemku, I am so thankful for your help Could you please help me more ? Here is the way I control output file for energy minimization step , integrator = cg nstcgsteep = 1000 emtol = 100.0 emstep = 0.01 nsteps = 5000 ; Output control nstxout = 0 nstvout = 0 nstfout = 0 nstenergy = 50 nstlog = 50 nstxout-compressed = 50 But, the parameter file in the mdout.mdp file like this ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 50 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 50 nstcalcenergy= 100 nstenergy= 50 ; Output frequency and precision for .xtc file nstxout-compressed = 0 compressed-x-precision = 1000 I do not know why this happen ? IIRC you can't write an .xtc during EM, only during actual dynamics. There's probably some magic that grompp does to translate this, but I've never looked into it. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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] question
On 5/19/15 11:19 AM, Andrew Bostick wrote: Dear Tsjerk, Justin and Mark Very thanks for your answers and guidance. I installed gromacs 5.0.5. I used gmx pdb2gmx -f be_near.pdb -ignh -merge all. I want to have a link between two chains (CD atom of GLU residue from chaim B and NZ atom of LYS residue from chain E) to get isopeptide bond between these two atoms. I used the all for -merge option. Is this true? After gmx pdb2gmx, I encountered with: Linking CYS-252 SG-248 and CYS-312 SG-743... Linking CYS-358 SG-1094 and CYS-416 SG-1565... Linking GLU-380 CD-1269 and LYS-540 NZ-2499... Start terminus PRO-220: PRO-NH2+ End terminus HIS-434: COO- Start terminus GLY-435: GLY-NH3+ End terminus LYS-551: COO- Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 332 residues with 3314 atoms Making bonds... WARNING: atom H is missing in residue GLU 380 in the pdb file You might need to add atom H to the hydrogen database of building block GLU2 in the file aminoacids.hdb (see the manual) WARNING: atom H is missing in residue LYS 540 in the pdb file You might need to add atom H to the hydrogen database of building block LYS2 in the file aminoacids.hdb (see the manual) WARNING: atom HZ1 is missing in residue LYS 540 in the pdb file You might need to add atom HZ1 to the hydrogen database of building block LYS2 in the file aminoacids.hdb (see the manual) WARNING: atom HZ2 is missing in residue LYS 540 in the pdb file You might need to add atom HZ2 to the hydrogen database of building block LYS2 in the file aminoacids.hdb (see the manual) -- Program gmx, VERSION 5.0.5 Source code file: /export/apps/gromacs/gromacs-5.0.5/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1587 Fatal error: There were 4 missing atoms in molecule Protein_chain_B, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- I added following lines to aminoacids.hdb file of gromose43a1 force field. LYS2 2 1 1 H N -C CA 2 4 HZ NZ CE CD You don't want to be adding 2 HZ here, just one since it is a peptide bond. GLU21 1 1 H N -C CA Then, this error was solved. Is my manner true? Then, I checked topology file: ; residue 380 GLU rtp GLU2 q 0.0 1595 N380GLU N705 -0.2814.0067 ; qtot -2.28 1596 H380GLU H705 0.28 1.008 ; qtot -2 1597CH1380GLU CA706 0 13.019 ; qtot -2 1598CH2380GLU CB706 0 14.027 ; qtot -2 1599CH2380GLU CG706 0 14.027 ; qtot -2 1600 C380GLU CD707 0.38 12.011 ; qtot -1.62 1601 OM380GLUOE1707 -0.3815.9994 ; qtot -2 1602 OM380GLUOE2707 015.9994 ; qtot -2 1603 C380GLU C708 0.38 12.011 ; qtot -1.62 1604 O380GLU O708 -0.3815.9994 ; qtot -2 and ; residue 540 LYS rtp LYS2 q 0.0 3198 N540LYS N 1422 -0.2814.0067 ; qtot -5.28 3199 H540LYS H 1422 0.28 1.008 ; qtot -5 3200CH1540LYS CA 1423 0 13.019 ; qtot -5 3201CH2540LYS CB 1423 0 14.027 ; qtot -5 3202CH2540LYS CG 1424 0 14.027 ; qtot -5 3203CH2540LYS CD 1424 0 14.027 ; qtot -5 3204CH2540LYS CE 1424 0 14.027 ; qtot -5 3205 NT540LYS NZ 1425 -0.2814.0067 ; qtot -5.28 3206 H540LYSHZ1 1425 0.28 1.008 ; qtot -5 3207 H540LYSHZ2 1425 0 1.008 ; qtot -5 3208 C540LYS C 1426 0.38 12.011 ; qtot -4.62 3209 O540LYS O 1426 -0.3815.9994 ; qtot -5 Then, I did following steps: gmx editconf -f conf.gro -o box.gro -d 0.8 -bt cubic -c gmx solvate -cp box.gro -cs spc216.gro -p topol.top -o sol.gro gmx grompp -f ions.mdp -c sol.gro -p topol.top -o ions.tpr After using last command, I encountered with: NOTE 1 [file ions.mdp]: With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 1332188956 Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file topol.top, line 5321]: No default G96Bond
[gmx-users] question
Dear Tsjerk, Justin and Mark Very thanks for your answers and guidance. I installed gromacs 5.0.5. I used gmx pdb2gmx -f be_near.pdb -ignh -merge all. I want to have a link between two chains (CD atom of GLU residue from chaim B and NZ atom of LYS residue from chain E) to get isopeptide bond between these two atoms. I used the all for -merge option. Is this true? After gmx pdb2gmx, I encountered with: Linking CYS-252 SG-248 and CYS-312 SG-743... Linking CYS-358 SG-1094 and CYS-416 SG-1565... Linking GLU-380 CD-1269 and LYS-540 NZ-2499... Start terminus PRO-220: PRO-NH2+ End terminus HIS-434: COO- Start terminus GLY-435: GLY-NH3+ End terminus LYS-551: COO- Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 332 residues with 3314 atoms Making bonds... WARNING: atom H is missing in residue GLU 380 in the pdb file You might need to add atom H to the hydrogen database of building block GLU2 in the file aminoacids.hdb (see the manual) WARNING: atom H is missing in residue LYS 540 in the pdb file You might need to add atom H to the hydrogen database of building block LYS2 in the file aminoacids.hdb (see the manual) WARNING: atom HZ1 is missing in residue LYS 540 in the pdb file You might need to add atom HZ1 to the hydrogen database of building block LYS2 in the file aminoacids.hdb (see the manual) WARNING: atom HZ2 is missing in residue LYS 540 in the pdb file You might need to add atom HZ2 to the hydrogen database of building block LYS2 in the file aminoacids.hdb (see the manual) -- Program gmx, VERSION 5.0.5 Source code file: /export/apps/gromacs/gromacs-5.0.5/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1587 Fatal error: There were 4 missing atoms in molecule Protein_chain_B, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- I added following lines to aminoacids.hdb file of gromose43a1 force field. LYS2 2 1 1 H N -C CA 2 4 HZ NZ CE CD GLU21 1 1 H N -C CA Then, this error was solved. Is my manner true? Then, I checked topology file: ; residue 380 GLU rtp GLU2 q 0.0 1595 N380GLU N705 -0.2814.0067 ; qtot -2.28 1596 H380GLU H705 0.28 1.008 ; qtot -2 1597CH1380GLU CA706 0 13.019 ; qtot -2 1598CH2380GLU CB706 0 14.027 ; qtot -2 1599CH2380GLU CG706 0 14.027 ; qtot -2 1600 C380GLU CD707 0.38 12.011 ; qtot -1.62 1601 OM380GLUOE1707 -0.3815.9994 ; qtot -2 1602 OM380GLUOE2707 015.9994 ; qtot -2 1603 C380GLU C708 0.38 12.011 ; qtot -1.62 1604 O380GLU O708 -0.3815.9994 ; qtot -2 and ; residue 540 LYS rtp LYS2 q 0.0 3198 N540LYS N 1422 -0.2814.0067 ; qtot -5.28 3199 H540LYS H 1422 0.28 1.008 ; qtot -5 3200CH1540LYS CA 1423 0 13.019 ; qtot -5 3201CH2540LYS CB 1423 0 14.027 ; qtot -5 3202CH2540LYS CG 1424 0 14.027 ; qtot -5 3203CH2540LYS CD 1424 0 14.027 ; qtot -5 3204CH2540LYS CE 1424 0 14.027 ; qtot -5 3205 NT540LYS NZ 1425 -0.2814.0067 ; qtot -5.28 3206 H540LYSHZ1 1425 0.28 1.008 ; qtot -5 3207 H540LYSHZ2 1425 0 1.008 ; qtot -5 3208 C540LYS C 1426 0.38 12.011 ; qtot -4.62 3209 O540LYS O 1426 -0.3815.9994 ; qtot -5 Then, I did following steps: gmx editconf -f conf.gro -o box.gro -d 0.8 -bt cubic -c gmx solvate -cp box.gro -cs spc216.gro -p topol.top -o sol.gro gmx grompp -f ions.mdp -c sol.gro -p topol.top -o ions.tpr After using last command, I encountered with: NOTE 1 [file ions.mdp]: With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 1332188956 Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file topol.top, line 5321]: No default G96Bond types ERROR 2 [file topol.top, line 14911]: No default G96Angle types ERROR 3 [file topol.top, line 14913]: No default G96Angle types ERROR 4 [file
Re: [gmx-users] Fwd: Bad performance in free energy calulations
Hi, somewhat off-topic but I wonder why in your free energy protocol you only vary the vdW and electrostatic lambdas. What about the others? Your mutation also transforms bonded terms and masses. One minor point is that your duplication of atomtypes (with i and m prefixes) seems pretty redundant to me. Cheers, Hannes. -- 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] Fwd: Bad performance in free energy calulations
Hi, mdrun doesn't see any problems, but if something else is reporting 25% utilization then that probably means you have something else running on your machine, which is a terrible idea for running mdrun. You should expect some slowdown wrt to the non-free-energy version of the run - the implementation of the short-ranged loops for the perturbed atoms is not as great as the rest. Mark On Tue, May 19, 2015 at 3:13 PM Julian Zachmann frankjulian.zachm...@uab.cat wrote: Dear Gromacs users, I want to do free energy calculations following this http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html tutorial. My system contains a GPCR, membrane, small ligand, solvate - in total 60.000 atoms. I want to perturb the ligand (31 atoms, 3 hydrogen atoms get converted to dummy atoms, one carbon atom get converted to a carbon atom, the other 27 ligand atoms just change slightly their charges). Apart from the perturbation and an extra simulated annealing step in the equilibration, I am following the tutorial as close as possible. My calculations work, but the computer performance is really bad. I am using only 8 processors for each Lambda, so domain decomposition is not really an issue (see below) but the CPUs run with only 25% load. Which could be the reason? Any ideas? I have made all files available under this link https://drive.google.com/folderview?id=0B2M9aqeJrxnYfjRLbzZ0VkFBTlFraEJaWWJ3MzVSaHlUN2cyVzV6X2ZibjRkek81UVM5S0kusp=sharing . Thank you very much for your help!! Julian D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 74451.3 av. #atoms communicated per step for LINCS: 2 x 4495.3 Average load imbalance: 2.9 % Part of the total run time spent waiting due to load imbalance: 1.4 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 2 % R E A L C Y C L E A N D T I M E A C C O U N T I N G On 8 MPI ranks Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum% - Domain decomp. 81150 3.136 65.226 0.3 DD comm. load 81150 0.208 4.335 0.0 DD comm. bounds81150 0.257 5.355 0.0 Neighbor search81151 11.329235.608 1.2 Comm. coord. 81 4850 11.368236.425 1.2 Force 81 5001 466.392 9699.934 50.6 Wait + Comm. F 81 5001 10.598220.418 1.2 PME mesh 81 5001 386.976 8048.244 42.0 NB X/F buffer ops. 81 14701 1.670 34.724 0.2 Write traj.81 3 0.133 2.768 0.0 Update 81 5001 1.474 30.664 0.2 Constraints81 10002 20.387423.998 2.2 Comm. energies 81501 2.255 46.891 0.2 Rest 4.983103.631 0.5 - Total921.165 19158.221 100.0 - Breakdown of PME mesh computation - PME redist. X/F81 15003 134.013 2787.183 14.5 PME spread/gather 81 20004 179.277 3728.576 19.5 PME 3D-FFT 81 20004 22.603470.092 2.5 PME 3D-FFT Comm. 81 20004 47.072979.004 5.1 PME solve Elec 81 10002 3.941 81.965 0.4 - Core t (s) Wall t (s)(%) Time: 3693.315 921.165 400.9 (ns/day)(hour/ns) Performance:0.938 25.583 Finished mdrun on rank 0 Tue May 19 14:01:45 2015 -- 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
Re: [gmx-users] Fwd: Bad performance in free energy calulations
somewhat off-topic but I wonder why in your free energy protocol you only vary the vdW and electrostatic lambdas. What about the others? Your mutation also transforms bonded terms and masses. Minor point - if you are taking the difference between two mutations (say, with and without a ligand), then it's better to leave the masses untouched -- any contribution will cancel. There are some weird issues with changing masses in the constraint terms and their contribution to the free energies that need to be accounted for post-hoc. -- 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] question
Dear Justin Based on your answer (You don't want to be adding 2 HZ here, just one since it is a peptide bond.), I modified LYS2 in aminoacids.hdb file LYS2 2 1 1 H N -C CA 1 4 HZ NZ CE CD But, after pdb2gmx, I encountered with WARNING: atom HZ1 is missing in residue LYS 540 in the pdb file You might need to add atom HZ1 to the hydrogen database of building block LYS2 in the file aminoacids.hdb (see the manual) WARNING: atom HZ2 is missing in residue LYS 540 in the pdb file You might need to add atom HZ2 to the hydrogen database of building block LYS2 in the file aminoacids.hdb (see the manual). What is the reason of this issue? Is there problem in my rtp file (about LYS2 and GLU2 entries)? [ GLU2 ] [ atoms ] N N-0.28000 0 H H 0.28000 0 CA CH1 0.0 1 CB CH2 0.0 1 CG CH2 0.0 1 CD C 0.380 2 OE1OM -0.380 2 OE2OM 0.0 2 C C 0.380 3 O O -0.380 3 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CBCGgb_26 CGCDgb_26 CD OE1gb_5 CD OE2gb_5 [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 O C+N ga_32 NCACB ga_12 CCACB ga_12 CACBCG ga_14 CBCGCD ga_14 CGCD OE1 ga_21 CGCD OE2 ga_21 OE1CD OE2 ga_37 [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N O gi_1 CA N CCB gi_2 CD OE1 OE2CG gi_1 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_4 -C NCA C gd_19 NCA C+N gd_20 NCACBCG gd_17 CACBCGCD gd_17 CBCGCD OE2 gd_2 [ LYS2 ] [ atoms ] N N-0.28000 0 H H 0.28000 0 CA CH1 0.0 1 CB CH2 0.0 1 CG CH2 0.0 2 CD CH2 0.0 2 CE CH2 0.0 2 NZNT-0.28000 3 HZ1 H 0.28000 3 HZ2 H 0.0 3 C C 0.380 4 O O -0.380 4 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CBCGgb_26 CGCDgb_26 CDCEgb_26 CENZgb_20 NZ HZ1gb_2 NZ HZ2gb_2 [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 O C+N ga_32 NCACB ga_12 CCACB ga_12 CACBCG ga_14 CBCGCD ga_14 CGCDCE ga_14 CDCENZ ga_14 CENZ HZ1 ga_10 CENZ HZ2 ga_10 HZ1NZ HZ2 ga_9 [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N O gi_1 CA N CCB gi_2 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_4 -C NCA C gd_19 NCA C+N gd_20 NCACBCG gd_17 CACBCGCD gd_17 CBCGCDCE gd_17 CGCDCENZ gd_17 CDCENZ HZ1 gd_14 Thanks in advance. -- 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] Fwd: Bad performance in free energy calulations
On 5/19/15 12:12 PM, Hannes Loeffler wrote: On Tue, 19 May 2015 12:03:41 -0400 Michael Shirts mrshi...@gmail.com wrote: Yep, that's what I generally do. Almost all alchemical changes involve a difference in two calculations (since the alchemical change itself is unphysical). Even one-calculation solvation free energy calculations are actually calculating the difference in free energy from liquid to vapor state. This reminds me: there was recently a discussion around couple-moltype on this list. My understanding is that this can be used for absolute free energies. But what I really want to make sure is this: as far as I can see in the code and I think the manual says that too is that when couple-moltype is not set in the .mdp none of the other couple- parameters have any effect should I set any of the to something. Do I get this right? Right, they're ignored. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Query
On 5/19/15 1:15 PM, Priya Das wrote: Yes Justin...i watched the dynamic structure carefully. As it is a transmembrane protein it is stringently moving. The dynamic movement of the structure seems fine. I used the backbone of protein for calculating Rmsd. Consider everything else I said. I also want to know the ligand stability, for it i need to check the least square fit of ligand , right? There are many ways to assess this. RMSD is just one possible metric. -Justin On May 19, 2015 5:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/19/15 6:29 AM, Priya Das wrote: Dear all, While generating RMSD plots of protein in presence of ligand, i am getting a RMSD of around 4.5 Angstrom around 10 ns after which the system is almost stable. Is it an acceptable RMSD? What is the acceptable range for RMSD for structures? There is no general rule, and a number without context is meaningless. How did you calculate the RMSD - backbone? heavy atoms? all atoms? Does your protein have a lot of variable loops, and did you consider these? Or did you just consider structured parts of the protein? Did you include termini? Did you watch the trajectory to see what's happening? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] question
On 5/19/15 2:45 PM, Andrew Bostick wrote: Dear Justin Based on your answer (You don't want to be adding 2 HZ here, just one since it is a peptide bond.), I modified LYS2 in aminoacids.hdb file LYS2 2 1 1 H N -C CA 1 4 HZ NZ CE CD But, after pdb2gmx, I encountered with WARNING: atom HZ1 is missing in residue LYS 540 in the pdb file You might need to add atom HZ1 to the hydrogen database of building block LYS2 in the file aminoacids.hdb (see the manual) WARNING: atom HZ2 is missing in residue LYS 540 in the pdb file You might need to add atom HZ2 to the hydrogen database of building block LYS2 in the file aminoacids.hdb (see the manual). What is the reason of this issue? Is there problem in my rtp file (about LYS2 and GLU2 entries)? Yes. This: [ LYS2 ] [ atoms ] N N-0.28000 0 H H 0.28000 0 CA CH1 0.0 1 CB CH2 0.0 1 CG CH2 0.0 2 CD CH2 0.0 2 CE CH2 0.0 2 NZNT-0.28000 3 HZ1 H 0.28000 3 HZ2 H 0.0 3 Here, you specify two HZ atoms, when you actually only want one (look at the structure of a peptide bond!). The .hdb entry specifies one HZ to be built (with the name HZ), but your .rtp tells pdb2gmx there should be two, HZ1 and HZ2. That, of course, is not correct, as is assigning a zero charge to any H atom here. -Justin C C 0.380 4 O O -0.380 4 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CBCGgb_26 CGCDgb_26 CDCEgb_26 CENZgb_20 NZ HZ1gb_2 NZ HZ2gb_2 [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 O C+N ga_32 NCACB ga_12 CCACB ga_12 CACBCG ga_14 CBCGCD ga_14 CGCDCE ga_14 CDCENZ ga_14 CENZ HZ1 ga_10 CENZ HZ2 ga_10 HZ1NZ HZ2 ga_9 [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N O gi_1 CA N CCB gi_2 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_4 -C NCA C gd_19 NCA C+N gd_20 NCACBCG gd_17 CACBCGCD gd_17 CBCGCDCE gd_17 CGCDCENZ gd_17 CDCENZ HZ1 gd_14 Thanks in advance. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Fwd: Bad performance in free energy calulations
On Tue, 19 May 2015 17:48:17 +0200 Julian Zachmann frankjulian.zachm...@uab.cat wrote: Concerning the changes of the atom types: the changes in the charges are really small and the results will probably be the same if I would not convert the whole ligand, just the 4 atoms which are changing. However, as i had both ligands parametrised, I thought it would be a good idea to really convert the whole ligand from one to the other, and change all charges on all atoms. That's not what I meant. I was wondering why you define a, say, ic3 type and an mc3 type. They are identical! The charges are explicitly listed for both states so I think the atom types only affect the vdW terms. Cheers, Hannes. -- 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] Fwd: Bad performance in free energy calulations
On Tue, 19 May 2015 11:37:11 -0400 Michael Shirts mrshi...@gmail.com wrote: somewhat off-topic but I wonder why in your free energy protocol you only vary the vdW and electrostatic lambdas. What about the others? Your mutation also transforms bonded terms and masses. Minor point - if you are taking the difference between two mutations (say, with and without a ligand), then it's better to leave the masses untouched -- any contribution will cancel. There are some weird issues with changing masses in the constraint terms and their contribution to the free energies that need to be accounted for post-hoc. So you suggest to leave the mass lambdas simply at their initial (or final) value to be safe in case constraints are involved (and I am too lazy to check)? -- 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] Compiling GROMACS 5.0.5 on Fujitsu PRIMEHPC FX-10
Hi everyone, I try to compile GROMACS 5.0.5 on Fujitsu PRIMEHPC FX-10 with the command from installation instruction page http://www.gromacs.org/Documentation/Installation_Instructions_5.0#linear-algebra-libraries I use the Fujitsu compiler with the custom build toolchain as suggestion from the GROMACS webpage. The command is: ~/software/cmake/bin/cmake ../ -DCMAKE_INSTALL_PREFIX=/home/k0055/k005503/software/gromacs -DGMX_MPI=ON -DCMAKE_TOOLCHAIN_FILE=../cmake/Platform/Toolchain-Fujitsu-Sparc64-mpi.cmake -DCMAKE_PREFIX_PATH=/usr/local/fftw/3.3 -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_RELAXED_DOUBLE_PRECISION=ON But unfortunately, I got this message after running make. ../../lib/libgromacs_mdrun_mpi_d.a(tpi.c.o): In function `do_tpi': tpi.c:(.text+0x2130): undefined reference to `gmx_simd_check_and_reset_overflow' make[2]: *** [bin/mdrun_mpi_d] Error 1 make[1]: *** [src/programs/CMakeFiles/mdrun.dir/all] Error 2 make: *** [all] Error 2 Is there any suggestion on this problem? Thank you a lot. -- 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] g_clustsize
Hi, I have used g_clustsize to count the number of molecules (they differ by chain id) in the maximum populated cluster. Is it also possible to label these molecules? i.e. to print chain ids of these molecules with time in separate file? Thanks in advance -- 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] Query
Yes Justin...i watched the dynamic structure carefully. As it is a transmembrane protein it is stringently moving. The dynamic movement of the structure seems fine. I used the backbone of protein for calculating Rmsd. I also want to know the ligand stability, for it i need to check the least square fit of ligand , right? On May 19, 2015 5:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/19/15 6:29 AM, Priya Das wrote: Dear all, While generating RMSD plots of protein in presence of ligand, i am getting a RMSD of around 4.5 Angstrom around 10 ns after which the system is almost stable. Is it an acceptable RMSD? What is the acceptable range for RMSD for structures? There is no general rule, and a number without context is meaningless. How did you calculate the RMSD - backbone? heavy atoms? all atoms? Does your protein have a lot of variable loops, and did you consider these? Or did you just consider structured parts of the protein? Did you include termini? Did you watch the trajectory to see what's happening? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
[gmx-users] Help_Warning1
Dear All, I am new user of Gromacs and I am facing with a problem during a Tutorial that until now It was not solved. The following message appear: The switching range for PME-Switch should be 5% or less, energy conservation will be good anyhow, since ewald_rtol = 1e-05. I would like to know if someone could help me with some tips about what I need to do. The .mdp file is attached. Thanks in advance! Tammy Lira -- 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] Fwd: Bad performance in free energy calulations
Hello Hannes, As Michael said it is better to leave most things untouched and just change VDW and LJ - at least this is what I have been reading so far. Concerning the changes of the atom types: the changes in the charges are really small and the results will probably be the same if I would not convert the whole ligand, just the 4 atoms which are changing. However, as i had both ligands parametrised, I thought it would be a good idea to really convert the whole ligand from one to the other, and change all charges on all atoms. Probably it won't really make any difference. All the best, Julian 2015-05-19 17:37 GMT+02:00 Michael Shirts mrshi...@gmail.com: somewhat off-topic but I wonder why in your free energy protocol you only vary the vdW and electrostatic lambdas. What about the others? Your mutation also transforms bonded terms and masses. Minor point - if you are taking the difference between two mutations (say, with and without a ligand), then it's better to leave the masses untouched -- any contribution will cancel. There are some weird issues with changing masses in the constraint terms and their contribution to the free energies that need to be accounted for post-hoc. -- 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. -- Julian Zachmann Laboratori de Medicina Computacional Unitat de Bioestadistica. Facultat de Medicina Universitat Autonoma de Barcelona 08193 Bellaterra (Barcelona). Spain Phone: (3493) 581 2797 Fax: (3493) 581 2344 E-mail: frankjulian.zachm...@uab.cat http://lmc.uab.es -- 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] Fwd: Bad performance in free energy calulations
As Michael said it is better to leave most things untouched and just change VDW and LJ - at least this is what I have been reading so far. Well, I didn't quite say this. Changes in the bonded terms do not entirely cancel. Changes in masses do 100% cancel because of the seperability of momenta and position, and the masses only contributed to the total energy through the momenta. -- 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] Fwd: Bad performance in free energy calulations
Yep, that's what I generally do. Almost all alchemical changes involve a difference in two calculations (since the alchemical change itself is unphysical). Even one-calculation solvation free energy calculations are actually calculating the difference in free energy from liquid to vapor state. On Tue, May 19, 2015 at 11:58 AM, Hannes Loeffler hannes.loeff...@stfc.ac.uk wrote: On Tue, 19 May 2015 11:37:11 -0400 Michael Shirts mrshi...@gmail.com wrote: somewhat off-topic but I wonder why in your free energy protocol you only vary the vdW and electrostatic lambdas. What about the others? Your mutation also transforms bonded terms and masses. Minor point - if you are taking the difference between two mutations (say, with and without a ligand), then it's better to leave the masses untouched -- any contribution will cancel. There are some weird issues with changing masses in the constraint terms and their contribution to the free energies that need to be accounted for post-hoc. So you suggest to leave the mass lambdas simply at their initial (or final) value to be safe in case constraints are involved (and I am too lazy to check)? -- 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.
Re: [gmx-users] Fwd: Bad performance in free energy calulations
Concerning the changes of the atom types: the changes in the charges are really small and the results will probably be the same if I would not convert the whole ligand, just the 4 atoms which are changing. However, as i had both ligands parametrised, I thought it would be a good idea to really convert the whole ligand from one to the other, and change all charges on all atoms. That's not what I meant. I was wondering why you define a, say, ic3 type and an mc3 type. They are identical! The charges are explicitly listed for both states so I think the atom types only affect the vdW terms. There is no specific reason for it. After the parametrisation of the ligands I just took for both of them all atom types and use them for the ligand conversion - whether they are identical, only slightly different, or not. 2015-05-19 18:00 GMT+02:00 Hannes Loeffler hannes.loeff...@stfc.ac.uk: On Tue, 19 May 2015 17:48:17 +0200 Julian Zachmann frankjulian.zachm...@uab.cat wrote: Concerning the changes of the atom types: the changes in the charges are really small and the results will probably be the same if I would not convert the whole ligand, just the 4 atoms which are changing. However, as i had both ligands parametrised, I thought it would be a good idea to really convert the whole ligand from one to the other, and change all charges on all atoms. That's not what I meant. I was wondering why you define a, say, ic3 type and an mc3 type. They are identical! The charges are explicitly listed for both states so I think the atom types only affect the vdW terms. Cheers, Hannes. -- 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. -- Julian Zachmann Laboratori de Medicina Computacional Unitat de Bioestadistica. Facultat de Medicina Universitat Autonoma de Barcelona 08193 Bellaterra (Barcelona). Spain Phone: (3493) 581 2797 Fax: (3493) 581 2344 E-mail: frankjulian.zachm...@uab.cat http://lmc.uab.es -- 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] Fwd: Bad performance in free energy calulations
On Tue, 19 May 2015 12:03:41 -0400 Michael Shirts mrshi...@gmail.com wrote: Yep, that's what I generally do. Almost all alchemical changes involve a difference in two calculations (since the alchemical change itself is unphysical). Even one-calculation solvation free energy calculations are actually calculating the difference in free energy from liquid to vapor state. This reminds me: there was recently a discussion around couple-moltype on this list. My understanding is that this can be used for absolute free energies. But what I really want to make sure is this: as far as I can see in the code and I think the manual says that too is that when couple-moltype is not set in the .mdp none of the other couple- parameters have any effect should I set any of the to something. Do I get this right? Many thanks for the answers, Hannes. On Tue, May 19, 2015 at 11:58 AM, Hannes Loeffler hannes.loeff...@stfc.ac.uk wrote: On Tue, 19 May 2015 11:37:11 -0400 Michael Shirts mrshi...@gmail.com wrote: somewhat off-topic but I wonder why in your free energy protocol you only vary the vdW and electrostatic lambdas. What about the others? Your mutation also transforms bonded terms and masses. Minor point - if you are taking the difference between two mutations (say, with and without a ligand), then it's better to leave the masses untouched -- any contribution will cancel. There are some weird issues with changing masses in the constraint terms and their contribution to the free energies that need to be accounted for post-hoc. So you suggest to leave the mass lambdas simply at their initial (or final) value to be safe in case constraints are involved (and I am too lazy to check)? -- 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.
Re: [gmx-users] Compiling GROMACS 5.0.5 on Fujitsu PRIMEHPC FX-10
Hi, Thanks, sorry about that. We'll fix that for next release. You can simply remove the call on line 472 of src/gromacs/mdlib/tpi.c Mark On Tue, May 19, 2015 at 5:59 PM Duy Tran Phuoc tranpdu...@gmail.com wrote: Hi everyone, I try to compile GROMACS 5.0.5 on Fujitsu PRIMEHPC FX-10 with the command from installation instruction page http://www.gromacs.org/Documentation/Installation_Instructions_5.0#linear-algebra-libraries I use the Fujitsu compiler with the custom build toolchain as suggestion from the GROMACS webpage. The command is: ~/software/cmake/bin/cmake ../ -DCMAKE_INSTALL_PREFIX=/home/k0055/k005503/software/gromacs -DGMX_MPI=ON -DCMAKE_TOOLCHAIN_FILE=../cmake/Platform/Toolchain-Fujitsu-Sparc64-mpi.cmake -DCMAKE_PREFIX_PATH=/usr/local/fftw/3.3 -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_RELAXED_DOUBLE_PRECISION=ON But unfortunately, I got this message after running make. ../../lib/libgromacs_mdrun_mpi_d.a(tpi.c.o): In function `do_tpi': tpi.c:(.text+0x2130): undefined reference to `gmx_simd_check_and_reset_overflow' make[2]: *** [bin/mdrun_mpi_d] Error 1 make[1]: *** [src/programs/CMakeFiles/mdrun.dir/all] Error 2 make: *** [all] Error 2 Is there any suggestion on this problem? Thank you a lot. -- 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.
Re: [gmx-users] g_clustsize
Hi, No, but you can probably use -mcn to get an index group of the atoms, and work backwards from there. See gmx clustsize -h Mark On Tue, May 19, 2015 at 6:07 PM pratibha kapoor kapoorpratib...@gmail.com wrote: Hi, I have used g_clustsize to count the number of molecules (they differ by chain id) in the maximum populated cluster. Is it also possible to label these molecules? i.e. to print chain ids of these molecules with time in separate file? Thanks in advance -- 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.
