[gmx-users] How to set a system consists of membranes and cholestrols
Dear gmx_users, Hello, I want to simulate membrane system that contains lipids, cholestrols and glycolipids. Is there any suggestions, advice and some useful links? Best regards, Batsaikhan -- 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] Can I use gromos43a1p-4.5.1.tar.gz in gromacs5.0?
Dear Gmx users, I want to simulate a protein which has phosphorelated residues. Can I use gromos43a1p-4.5.1.tar.gz in gromacs5.0 or 4.6? I have got following error: Program pdb2gmx, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/kernel/pgutil.c, line: 126 Fatal error: Residue 2000697817 named THR of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Best regards, Batsaikhan -- 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] How much different run (with posre.itp) from no posre.itp?
Dear gmx-users, I run 3 different conformation of a protein. I run 2 of them no posre.itp and another one has posre.itp. How much different these two run? Sincerely, Batsaikhan -- 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] How long run should be enough for Free Energy Calculation of a protein?
I want to calculate free energy of 2 different types of 71 amino acids long protein. I run General Equilibration (NPT). Then I run free energy calculation of 200 ps. When calculation start, I got following warming message: ** WARNING: Listed nonbonded interaction between particles 27 and 159 at distance 2.056 which is larger than the table limit 2.029 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. *** Question: Is these calculation reliable? Best regards, Batsaikhan On Sunday, October 19, 2014 2:31 PM, Batdorj Batsaikhan batsaikhan...@yahoo.com wrote: Dear gmx user, please give me advice about above calculations. Thanks. Batsaikhan On Thursday, October 16, 2014 2:51 PM, Batdorj Batsaikhan batsaikhan...@yahoo.com wrote: I want to calculate free energy of 2 different types of 71 amino acids long protein. I run General Equilibration (NPT). Then I run free energy calculation of 200 ps. When calculation start, I got following warming message: ** WARNING: Listed nonbonded interaction between particles 27 and 159 at distance 2.056 which is larger than the table limit 2.029 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. *** Question: Is these calculation reliable? Best regards, Batsaikhan On Wednesday, October 15, 2014 7:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/14/14 11:37 PM, Batdorj Batsaikhan wrote: Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? How is it that you're attempting to calculate this quantity? -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] How long run should be enough for Free Energy Calculation of a protein?
Dear gmx user, please give me advice about above calculations. Thanks. Batsaikhan On Thursday, October 16, 2014 2:51 PM, Batdorj Batsaikhan batsaikhan...@yahoo.com wrote: I want to calculate free energy of 2 different types of 71 amino acids long protein. I run General Equilibration (NPT). Then I run free energy calculation of 200 ps. When calculation start, I got following warming message: ** WARNING: Listed nonbonded interaction between particles 27 and 159 at distance 2.056 which is larger than the table limit 2.029 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. *** Question: Is these calculation reliable? Best regards, Batsaikhan On Wednesday, October 15, 2014 7:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/14/14 11:37 PM, Batdorj Batsaikhan wrote: Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? How is it that you're attempting to calculate this quantity? -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.
[gmx-users] Free energy calculation of
Dear gxm users, Now I am doing solvation free energy of a protein, I follow Sander Pronk's tutorial downloaded from Gromacs page. 1. How do I check system is equilibrated? 2. I run following command sh mklambdas.sh run.mdp topol.top equil.gro I got following error: mklambdas.sh: 12: mklambdas.sh: Syntax error: ( unexpected How can I fix this? Best regards, Batsaikhan -- 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] How long run should be enough for Free Energy Calculation of a protein?
Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? Batsaikhan -- 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] Can I calculate free energy of Tutorial 1 of Justin's tutorials?
Dear gmx users, Can I calculate free energy of Tutorial 1 of Justin's tutorials? Batsaikhan -- 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] Can I simulate heavy atoms in my system?
Dear gmx users, I want to check interaction between heavy atoms (Hg, Pb etc.) and a protein. Can I simulate heavy atoms in our system? Thank you. Best regards, Batsaikhan -- 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] do_dssp result over written on the one line
Dear gmx users, I done secondary structure analysis using do_dssp. then I converted xpm file to eps. following commands: $ gmx do_dssp -s md3.tpr -f md.xtc -o ss.xpm -tu ns -sss -xvg $ xpm2ps -f ss.xpm -o ss.eps but result of ss.eps is written on the one line. How to fix it? when I open ss.eps file I typed ghostscript ss.eps. Best regards, Batsaikhan -- 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] do_dssp result over written on the one line
Thank you Justin, It is working but how can I adjust x-axis. My figure y-axis is ok, and x-axis has not time. Best regards, Batsaikhan On Saturday, August 16, 2014 10:00 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/16/14, 7:30 AM, Batdorj Batsaikhan wrote: Dear gmx users, I done secondary structure analysis using do_dssp. then I converted xpm file to eps. following commands: $ gmx do_dssp -s md3.tpr -f md.xtc -o ss.xpm -tu ns -sss -xvg $ xpm2ps -f ss.xpm -o ss.eps but result of ss.eps is written on the one line. How to fix it? You need to increase the size of the y-axis relative to x by using an .m2p file with a suitable ybox/xbox ratio. The default output is generally very distorted because there are orders of magnitudes more frames (x-axis) than there are protein residues (y-axis) in most simulations. http://manual.gromacs.org/online/m2p.html -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 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] Can I delete trr file?
Thank you Justin. On Saturday, August 9, 2014 5:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/8/14, 10:58 PM, Batdorj Batsaikhan wrote: Dear gmx users, I am new user of gromacs. Our calculations are running, but we have a problem that has not enough disk space. Therefore I need to delete some file that are unimportant for analysis. Is there any analysis use trr file? Can I delete trr file? Not while mdrun is running; that will kill the run. The most important part of the run is the trajectory, so if you delete the .trr you'd better have the .xtc as well, otherwise there was no point in doing the simulation. Better planning (in terms of frequency for saving frames) and paying attention to what grompp tells you about how much data will be generated pay off here. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 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.
[gmx-users] Can I delete trr file?
Dear gmx users, I am new user of gromacs. Our calculations are running, but we have a problem that has not enough disk space. Therefore I need to delete some file that are unimportant for analysis. Is there any analysis use trr file? Can I delete trr file? Best regards, Batsaikhan -- 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] What files should I delete after simulation?
Dear Users, I have subsequent simulations of MD. I need to delete some unimportant files for analyses. What files should I delete? Best regards, Batsaikhan -- 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] How to add multiple simulations?
Dear all, I have each of 10 ns five simulations which were subsequently run. How can I join these simulations? Best regards, Batsaikhan -- 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] How can I add subsequent simulations?
Dear all, I have each of 10 ns five simulations which were subsequently run. How can I join these simulations? Best regards, Batsaikhan -- 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] What analysis do I need?
Dear all, I am new user, and I want to analyze conformation change of protein using MD. If you do not mind give me advice. What analysis do I need? How to use do_dssp? Thank you. Batsaikhan -- 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] How to fix protein went out water?
Dear gmx_users, I am working on simulation of protein in water. 10 ns after the protein went out from water. How to fix this? Can I continue my simulation? Best regards, Batsaikhan -- 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] How to fix protein went out water?
Thank you Justin and Thales. Best regards, Batsaikhan On Tuesday, June 17, 2014 11:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/17/14, 10:54 AM, Thales Kronenberger wrote: Hi Batsaikhan You should re-do the simulation, perfoming it within a box of water with PBC (you can do this with the editconf) There is no need to re-do anything. PBC means it is totally irrelevant whether the protein is conveniently centered in the box or not; the forces are the same. The protein drifting outside the box is a total non-issue, since there is no such thing as outside of a periodic system. All one needs to do is apply trjconv for convenient visualization, and no action needs to be taken to continue the run; mdrun doesn't care about our conventions for watching the trajectory. -Justin Kind regards Thales 2014-06-17 8:56 GMT-03:00 Batdorj Batsaikhan batsaikhan...@yahoo.com: Dear gmx_users, I am working on simulation of protein in water. 10 ns after the protein went out from water. How to fix this? Can I continue my simulation? Best regards, Batsaikhan -- 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 601 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] How to extend Amber FF parameters of Lipids
Dear gmx users, I would like to simulate lipid with a protein using AMBER force field. Have you any advice and useful links? Best regards, Batsaikhan -- 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] How to exit cluster during the simulation
Dear GMX users, I am a new user of gromacs on cluster. I use putty to connect to the cluster. I have a problem. How to exit cluster during the simulation? My last command is mpirun -np 8 mdrun_mpi ... in the past, I clicked X button of putty, mdrun did not finished. Thank you. -- 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] How to exit cluster during the simulation
Thank you. Also how to know cpu performance and resting time of simulation after exit. On Sunday, June 15, 2014 12:45 PM, 陈功 gchen...@gmail.com wrote: Seems like : nohup mpirun -np 8 mdrun_mpi -v -deffnm your_tpr output.info From: Batdorj Batsaikhan Date: 2014-06-15 11:53 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] How to exit cluster during the simulation Dear GMX users, I am a new user of gromacs on cluster. I use putty to connect to the cluster. I have a problem. How to exit cluster during the simulation? My last command is mpirun -np 8 mdrun_mpi ... in the past, I clicked X button of putty, mdrun did not finished. Thank you. -- 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.
