Re: [gmx-users] MD simullations with Morse potential
Hi Justin, Thanks very much for your reply! Regarding to your two explanations, I guess it might be the first one. I have also tried to do a simulation of a three-residue (Gly-Ser-Asn) system with water, but it still did not work. Could you also give some test for this morse potential? Thanks very much! All the best, Qinghua On 04/26/2014 12:31 AM, Justin Lemkul [via GROMACS] wrote: On 4/25/14, 5:37 PM, fantasticqhl wrote: Dear Justin, Thanks very much for your reply! I guess the use of the Parrinello-Rahman barostat should not be a problem because the optimization ran successfully if I turned off the morse potential. Actually, I have already done the nvt optimization without morse potential before I moved to npt optimization with morse potential, the error was the same for nvt with morse potential. I just do not know why the morse potential was not working. Do you have some other ideas which may result in the problem? Thanks very much! Well, Morse potentials aren't the functional form with which any of the biomolecular force fields in Gromacs were parametrized, so either (1) there's a bug that needs to be fixed or (2) you're doing something incompatible and the model physics is breaking down. -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 [hidden email] /user/SendEmail.jtp?type=nodenode=5016073i=0 | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul http://mackerell.umaryland.edu/%7Ejalemkul == -- 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 [hidden email] /user/SendEmail.jtp?type=nodenode=5016073i=1. If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/MD-simullations-with-Morse-potential-tp5016062p5016073.html To unsubscribe from MD simullations with Morse potential, click here http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5016062code=ZmFudGFzdGljcWhsQGdtYWlsLmNvbXw1MDE2MDYyfDE5NzE0ODU3Nzc=. NAML http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://gromacs.5086.x6.nabble.com/MD-simullations-with-Morse-potential-tp5016062p5016087.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] MD simullations with Morse potential
Hi Tsjerk, Thanks! Is morse potential working for you? I am using Gromos 53a6 force field with spc water, and the Gromacs version is 4.5.4, and I also tried 4.6.5. I just tried to do a simulation for just one residue (Gly) with water. However, all tests were not working! Could you tell me how you did the equilibrations? Thanks very much! All the best, Qinghua On 04/27/2014 11:30 AM, Tsjerk Wassenaar [via GROMACS] wrote: Hi Qinghua, I have run simulations with morse bonds a while back, in combination with the Gromos 45a3 force field. I only had a few of those bonds, though. Which Gromacs version are you using and which force field? Cheers, Tsjerk On Apr 27, 2014 10:44 AM, fantasticqhl [hidden email] /user/SendEmail.jtp?type=nodenode=5016089i=0 wrote: -- View this message in context: http://gromacs.5086.x6.nabble.com/MD-simullations-with-Morse-potential-tp5016062p5016090.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] NPT simulation stage
dear justin Thank you for your reply. My system is about 123,000 atoms and my box is cubic. I'm following conditions apply: pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com But the average pressure is not good repeatability. To fix this problem I did two NPT simulation stageThe first 100ps by brendsand barostat then 100ps by Parrinello-Rahman barostatbut Still not good repeatability. I frequently change tau_p but I did not get any results. Increase the NPT simulation time did not solve the problem. I strongly need your help Thank you sincerely for your kindness On Friday, April 25, 2014 5:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/25/14, 2:36 AM, Mahboobeh Eslami wrote: hi GMX users please help me i want to simulate protein-ligand complex by gromacs4.6.5 when i repeat NPT simulation stage many times, simulation results are very different for the pressure average.I sincerely thank you for your guidance Pressure is probably the most ill-defined quantity in MD simulations. It can fluctuate dramatically. Without the actual numbers, it's hard to comment, but issues related to pressure have been discussed extensively over the list in the past and there is useful information in http://www.gromacs.org/Documentation/Terminology/Pressure. -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] make install creating infinite recursive directories: addendum
OK. The GROMACS developers intended the user to follow normal practice, such as doing the build in user space in the file system, and then installing as root, and installing to somewhere other than the source tarball location. Unpacking a source tarball in /opt and building from there (as root or not) is asking for various kinds of trouble. That (apparently) CMake gets confused by the source and install directory being the same comes under the heading of not our problem ;-) I will try to remember to add don't install to your tarball location to the install guide when next I update it. Cheers, Mark On Sun, Apr 27, 2014 at 10:46 AM, Harry Mark Greenblatt harry.greenbl...@weizmann.ac.il wrote: BSD Dear All, It seems the problem of creating recursive .../share/gromacs/ directories during the make install step occurs only when the target install directory is the original un-tarred directory. Thus, if the tar file is unpacked in /opt, and so generates, for example, /opt/gromacs-4.6.5, and this directory is specified as CMAKE_INSTALL_PREFIX, the problem arises. If, however, one specifies a different directory for CMAKE_INSTALL_PREFIX, such as /opt/gromacs465, the make install step has no problem. I don't know if this what the developers intended, but this was not an issue in 4.5.x. Harry - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenbl...@weizmann.ac.il mailto:arry.greenbl...@weizmann.ac.il Weizmann Institute of SciencePhone: 972-8-934-3625 234 Herzl St.Facsimile: 972-8-934-4159 Rehovot, 76100 Israel -- 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] make install creating infinite recursive directories: addendum
BSD Dear Mark, OK. The GROMACS developers intended the user to follow normal practice, such as doing the build in user space in the file system, and then installing as root, and installing to somewhere other than the source tarball location. Unpacking a source tarball in /opt and building from there (as root or not) is asking for various kinds of trouble. That (apparently) CMake gets confused by the source and install directory being the same comes under the heading of not our problem ;-) Well, interestingly enough, the CMake package itself didn't have a problem installing into its own directory. Anyhow, at least the resolution of the problem is pretty straightforward. Thanks Harry - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenbl...@weizmann.ac.ilmailto:arry.greenbl...@weizmann.ac.il Weizmann Institute of SciencePhone: 972-8-934-3625 234 Herzl St.Facsimile: 972-8-934-4159 Rehovot, 76100 Israel -- 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] NPT simulation stage
On 4/27/14, 6:03 AM, Mahboobeh Eslami wrote: dear justin Thank you for your reply. My system is about 123,000 atoms and my box is cubic. I'm following conditions apply: pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 refcoord_scaling = com But the average pressure is not good repeatability. To fix this problem I did two NPT simulation stage The first 100ps by brendsand barostat then 100ps by Parrinello-Rahman barostatbut Still not good repeatability. I frequently change tau_p but I did not get any results. Increase the NPT simulation time did not solve the problem. I strongly need your help Thank you sincerely for your kindness What I was asking for previously were the actual results - i.e. what values of pressure you achieved. Please provide the exact g_energy output. When you increased the time, how long were the new runs? 100 ps is fairly short for any NPT process. Some systems may take a few ns to converge, depending on what their contents are. -Justin On Friday, April 25, 2014 5:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/25/14, 2:36 AM, Mahboobeh Eslami wrote: hi GMX users please help me i want to simulate protein-ligand complex by gromacs4.6.5 when i repeat NPT simulation stage many times, simulation results are very different for the pressure average.I sincerely thank you for your guidance Pressure is probably the most ill-defined quantity in MD simulations. It can fluctuate dramatically. Without the actual numbers, it's hard to comment, but issues related to pressure have been discussed extensively over the list in the past and there is useful information in http://www.gromacs.org/Documentation/Terminology/Pressure. -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 mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- == 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] NPT simulation stage
Hi Lemkul, I am trying to simulate guanidium in water. My system contains 198 guanidium residues. But when I'm trying to use the grompp command ,I'm facing the problem of fudgeQQ, qi ,qj. I don't know what that means. I don't know how to rectify the error too. Plus if there are too many solvet molecules, how do I delete it ? Thanks, Swetha 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: Sunday, April 27, 2014 9:17 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] NPT simulation stage On 4/27/14, 6:03 AM, Mahboobeh Eslami wrote: dear justin Thank you for your reply. My system is about 123,000 atoms and my box is cubic. I'm following conditions apply: pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 refcoord_scaling = com But the average pressure is not good repeatability. To fix this problem I did two NPT simulation stage The first 100ps by brendsand barostat then 100ps by Parrinello-Rahman barostatbut Still not good repeatability. I frequently change tau_p but I did not get any results. Increase the NPT simulation time did not solve the problem. I strongly need your help Thank you sincerely for your kindness What I was asking for previously were the actual results - i.e. what values of pressure you achieved. Please provide the exact g_energy output. When you increased the time, how long were the new runs? 100 ps is fairly short for any NPT process. Some systems may take a few ns to converge, depending on what their contents are. -Justin On Friday, April 25, 2014 5:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/25/14, 2:36 AM, Mahboobeh Eslami wrote: hi GMX users please help me i want to simulate protein-ligand complex by gromacs4.6.5 when i repeat NPT simulation stage many times, simulation results are very different for the pressure average.I sincerely thank you for your guidance Pressure is probably the most ill-defined quantity in MD simulations. It can fluctuate dramatically. Without the actual numbers, it's hard to comment, but issues related to pressure have been discussed extensively over the list in the past and there is useful information in http://www.gromacs.org/Documentation/Terminology/Pressure. -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 mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- == 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.
Re: [gmx-users] guanidinium in water
Hi Lemkul, genbox -cp test.gro -cs spc216.gro -box 24 24 24 -o watGND.gro Actually I want to do a simulation for 7M concentration. So, since the conc of 3M is already done, I did a small calculation of mass of 3M/avogadro number = 7M* Mixed mass(Mgnd+Mcl/ratio)*V .From this,I got the volume.From this, the box size was 24 24 24 . Thus I used this in the genbox. Output configuration contains 1384837 atoms in 461568 residues Volume : 13824 (nm^3) Density: 998.941 (g/l) Number of SOL molecules: 461549 Next,grompp command grompp -f ions.mdp -c watGND.gro -p system.top -o ions.tpr My system.top file #include gromos43a1.ff/forcefield.itp #include spc.itp #include gnd.itp [ molecule ] ; Name guanidium in water [ molecule ] ; Compound#molecule GND 19 SOL 461549 CL-38 ~ My ions.mdp file ions.mdp - used as input into grompp to generate ions.tpr ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 0 ; For exact run continuation or redoing part of a run init_step= 0 ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 10 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 grompp -f ions.mdp -c watGND.gro -p system.top -o ions.tpr Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1631 Fatal error: Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This is the trouble Im facing. Hoping for a positive reply soon. Regards, Swetha 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: Sunday, April 27, 2014 11:38 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] guanidinium in water Please don't hijack an unrelated thread with a new question. I am re-titling this message; in the future, just send a new email when you have a new question. On 4/27/14, 11:11 AM, Swetha Srinivasan wrote: Hi Lemkul, I am trying to simulate guanidium in water. My system contains 198 guanidium residues. But when I'm trying to use the grompp command ,I'm facing the problem of fudgeQQ, qi ,qj. I don't know what that means. I don't know how to rectify the error too. Plus if there are too many solvet molecules, how do I delete it ? FudgeQQ is explained in the manual. Beyond that, you need to provide more details. What is in your topology? Did you create it yourself, or did you get it from some other source? What is the *exact* error message from grompp (copied and pasted from the terminal)? As for solvent removal, you'll have to tell us how you added solvent in the first place. Presumably this was done with genbox, in which case you can use -maxsol, but that's often not a good idea because it will leave voids in the simulation box. If the box is too large, you'll have to set up an appropriate one with editconf (or possibly genbox, but I'm still guessing here because you haven't provided any of your commands). -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. -- 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] guanidinium in water
On 4/27/14, 11:57 AM, Swetha Srinivasan wrote: Hi Lemkul, genbox -cp test.gro -cs spc216.gro -box 24 24 24 -o watGND.gro Actually I want to do a simulation for 7M concentration. So, since the conc of 3M is already done, I did a small calculation of mass of 3M/avogadro number = 7M* Mixed mass(Mgnd+Mcl/ratio)*V .From this,I got the volume.From this, the box size was 24 24 24 . Thus I used this in the genbox. Gromacs uses nm for all lengths and distances; I strongly suspect you assumed it was A. The topology section below definitely does not correspond to 7 M. Output configuration contains 1384837 atoms in 461568 residues Volume : 13824 (nm^3) Density: 998.941 (g/l) Number of SOL molecules: 461549 Next,grompp command grompp -f ions.mdp -c watGND.gro -p system.top -o ions.tpr My system.top file #include gromos43a1.ff/forcefield.itp #include spc.itp #include gnd.itp [ molecule ] ; Name guanidium in water [ molecule ] ; Compound#molecule GND 19 SOL 461549 CL-38 ~ My ions.mdp file ions.mdp - used as input into grompp to generate ions.tpr ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 0 ; For exact run continuation or redoing part of a run init_step= 0 ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 10 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 grompp -f ions.mdp -c watGND.gro -p system.top -o ions.tpr Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1631 Fatal error: Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This is the trouble Im facing. Hoping for a positive reply soon. OK, so you're specifying type-2 pairs. Again I ask: what is the source of this topology? Do you really intend to use this interaction? This pair type is rather unusual and requires you to specify van der Waals parameters (V, W) and charges (qi, qj), as well as fudge factor for the interactions (fudgeQQ) - hence 5 parameters. -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] (no subject)
Hi Lemkul, If you tell me the exact steps I need to follow,I would be able to execute it. Please help me out with this. Thanks, Swetha -- 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] (no subject)
Hi lemkul, How do I correct the topology file? And which file is it? Thanks, Swetha -- 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] guanidinium in water
Hi Lemkul, How do I correct this.Could you please help me? Thanks, Swetha 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: Sunday, April 27, 2014 12:25 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] guanidinium in water On 4/27/14, 12:20 PM, Swetha Srinivasan wrote: Hi Lemkul, I had already used a rhein-water system before. I just edited that and gave my inputs. I don't really know what that means, but the bottom line is you have an incorrectly formatted line in the topology. It's under [pairs], it's function type 2, and it doesn't specify parameters correctly. See manual section 5.3.4. -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. -- 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] guanidinium in water
Please don't spam the list with repeated pleas for help. Realize that this is an international mailing list with hundreds (or more) subscribers who give of their free time to help. I'm not going to be able to instantly answer all of your emails within minutes. I'll answer this most recent one with whatever information I can. On 4/27/14, 1:02 PM, Swetha Srinivasan wrote: Hi Lemkul, How do I correct this.Could you please help me? The error is in the topology. You still haven't given any evidence of how you made it, why you're using this type of interaction, or what atoms it applies to. Hint: post the content of the topology. If you don't know what a topology is, you should stop what you're doing immediately and work through as many tutorials as you can find. Time spent learning proper techniques will save you potentially months of wasted work based on whatever you might have done incorrectly. To create a mixture of guanidinium in water, you can follow the protocol described here: http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents. It's a very standard thing to do. Constructing the system is the easy part; defining the topology is a much harder thing to do, though guanidinium should have a fairly easily defined topology since it is part of the Arg side chain. -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] g_dipoles
Hello, I run g_dipoles for two different systems (System are ionic liquids). For one system when I run g_dipoles I get following message There are 256 molecules in the selection There are 256 charged molecules in the selection, will subtract their charge at their center of mass and I don't get this message for other system. Why program subtract their charge at their center of mass for one system and not for other. Nilesh -- 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_dipoles
On 4/27/14, 4:01 PM, Nilesh Dhumal wrote: Hello, I run g_dipoles for two different systems (System are ionic liquids). For one system when I run g_dipoles I get following message There are 256 molecules in the selection There are 256 charged molecules in the selection, will subtract their charge at their center of mass and I don't get this message for other system. Why program subtract their charge at their center of mass for one system and not for other. Based on whatever the topology says, g_dipoles doesn't find a net charge on whatever these molecules are. Without providing more information - what the molecules/selections are, what the topology(ies) is(are) - that's all that can be surmised at this point. -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] g_dipoles
On 4/27/14, 4:25 PM, Nilesh Dhumal wrote: On 4/27/14, 4:01 PM, Nilesh Dhumal wrote: Hello, I run g_dipoles for two different systems (System are ionic liquids). For one system when I run g_dipoles I get following message There are 256 molecules in the selection There are 256 charged molecules in the selection, will subtract their charge at their center of mass and I don't get this message for other system. Why program subtract their charge at their center of mass for one system and not for other. Based on whatever the topology says, g_dipoles doesn't find a net charge on whatever these molecules are. Without providing more information - what the molecules/selections are, what the topology(ies) is(are) - that's all that can be surmised at this point. -Justin There are 128 cations (EMI) and 128 anions (ETS). Total charge is ZERO here is molecular section from topology file. [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 #include emi.itp #include ets.itp [ molecules ] ; Compound#mols EMI128 ETS128 You said you had two different systems. What's the difference between them? -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] g_dipoles
On 4/27/14, 4:25 PM, Nilesh Dhumal wrote: On 4/27/14, 4:01 PM, Nilesh Dhumal wrote: Hello, I run g_dipoles for two different systems (System are ionic liquids). For one system when I run g_dipoles I get following message There are 256 molecules in the selection There are 256 charged molecules in the selection, will subtract their charge at their center of mass and I don't get this message for other system. Why program subtract their charge at their center of mass for one system and not for other. Based on whatever the topology says, g_dipoles doesn't find a net charge on whatever these molecules are. Without providing more information - what the molecules/selections are, what the topology(ies) is(are) - that's all that can be surmised at this point. -Justin There are 128 cations (EMI) and 128 anions (ETS). Total charge is ZERO here is molecular section from topology file. [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 #include emi.itp #include ets.itp [ molecules ] ; Compound#mols EMI128 ETS128 For other system I have different anion. I didn't specify the number of residues in molecular section. [ system ] ; Name Grunge ROck MAChoS t= 2.0 [ molecules ] ; Compound#mols Ion 1 Nilesh You said you had two different systems. What's the difference between them? -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. -- 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] SWCNT interaction with the outside of an ion channel
Hi dear gromacs users, I am planning to study the interaction between a SWCNT and the outside of an ion channel, in order to do this i am preparing a Umbrella Sampling Simulation, were i put the CNT, (3nm or 2nm) from the ion channel's pore, and the CNT axis is parallel to the pore axis, in order to compute the PMF between the CNT and the external residues of the ion channel , in order to do this i was thinking first just run unconstrained MD of the CNT and understand the potential energy surface, and then run the US using constraints XY (Z axis) due to CNT might move or should i not use constraints at running US ? , I was wondering if you could give me some advice about this, it is my point of view well think? or should i think in a different methodology ? Thank you in advance Andrés -- View this message in context: http://gromacs.5086.x6.nabble.com/SWCNT-interaction-with-the-outside-of-an-ion-channel-tp5016110.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] constraint center of mass
Dear Gmx Users, Is there a way to constraint a protein's center of the mass (COM) at certain (X, Y, Z) position? Thanks! Thoms -- 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] LINCS warning
Dear Gromacs user, After I give the command for nvt, I get the following error: starting mdrun 'Protein in water' 15 steps,300.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.410417, max 7.601056 (between atoms 188 and 192) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 177179 40.70.1342 0.2195 0.1330 179181 69.60.1484 0.2977 0.1470 179180 51.10.1005 0.1744 0.1000 181195 75.80.1543 0.2575 0.1530 181182 77.00.1549 0.6596 0.1530 182183 47.80.1549 0.3570 0.1530 183186 76.80.1407 1.1049 0.1390 183184 76.10.1406 0.9974 0.1390 186187 69.80.1097 0.3696 0.1090 188192 79.10.1403 1.1955 0.1390 188189 72.00.1099 0.3759 0.1090 190192 77.90.1404 1.1212 0.1390 190191 71.50.1099 0.3818 0.1090 195197 34.80.1345 0.1997 0.1330 195196 39.90.1237 0.1807 0.1230 4571 4569 40.00.1404 0.0953 0.1400 4570 4569 91.20.1245 0.1846 0.1230 4572 4571 31.30.1005 0.1253 0.1000 184188 41.10.1397 0.2396 0.1390 184185 72.10.1097 0.4012 0.1090 193194 82.90.1015 0.6012 0.1000 Wrote pdb files with previous and current coordinates step 0 Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2524.656192, max 85802.020979 (between atoms 170 and 177) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 170177 81.90.1793 13127.8622 0.1530 177179 94.90.2195 12873.2695 0.1330 179181 88.60.2977 4411.0838 0.1470 181195 96.60.2575 963.1998 0.1530 195197 87.40.1997 250.2422 0.1330 195196 80.60.1807 246.3256 0.1230 181182 83.50.6596 33817.6412 0.1530 182183 90.90.3570 1629245.5886 0.1530 179180 150.70.1744 806.4780 0.1000 177178 86.50.1487 13025.8466 0.1230 170171 123.70.1636 1099.0521 0.1530 172174 112.90.1334 124.2084 0.1330 172173 119.80.1234 122.9154 0.1230 174176 41.30.1000 19.2568 0.1000 141149 30.50.1530 0.1924 0.1530 149151 125.20.1330 18.9674 0.1330 149150 34.10.1230 0.1614 0.1230 151153 35.80.1471 28.7745 0.1470 151152 83.30.1000 18.9746 0.1000 166167 115.50.1238 341.2685 0.1230 153166 117.80.1538 365.5008 0.1530 153154 37.00.1531 14.8979 0.1530 154155 90.80.1530 15.6791 0.1530 155158 33.40.1390 0.1782 0.1390 155156 32.80.1390 0.1771 0.1390 168170 141.40.1596 1274.6369 0.1470 168169 93.70.1015 232.5375 0.1000 Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 12958124.333813, max 292691795.227618 (between atoms 184 and 188) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 203204 32.10.1470 0.1744 0.1470 201202 74.00.1532 1.1957 0.1530 202203 117.70.1530 0.3991 0.1530 208210 59.20.1359 3.5580 0.1330 208209 73.20.1256 1.9933 0.1230 210212 74.80.1480 1.9178 0.1470 210211 93.80.1007 1.5815 0.1000 177179 94.90.2195 12873.2691 0.1330 177178 86.50.1487 13025.8467 0.1230 170177 81.90.1793 13127.8623 0.1530 170171 123.70.1636 1099.0521 0.1530 172174 112.90.1334 124.2084 0.1330 174176 41.30.1000 19.2568 0.1000 172173 119.80.1234 122.9154 0.1230 168170 141.40.1596 1274.6369 0.1470 168169 93.70.1015 232.5375 0.1000 166167 115.50.1238 341.2681 0.1230 153166 117.80.1538 365.5039 0.1530 153154 37.00.1531 14.8978 0.1530 151153 35.80.1471 28.7776 0.1470 179181 88.60.2977 4411.0814 0.1470 179180 150.70.1744 806.4798 0.1000 212217 118.10.1531 1.2961 0.1530 212213 109.40.1531 1.3254 0.1530 213214 39.00.1530 0.2085 0.1530 155156 32.80.1390 0.1771 0.1390 155158 33.40.1390 0.1782 0.1390 154155 90.80.1530 15.6794 0.1530 151
