Re: [gmx-users] Free energy change with harmonic restraints
This may be of help: http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Natalie Nguyen [nguy...@wittenberg.edu] Sent: 09 July 2015 14:19 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Free energy change with harmonic restraints Dear Asaf, Thank you for the quick reply! I was wondering if it was possible to use thermodynamic integration to represent growing harmonic restraints aside from using an analytical method. I will cite this article most definitely! Natalie Nguyen From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of asaffa...@post.tau.ac.il asaffa...@post.tau.ac.il Sent: Thursday, July 09, 2015 7:45 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Free energy change with harmonic restraints Dear Natalie, You have in http://xxx.tau.ac.il/pdf/1502.07196v3.pdf exact free energy of harmonic covalent bond and bond angle terms (or restrains). See Eqs. (2) and (3). There are also previous studies in the references there. For the dihedral term I assume it can also be calculated exactly (I might upload it). There is also to think if there are other contributions. If you are using it please cite. Best regards, Asaf Quoting Natalie Nguyen nguy...@wittenberg.edu: Dear all, I am trying to measure the free energy change associated with adding/removing harmonic restraints imposed on a ligand that is attached to a protein. Is there any way to set this up? Thank you ahead of time! Natalie Nguyen -- 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] Free energy change with harmonic restraints
The equations in the articles are relevant for the step Removal of Restraints in that link. Please note that these equations have been verified in http://arxiv.org/abs/1501.01514 Best regards, Asaf Quoting hannes.loeff...@stfc.ac.uk: This may be of help: http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Natalie Nguyen [nguy...@wittenberg.edu] Sent: 09 July 2015 14:19 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Free energy change with harmonic restraints Dear Asaf, Thank you for the quick reply! I was wondering if it was possible to use thermodynamic integration to represent growing harmonic restraints aside from using an analytical method. I will cite this article most definitely! Natalie Nguyen From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of asaffa...@post.tau.ac.il asaffa...@post.tau.ac.il Sent: Thursday, July 09, 2015 7:45 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Free energy change with harmonic restraints Dear Natalie, You have in http://xxx.tau.ac.il/pdf/1502.07196v3.pdf exact free energy of harmonic covalent bond and bond angle terms (or restrains). See Eqs. (2) and (3). There are also previous studies in the references there. For the dihedral term I assume it can also be calculated exactly (I might upload it). There is also to think if there are other contributions. If you are using it please cite. Best regards, Asaf Quoting Natalie Nguyen nguy...@wittenberg.edu: Dear all, I am trying to measure the free energy change associated with adding/removing harmonic restraints imposed on a ligand that is attached to a protein. Is there any way to set this up? Thank you ahead of time! Natalie Nguyen -- 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx error residue not found in residue topology database
Thank You Mr. Peter I just checked your response and that really helps. Gaussian allows you to save the file in different format(.pdb inclusive), I just choosed to save in .pdb format. I don’t know if I did the right thing. hahaha... On Jul 9, 2015, at 8:17 PM, su sun.i...@gmail.com wrote: Peter, This question was for Ali.H.. Sent from my iPhone On 09-Jul-2015, at 5:20 pm, Peter Stern peter.st...@weizmann.ac.il wrote: I never did that. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of su Sent: Wednesday, July 08, 2015 11:26 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] pdb2gmx error residue not found in residue topology database How you converted the gaussian file into .pdb? Because once i did the same and suffered from some missing co ordinates. Sent from my iPhone On 08-Jul-2015, at 11:16 pm, Peter Stern peter.st...@weizmann.ac.il wrote: Look at the file: residuetypes.dat in the ../top/ directory of your installation. It lists all the residue names and more. Peter Stern Weizmann Institute Sent from my iPad On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd hamisu.kaza...@yahoo.com wrote: Dear gmx-users, I am really new in this field of endeavour and I am trying investigate the solubility of peptides in organic solvents, I built a simple tripeptide (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to .pdb. I am now trying to use pdb2gmx tool to generate topology for my peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was promoted with an error residue not found in residue topology database” I checked GROMACS website at http://www.gromacs.org/Documentation/Errors I learned the residue must have the same name as in the force field, please I don’t know the naming convention of this force field please HELP. Thanks Ali H. Department of Chemistry University Dutse -- 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. -- 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] Free energy change with harmonic restraints
Dear Natalie, You are welcome. Could you please explain in more detail so maybe I can help? Do you want to change the strength of the restraints and measure the free energy difference associated with this change? Thanks. p.s there is also http://arxiv.org/pdf/1307.1620v7.pdf with the same equations. Best regards, Asaf Quoting Natalie Nguyen nguy...@wittenberg.edu: Dear Asaf, Thank you for the quick reply! I was wondering if it was possible to use thermodynamic integration to represent growing harmonic restraints aside from using an analytical method. I will cite this article most definitely! Natalie Nguyen From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of asaffa...@post.tau.ac.il asaffa...@post.tau.ac.il Sent: Thursday, July 09, 2015 7:45 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Free energy change with harmonic restraints Dear Natalie, You have in http://xxx.tau.ac.il/pdf/1502.07196v3.pdf exact free energy of harmonic covalent bond and bond angle terms (or restrains). See Eqs. (2) and (3). There are also previous studies in the references there. For the dihedral term I assume it can also be calculated exactly (I might upload it). There is also to think if there are other contributions. If you are using it please cite. Best regards, Asaf Quoting Natalie Nguyen nguy...@wittenberg.edu: Dear all, I am trying to measure the free energy change associated with adding/removing harmonic restraints imposed on a ligand that is attached to a protein. Is there any way to set this up? Thank you ahead of time! Natalie Nguyen -- 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] Free energy change with harmonic restraints
Dear Asaf, Thank you for the quick reply! I was wondering if it was possible to use thermodynamic integration to represent growing harmonic restraints aside from using an analytical method. I will cite this article most definitely! Natalie Nguyen From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of asaffa...@post.tau.ac.il asaffa...@post.tau.ac.il Sent: Thursday, July 09, 2015 7:45 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Free energy change with harmonic restraints Dear Natalie, You have in http://xxx.tau.ac.il/pdf/1502.07196v3.pdf exact free energy of harmonic covalent bond and bond angle terms (or restrains). See Eqs. (2) and (3). There are also previous studies in the references there. For the dihedral term I assume it can also be calculated exactly (I might upload it). There is also to think if there are other contributions. If you are using it please cite. Best regards, Asaf Quoting Natalie Nguyen nguy...@wittenberg.edu: Dear all, I am trying to measure the free energy change associated with adding/removing harmonic restraints imposed on a ligand that is attached to a protein. Is there any way to set this up? Thank you ahead of time! Natalie Nguyen -- 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] How to justify when the trajectory reached equilibrium
Thank you, Justin. I am trying to simulate a protein-ligand complex to see the conformation transition during the simulation... We propose that the receptor pocket may be subject to a conformational change upon ligand-binding, so I want to verify it by MD... I am really a newbie in molecular simulation and all I did to analysis were time evolution of RMSD, interaction energy, and visualization. I try to do some principal component analysis, but literature said that PCA must be performed after equilibrium... Could you give me more info on block-averaging, or any other advice that will help? Best, Qing At 2015-07-09 19:41:09, Justin Lemkul jalem...@vt.edu wrote: On 7/8/15 9:48 PM, Qing Lv wrote: Hi, I did a 70-ns MD simulation. I wonder how to justify when the trajectory reached equilibrium... Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and kept stable after that. Could I justify that the system reached equilibrium at 12 ns? Are there any methods/criteria to justify the equilibrium other than RMSD evolution? RMSD is pretty useless in telling you anything about convergence. Great, your structure probably isn't changing a whole lot (but RMSD can also hide interesting things). Assess convergence based on the quantities of interest - why did you do the simulation? What behavior are you trying to observe, and what measurables do you use to assess it? If those metrics are invariant with time (e.g. via block-averaging or something) then your simulation is likely converged. -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] after extending simulation
Dear all, I extend a simulation (GROMACS 5.0.5) with these command lines: convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr mdrun -s md_0_2.tpr -cpi md_0_1.cpt And now? What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation? Please help me! Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- 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] after extending simulation
So, I’m ok! I can read the only one .gro file created at the first simulation as the final .gro file after all extensions. That’s right? On Jul 9, 2015, at 7:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:49 PM, Andrea Spinelli wrote: I’m sorry, I miss something with cut and paste command. On terminal I wrote: gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt There is no gromacs coordinate file in VMD, I have to convert a md_0_2.tpr into try or try file? The contents of md_0_1.tpr and md_0_2.tpr are identical except that the latter contains a different number of steps. When providing mdrun with a .cpt file, it carries out the run from that point, so the starting point of the run (time = 0) is always the same. The final coordinates are always written to a .gro file unless you specify a different format (which your above command does not). Whatever that file is called depends on the first run (md_0_1), because the file names are stored in the .cpt file; they will be appended to by default. The final .gro file has an appended name rather than being overwritten, IIRC. -Justin On Jul 9, 2015, at 7:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:25 PM, Andrea Spinelli wrote: Dear all, I extend a simulation (GROMACS 5.0.5) with these command lines: convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr mdrun -s md_0_2.tpr -cpi md_0_1.cpt And now? Well, the above sequence of commands won't do anything because (1) it's gmx convert-tpr not just convert-tpr and (2) if you create next.tpr and try to run md_0_2.tpr then mdrun will exit. What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation? Load it like any coordinate file. -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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- == 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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- 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] Free energy change with harmonic restraints
Dear Asaf, Thank you again for putting in the time to respond to me so quickly. What I have been trying to do was start from a system that is not restrained and grow the restraints onto the ligand, measuring the change in free energy of this. The harmonic restraints used are that of the umbrella pull code with a force constant of k= 1000 kJ/mol*nm^2. It is mentioned In the Gromacs manual for mdp options that the pull code can be controlled with restraint-lambdas, but there is not much detail other than this. I imagine that lambda =0 would represent a nonexistent potential with k= 0 and at lambda = 1 a full strength potential would be imposed. Please feel free to ask me to add more detail! Warm regards, Natalie From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of asaffa...@post.tau.ac.il asaffa...@post.tau.ac.il Sent: Thursday, July 09, 2015 10:38 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Free energy change with harmonic restraints Dear Natalie, You are welcome. Could you please explain in more detail so maybe I can help? Do you want to change the strength of the restraints and measure the free energy difference associated with this change? Thanks. p.s there is also http://arxiv.org/pdf/1307.1620v7.pdf with the same equations. Best regards, Asaf Quoting Natalie Nguyen nguy...@wittenberg.edu: Dear Asaf, Thank you for the quick reply! I was wondering if it was possible to use thermodynamic integration to represent growing harmonic restraints aside from using an analytical method. I will cite this article most definitely! Natalie Nguyen From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of asaffa...@post.tau.ac.il asaffa...@post.tau.ac.il Sent: Thursday, July 09, 2015 7:45 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Free energy change with harmonic restraints Dear Natalie, You have in http://xxx.tau.ac.il/pdf/1502.07196v3.pdf exact free energy of harmonic covalent bond and bond angle terms (or restrains). See Eqs. (2) and (3). There are also previous studies in the references there. For the dihedral term I assume it can also be calculated exactly (I might upload it). There is also to think if there are other contributions. If you are using it please cite. Best regards, Asaf Quoting Natalie Nguyen nguy...@wittenberg.edu: Dear all, I am trying to measure the free energy change associated with adding/removing harmonic restraints imposed on a ligand that is attached to a protein. Is there any way to set this up? Thank you ahead of time! Natalie Nguyen -- 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. -- 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] after extending simulation
I’m sorry, I miss something with cut and paste command. On terminal I wrote: gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt There is no gromacs coordinate file in VMD, I have to convert a md_0_2.tpr into try or try file? On Jul 9, 2015, at 7:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:25 PM, Andrea Spinelli wrote: Dear all, I extend a simulation (GROMACS 5.0.5) with these command lines: convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr mdrun -s md_0_2.tpr -cpi md_0_1.cpt And now? Well, the above sequence of commands won't do anything because (1) it's gmx convert-tpr not just convert-tpr and (2) if you create next.tpr and try to run md_0_2.tpr then mdrun will exit. What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation? Load it like any coordinate file. -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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- 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 justify when the trajectory reached equilibrium
On 7/9/15 10:11 AM, Qing Lv wrote: Thank you, Justin. I am trying to simulate a protein-ligand complex to see the conformation transition during the simulation... We propose that the receptor pocket may be subject to a conformational change upon ligand-binding, so I want to verify it by MD... I am really a newbie in molecular simulation and all I did to analysis were time evolution of RMSD, interaction energy, and visualization. I try to do some principal component analysis, but literature said that PCA must be performed after equilibrium... If you are hypothesizing a conformational change, then you need a way to quantify that change - distances, angles, etc. Could you give me more info on block-averaging, or any other advice that will help? It means to evaluate quantities over successive blocks of time (e.g. using -b and -e that all GROMACS analysis tools support) and check to see whether or not the quantities of interest are varying over time or if they are stable, i.e. converged. -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] after extending simulation
On 7/9/15 1:25 PM, Andrea Spinelli wrote: Dear all, I extend a simulation (GROMACS 5.0.5) with these command lines: convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr mdrun -s md_0_2.tpr -cpi md_0_1.cpt And now? Well, the above sequence of commands won't do anything because (1) it's gmx convert-tpr not just convert-tpr and (2) if you create next.tpr and try to run md_0_2.tpr then mdrun will exit. What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation? Load it like any coordinate file. -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] after extending simulation
On 7/9/15 1:49 PM, Andrea Spinelli wrote: I’m sorry, I miss something with cut and paste command. On terminal I wrote: gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt There is no gromacs coordinate file in VMD, I have to convert a md_0_2.tpr into try or try file? The contents of md_0_1.tpr and md_0_2.tpr are identical except that the latter contains a different number of steps. When providing mdrun with a .cpt file, it carries out the run from that point, so the starting point of the run (time = 0) is always the same. The final coordinates are always written to a .gro file unless you specify a different format (which your above command does not). Whatever that file is called depends on the first run (md_0_1), because the file names are stored in the .cpt file; they will be appended to by default. The final .gro file has an appended name rather than being overwritten, IIRC. -Justin On Jul 9, 2015, at 7:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:25 PM, Andrea Spinelli wrote: Dear all, I extend a simulation (GROMACS 5.0.5) with these command lines: convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr mdrun -s md_0_2.tpr -cpi md_0_1.cpt And now? Well, the above sequence of commands won't do anything because (1) it's gmx convert-tpr not just convert-tpr and (2) if you create next.tpr and try to run md_0_2.tpr then mdrun will exit. What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation? Load it like any coordinate file. -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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- == 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] after extending simulation
On 7/9/15 2:10 PM, Andrea Spinelli wrote: So, I’m ok! I can read the only one .gro file created at the first simulation as the final .gro file after all extensions. That’s right? No, you should get a .gro file at the end of each run. But that's missing out on most of the information; loading the trajectory is of course more informative than any single snapshot. -Justin On Jul 9, 2015, at 7:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:49 PM, Andrea Spinelli wrote: I’m sorry, I miss something with cut and paste command. On terminal I wrote: gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt There is no gromacs coordinate file in VMD, I have to convert a md_0_2.tpr into try or try file? The contents of md_0_1.tpr and md_0_2.tpr are identical except that the latter contains a different number of steps. When providing mdrun with a .cpt file, it carries out the run from that point, so the starting point of the run (time = 0) is always the same. The final coordinates are always written to a .gro file unless you specify a different format (which your above command does not). Whatever that file is called depends on the first run (md_0_1), because the file names are stored in the .cpt file; they will be appended to by default. The final .gro file has an appended name rather than being overwritten, IIRC. -Justin On Jul 9, 2015, at 7:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:25 PM, Andrea Spinelli wrote: Dear all, I extend a simulation (GROMACS 5.0.5) with these command lines: convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr mdrun -s md_0_2.tpr -cpi md_0_1.cpt And now? Well, the above sequence of commands won't do anything because (1) it's gmx convert-tpr not just convert-tpr and (2) if you create next.tpr and try to run md_0_2.tpr then mdrun will exit. What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation? Load it like any coordinate file. -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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- == 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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- == 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] after extending simulation
I don’t obtain a .gro file after each extension. What is wrong? On Jul 9, 2015, at 8:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 2:10 PM, Andrea Spinelli wrote: So, I’m ok! I can read the only one .gro file created at the first simulation as the final .gro file after all extensions. That’s right? No, you should get a .gro file at the end of each run. But that's missing out on most of the information; loading the trajectory is of course more informative than any single snapshot. -Justin On Jul 9, 2015, at 7:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:49 PM, Andrea Spinelli wrote: I’m sorry, I miss something with cut and paste command. On terminal I wrote: gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt There is no gromacs coordinate file in VMD, I have to convert a md_0_2.tpr into try or try file? The contents of md_0_1.tpr and md_0_2.tpr are identical except that the latter contains a different number of steps. When providing mdrun with a .cpt file, it carries out the run from that point, so the starting point of the run (time = 0) is always the same. The final coordinates are always written to a .gro file unless you specify a different format (which your above command does not). Whatever that file is called depends on the first run (md_0_1), because the file names are stored in the .cpt file; they will be appended to by default. The final .gro file has an appended name rather than being overwritten, IIRC. -Justin On Jul 9, 2015, at 7:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:25 PM, Andrea Spinelli wrote: Dear all, I extend a simulation (GROMACS 5.0.5) with these command lines: convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr mdrun -s md_0_2.tpr -cpi md_0_1.cpt And now? Well, the above sequence of commands won't do anything because (1) it's gmx convert-tpr not just convert-tpr and (2) if you create next.tpr and try to run md_0_2.tpr then mdrun will exit. What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation? Load it like any coordinate file. -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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- == 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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- == 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. Andrea
[gmx-users] g_hbond
Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? Default -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor or distance between donor---acceptor? Thanks, 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_hbond
Thanks. I will use two groups. Nilesh On 7/9/15 9:13 PM, Nilesh Dhumal wrote: On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? If the system is pure water, you do not need any special index groups. I have DMSO in the system. I just mentioned water to make it simple. I am interested in O--H---O(DMSO) interactions? How should I specify this? With one triplet O--H---O(DMSO) or two groups one O--H and second O(DMSO) The latter - just use DMSO and water groups. O can be a donor or acceptor, and g_hbond intelligently figures out whether or not a given atom is a donor or acceptor (or both). -Justin Default -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor or distance between donor---acceptor? Read the first sentence of the help description. -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. -- 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 regarding box size
Hi all, I have a system with 300k atoms, but computationally it is expensive for me doing simulation with such a big system, Is it possible to reduce the box size? If yes how? (the .gro file is uploaded). I know from Justin tutorial genconf -nboxvector 1 1 1 Does the numbers after -nbox have to integer? The size of box required to contain protein with 1.5nm of water on each side. Sorry I could not figure it out what to do and how to tackle this simple task. re bulding the simulation from scratch is an option but thought might find quicker and smarter way here. I want to have optimum size in each direction so that the protein does not see its periodic image. Appreciate any specific thoughts on my system and the box size I have got now. https://drive.google.com/file/d/0B0YMTXH1gmQsdFVKWkdPLURCUVk/view?usp=sharing Cheers James -- 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_hbond
On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? If the system is pure water, you do not need any special index groups. I have DMSO in the system. I just mentioned water to make it simple. I am interested in O--H---O(DMSO) interactions? How should I specify this? With one triplet O--H---O(DMSO) or two groups one O--H and second O(DMSO) Default -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor or distance between donor---acceptor? Read the first sentence of the help description. -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.
Re: [gmx-users] on trjconv command
Hi Brett, I think the following command will work: trjconv -f source.xtc -skip 5 -o target.xtc Qing At 2015-07-10 10:10:39, Brett brettliu...@163.com wrote: Dear All, Will you please show me the command based on the following cited content from the website on how to convert a xtc file with 1 frame per 2 ps to a xtc file with 1 frame per 10 ps? I hope the command contains “-dt” and “-timestep”， and what the values should be for “-dt” and “-timestep”. Best regards Brett With -dt it is possible to reduce the number of frames in the output. This option relies on the accuracy of the times in your input trajectory, so if these are inaccurate use the -timestep option to modify the time (this can be done simultaneously). -- 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_hbond
On 7/9/15 9:13 PM, Nilesh Dhumal wrote: On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? If the system is pure water, you do not need any special index groups. I have DMSO in the system. I just mentioned water to make it simple. I am interested in O--H---O(DMSO) interactions? How should I specify this? With one triplet O--H---O(DMSO) or two groups one O--H and second O(DMSO) The latter - just use DMSO and water groups. O can be a donor or acceptor, and g_hbond intelligently figures out whether or not a given atom is a donor or acceptor (or both). -Justin Default -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor or distance between donor---acceptor? Read the first sentence of the help description. -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] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
Thanks for your explanations, Dr. Lemkul. I had already corrected a couple of the things you suggested. Gromacs won't actually let me run with Nose-Hoover and Parrinello-Rahman together (or at least, it gives a warning not to do that and stops). I'd like to run in NVT anyway, so I had set Pcoupl to 'no'. I had also increased the cutoffs and my nstlist is 20. I have now also changed the tcoupl to v-rescale, but unfortunately that alone didn't help. So I'm not sure exactly what I can inspect to find the source of my error. I know that temperature, pressure, and total energy are all warning signs of bad things if they misbehave, but they were all fairly constant throughout the simulation. (This is for the flexible-model simulation:) The starting energy for 1700 water molecules at 120K was -1.08744e+05, and it finished at -1.06047e+05 with no significant variations on any step. Pressure and temperature were also fine. I attempted to look at the results visually in vmd but I might have done something wrong because the .trr file has some error in it and vmd crashes. But the starting geometry after minimization looks fine: none of the molecules were moved out of their position in the crystal. For the constrained molecules, the energy stays about the same (about -1e+5) for the first 8 timesteps and then quickly blows up to +2e15 at step 12 before it obviously fails. I get shake warnings from step 0 though. In vmd, the first 8 steps look reasonable (checking the .pdb files that gromacs outputs when there are warnings) and all the molecules seem to hold their places in the crystal, but then at step 9 suddenly some of the molecules become misshapen with very long or very short bonds. Of course it goes downhill from there, but I can't figure out what's causing the problems since it's clearly happening from the very beginning (according to the shake warnings). What other things could I look at to troubleshoot my problem? Thanks for your help, Nathan - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Thursday, July 9, 2015 7:39:47 AM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) On 7/8/15 8:06 PM, Nathan K Houtz wrote: Hello, I deleted the email and can't respond to my last reply directly - sorry! I got this response from Mark Abraham: Hi, Try doing some EM and initial equilibration with no constraints at all, perhaps? Mark I tried commenting out the shake commands, and got a short (5000 step) simulation to run just fine without blowing up. Before, I would get shake warnings from the first few steps and a segmentation fault around step 13 or 14. I would like to be able to simulate with rigid molecules, though. Why would the simulation work with flexible molecules but not rigid ones? Flexible water allows weird geometry, which is probably coming up and causing your constraint algorithm to fail. I'd inspect the outcome carefully. Just because it runs doesn't mean it's right. Also, in the example .mdp file for tip4p water, there is the (outdated) option, 'unconstrained-start', which is now 'continuation'. I got errors when trying to make the input .tpr file when I attempted to set that option to 'yes'. The warning said it was because I want Gromacs to generate velocities to start the simulation, which is incompatible with that command. Is there another way I can try to start the simulation unconstrained? Or would you suggest another idea to fix my shake warnings? What this setting says is have the constraints already been solved (continuation = yes) or should mdrun constrain the starting configuration itself (continuation = no). The .mdp file has a number of weird settings. I would never use Nose-Hoover and Parrinello-Rahman when generating velocities; that's likely to be very unstable. See if a more forgiving thermostat and/or barostat resolves the issue, e.g. tcoupl = v-rescale and pcoupl = Berendsen. Also note that the cutoffs are very short (probably because they want to use a small box, but note that it *does* affect the physics) and nstlist = 1 is totally unnecessary. It doesn't hurt your physics, but it's a major waste of performance. -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
Re: [gmx-users] How to justify when the trajectory reached equilibrium
It means to evaluate quantities over successive blocks of time (e.g. using -b and -e that all GROMACS analysis tools support) and check to see whether or not the quantities of interest are varying over time or if they are stable, i.e. converged. Thank you, Justin. What size of blocks I need to divide in such an analysis? e.g., for a 100-ns trajectory, is it appropriate to divide it into 5-ns or 10-ns blocks to see if it has converged? Qing At 2015-07-10 01:39:42, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 10:11 AM, Qing Lv wrote: Thank you, Justin. I am trying to simulate a protein-ligand complex to see the conformation transition during the simulation... We propose that the receptor pocket may be subject to a conformational change upon ligand-binding, so I want to verify it by MD... I am really a newbie in molecular simulation and all I did to analysis were time evolution of RMSD, interaction energy, and visualization. I try to do some principal component analysis, but literature said that PCA must be performed after equilibrium... If you are hypothesizing a conformational change, then you need a way to quantify that change - distances, angles, etc. Could you give me more info on block-averaging, or any other advice that will help? It means to evaluate quantities over successive blocks of time (e.g. using -b and -e that all GROMACS analysis tools support) and check to see whether or not the quantities of interest are varying over time or if they are stable, i.e. converged. -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.
Re: [gmx-users] how to make 8M solutions??
Thanks. Regards, Sapna. Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Wed, Jul 8, 2015 at 12:08 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Since you know how to add n molecules, and you want a solution with a given molality, work out how many molecules that is, and then add that many molecules. Decide whether you care about the volume excluded by the protein when considering what that molality means. Mark On Wed, Jul 8, 2015 at 6:51 AM SAPNA BORAH sapnauser...@gmail.com wrote: Dear all, I am trying to add gdmcl to a protein, however I am unable to make molal solutions. I can add gdmcl by -nmol command but to make molal solutions is giving me a hard time. This is a basic query but it has been bugging me for quite a long time. Please put some light on doing this... I have been using the following commands to make the gdmcl box: editconf -f mod.pdb -bt cubic -d 0.1 -box 5 5 5 -o box.gro genbox -cp box.gro -ci file_1.pdb -p topol.top -o guan.pdb -nmol 100 editconf -f guan.pdb -bt cubic -d 1.2 -o box_2.gro genbox -cp box_2.gro -cs spc216.gro -p topol.top -o solvated.gro The simulations I have been running well with the included 100 GdmCl, however, the problem with making the molal solutions still remains. Regards, Sapna Sapna Mayuri Borah Research student Tezpur University, 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. -- 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] on trjconv command
Dear All, Will you please show me the command based on the following cited content from the website on how to convert a xtc file with 1 frame per 2 ps to a xtc file with 1 frame per 10 ps? I hope the command contains “-dt” and “-timestep”， and what the values should be for “-dt” and “-timestep”. Best regards Brett With -dt it is possible to reduce the number of frames in the output. This option relies on the accuracy of the times in your input trajectory, so if these are inaccurate use the -timestep option to modify the time (this can be done simultaneously). -- 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_hbond
On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? If the system is pure water, you do not need any special index groups. Default -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor or distance between donor---acceptor? Read the first sentence of the help description. -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] (no subject)
Dear All, I have a 30 ns trajectory which I would like to extend up to 100 ns. For that I gave the following commands gmx convert-tpr -s md_0_1.tpr -extend 7 -o final_monomer.tpr gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append After completion of the extension two new trajectory files were generated- 'traj.trr' and 'traj_comp.xtc' . When I tried to check the length of the trajectory with gmxcheck -f traj_comp.xtc the output is Checking file traj_comp.xtc Reading frame 0 time 3.000 # Atoms 16867 Precision 0.001 (nm) Last frame 35000 time 10.000 This trajectory file contains coordinate values from 30ns to 100ns. I tried to calculate the rmsd with this file (both the trr and xtc file) but the graph abruptly starts from 30ns (instead of 0) and continues upto 100ns.For the calculation I need the total trajectory from time 0 to time 100ns.I think I am missing something. Can anyone please suggest anything here? Which one is the total trajectory file then? Thanks in advancePaulami -- 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] Problem with the MDS extended trajectory in Gromacs 5.04
Dear All, I have a 30 ns trajectory which I would like to extend up to 100 ns. For that I gave the following commands gmx convert-tpr -s md_0_1.tpr -extend 7 -o final_monomer.tpr gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append After completion of the extension two new trajectory files were generated- 'traj.trr' and 'traj_comp.xtc' . When I tried to check the length of the trajectory with gmxcheck -f traj_comp.xtc the output is Checking file traj_comp.xtc Reading frame 0 time 3.000 # Atoms 16867 Precision 0.001 (nm) Last frame 35000 time 10.000 This trajectory file contains coordinate values from 30ns to 100ns. I tried to calculate the rmsd with this file (both the trr and xtc file) but the graph abruptly starts from 30ns (instead of 0) and continues upto 100ns.For the calculation I need the total trajectory from time 0 to time 100ns.I think I am missing something. Can anyone please suggest anything here? Which one is the total trajectory file then? Thanks in advancePaulami -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx error residue not found in residue topology database
Peter, This question was for Ali.H.. Sent from my iPhone On 09-Jul-2015, at 5:20 pm, Peter Stern peter.st...@weizmann.ac.il wrote: I never did that. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of su Sent: Wednesday, July 08, 2015 11:26 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] pdb2gmx error residue not found in residue topology database How you converted the gaussian file into .pdb? Because once i did the same and suffered from some missing co ordinates. Sent from my iPhone On 08-Jul-2015, at 11:16 pm, Peter Stern peter.st...@weizmann.ac.il wrote: Look at the file: residuetypes.dat in the ../top/ directory of your installation. It lists all the residue names and more. Peter Stern Weizmann Institute Sent from my iPad On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd hamisu.kaza...@yahoo.com wrote: Dear gmx-users, I am really new in this field of endeavour and I am trying investigate the solubility of peptides in organic solvents, I built a simple tripeptide (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to .pdb. I am now trying to use pdb2gmx tool to generate topology for my peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was promoted with an error residue not found in residue topology database” I checked GROMACS website at http://www.gromacs.org/Documentation/Errors I learned the residue must have the same name as in the force field, please I don’t know the naming convention of this force field please HELP. Thanks Ali H. Department of Chemistry University Dutse -- 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. -- 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] Multiple output trajectories with different sampling frequencies
Hi, On Wed, Jul 8, 2015 at 3:01 PM Machtens, Jan-Philipp j.macht...@fz-juelich.de wrote: Dear all, I have a problem where I am interested in fast processes in one part of the system and a slow process in another, distinct part of the system. Due to disk space limitation, I would like mdrun to write (either compressed or full precision) output trajectories for different parts of the system at different output/sampling frequencies. GROMACS does not take into account distinct parameters for compressed-x-grps, right ? Right, these take a single field (the first one). I mean the second nstxout-compressed and compressed-x-precision parameters are not taken into account: ; Output frequency and precision for .xtc file nstxout-compressed = 1 100 compressed-x-precision = 1000 1000 compressed-x-grps= Protein System__!Protein As a workaround I could write the whole system at low sampling rate to an uncompressed trajectory, and one part of the system could be written at high frequency to a compressed trajectory. But what if I want a trr file also for the high-frequency sampling group ? Do you know solutions better than writing the whole system to a full precision trajectory at high sampling frequency, followed by post-processing and possibly deleting the initial raw trajectory? There is no support in GROMACS for simplifying that workflow. In principle, the TNG support in GROMACS 5 makes available a file format that can handle writing such customized output (different groups at different precision and/or frequency) to a single file, but neither the .mdp input format nor mdrun has been extended to support actually writing such files. Mark Many thanks! Cheers, Dr. Jan-Philipp Machtens Institute of Complex Systems - Zelluläre Biophysik (ICS-4) Forschungszentrum Jülich, Germany Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] pdb2gmx error residue not found in residue topology database
I never did that. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of su Sent: Wednesday, July 08, 2015 11:26 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] pdb2gmx error residue not found in residue topology database How you converted the gaussian file into .pdb? Because once i did the same and suffered from some missing co ordinates. Sent from my iPhone On 08-Jul-2015, at 11:16 pm, Peter Stern peter.st...@weizmann.ac.il wrote: Look at the file: residuetypes.dat in the ../top/ directory of your installation. It lists all the residue names and more. Peter Stern Weizmann Institute Sent from my iPad On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd hamisu.kaza...@yahoo.com wrote: Dear gmx-users, I am really new in this field of endeavour and I am trying investigate the solubility of peptides in organic solvents, I built a simple tripeptide (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to .pdb. I am now trying to use pdb2gmx tool to generate topology for my peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was promoted with an error residue not found in residue topology database” I checked GROMACS website at http://www.gromacs.org/Documentation/Errors I learned the residue must have the same name as in the force field, please I don’t know the naming convention of this force field please HELP. Thanks Ali H. Department of Chemistry University Dutse -- 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] Free energy change with harmonic restraints
Dear Natalie, You have in http://xxx.tau.ac.il/pdf/1502.07196v3.pdf exact free energy of harmonic covalent bond and bond angle terms (or restrains). See Eqs. (2) and (3). There are also previous studies in the references there. For the dihedral term I assume it can also be calculated exactly (I might upload it). There is also to think if there are other contributions. If you are using it please cite. Best regards, Asaf Quoting Natalie Nguyen nguy...@wittenberg.edu: Dear all, I am trying to measure the free energy change associated with adding/removing harmonic restraints imposed on a ligand that is attached to a protein. Is there any way to set this up? Thank you ahead of time! Natalie Nguyen -- 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] Grompp checkpoint bug?
Hi,
I thought this was supposed to work (I wrote that doc sentence, but have
forgotten what's in the code). Can you please open an issue at
redmine.gromacs.org and attach suitable files so I can see how grompp is
working for you?
Thanks,
Mark
On Thu, Jul 9, 2015 at 8:06 AM Dries Van Rompaey dries.vanromp...@gmail.com
wrote:
Hi everyone,
I’m experiencing some discrepancies when I pass the checkpoint file to
grompp using the -t checkpoint flag:
grompp -f md.mdp -o md.tpr -p topol.top -c md_res_1.gro -t md_res_1.cpt
This command results in a tpr file without any variables for barostat and
thermostat:
box (3x3):
box[0]={ 6.70916e+00, 0.0e+00, 0.0e+00}
box[1]={ 0.0e+00, 6.70916e+00, 0.0e+00}
box[2]={ 3.35458e+00, 3.35458e+00, 4.74410e+00}
box_rel (3x3):
box_rel[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
box_rel[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
box_rel[2]={ 5.0e-01, 5.0e-01, 7.07108e-01}
boxv (3x3):
boxv[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
boxv[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
boxv[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev (3x3):
pres_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev (3x3):
svir_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev (3x3):
fvir_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
nosehoover_xi: not available
These values are, however, present in the cpt file:
box (3x3):
box[0]={ 6.69977e+00, 0.0e+00, 0.0e+00}
box[1]={ 0.0e+00, 6.69977e+00, 0.0e+00}
box[2]={ 3.34989e+00, 3.34989e+00, 4.73746e+00}
box-rel (3x3):
box-rel[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
box-rel[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
box-rel[2]={ 5.0e-01, 5.0e-01, 7.07108e-01}
box-v (3x3):
box-v[0]={ 3.46479e-02, 0.0e+00, 0.0e+00}
box-v[1]={ 0.0e+00, 3.46479e-02, 0.0e+00}
box-v[2]={ 1.73240e-02, 1.73240e-02, 2.44998e-02}
pres_prev (3x3):
pres_prev[0]={ 5.48752e+02, 2.40244e+02, -2.50854e+02}
pres_prev[1]={ 2.39676e+02, -8.38463e+01, -4.59079e+02}
pres_prev[2]={-2.52490e+02, -4.60009e+02, 7.15652e-01}
nosehoover-xi: -0.2659910.015571
Running the tpr file and additionally providing the checkpoint through the
‘mdrun -cpi’ command produces a different output than running mdrun using
the same tpr (even though the checkpoint has already been passed into
grompp).
This seems to be contrary to the intended behaviour, as the manual states:
'If you wish to change the ensemble or things like output frequency, then
supplying the checkpoint file to gmx grompp with -t along with a new .mdp
http://manual.gromacs.org/online/mdp.html file with -f is the
recommended
procedure.’
If what I’m seeing is, in fact, the intended behaviour, it might be useful
to explicitly mention the need to supplement grompp with the energy files
as well in order to keep the barostat variables.
Kind regards
Dries
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Re: [gmx-users] Energy minimization
On 7/8/15 8:03 PM, Malihe Hasanzadeh wrote: Hi, I want to do MD simulation of protein-DNA-ligand using Gromacs 5.0.4.,when I do energy minimization, my system is converged but has positive potential energy. also this step only takes 3 second! for next step (pr), gives error: your system is not equilibrated well and blowing up! I chcked my em.pdb file and I saw the Sol box is separated from protein and DNA! This is probably just a PBC effect; use trjconv. Could you please help me, what should I do?what part of my set is wrong? Your EM outcome suggests an unresolvable clash in the system, so it's pointless to try dynamics unless you get a force below the specified tolerance (or at least of some other reasonable magnitude). mdrun tells you where the maximum force is, so that's where you should start looking. Beyond that, you'll have to give us a complete description of what you've done to prepare the system, parametrize the ligand, etc. General troubleshooting that you should always follow: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System my em.mdp: define = -DFLEXIBLE I'm assuming you're trying to use rigid water during the subsequent dynamics (you should), so you'll want to re-minimize without flexible water. Occasionally, the waters distort and SETTLE cannot fix the geometry. This is not likely the source of your problem, just an FYI. -Justin integrator = cg ; steep nsteps = 4000 nstlist = 1 constraints = none emtol = 100.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 nstcalcenergy = 1.2 ewald_rtol = 1e-05 coulombtype = PME cutoff-scheme = Group ns_type = grid rlist = 1.4 rcoulomb =1.4 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes Sincerely, Malihe -- == 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 with the MDS extended trajectory in GROMACS 5.0.4
Hi, Say your initial mdrun command for 30 ns were as follow grompp_mpi -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o md_0_1.tpr and mdrun_mpi -deffnm md_0_1 Then you should get the files such as md_0_1.xtc, md_0_1.log, md_0_1.edr, md_0_1.cpt, md_0_1.trr and so on Then you obtain a new tpr file say new_100ns.tpr using tpbconv or gmx convert with appropriate flags. . Now, if you want to extend your simulation by a certain amount of time and want all your previous files appended the exact command should be something like mdrun_mpi -s new_100ns.tpr -v -deffnm md_0_1 -cpi md_0_1.cpt -append I did it once and coordinates were saved from 0ns all the way to 100ns and the same md_0_1.xtc, md_0_1.edr etc files were apeended without any difficulty. I am not quite sure but there's no harm in trying. Cheers, Soumadwip -- 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 with the MDS extended trajectory in Gromacs 5.04
I have used the following commands for the initial mdrun gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tprgmx mdrun -deffnm md_0_1 Can you please suggest now what went wrong? Paulami On Thursday, 9 July 2015 5:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 4:15 AM, PAULAMI CHATTERJEE wrote: Dear All, I have a 30 ns trajectory which I would like to extend up to 100 ns. For that I gave the following commands gmx convert-tpr -s md_0_1.tpr -extend 7 -o final_monomer.tpr gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append After completion of the extension two new trajectory files were generated- 'traj.trr' and 'traj_comp.xtc' . When I tried to check the length of the trajectory with gmxcheck -f traj_comp.xtc the output is Checking file traj_comp.xtc Reading frame 0 time 3.000 # Atoms 16867 Precision 0.001 (nm) Last frame 35000 time 10.000 This trajectory file contains coordinate values from 30ns to 100ns. I tried to calculate the rmsd with this file (both the trr and xtc file) but the graph abruptly starts from 30ns (instead of 0) and continues upto 100ns.For the calculation I need the total trajectory from time 0 to time 100ns.I think I am missing something. Indeed, you're missing your first trajectory. You specified -append but if you're changing file names then that won't happen and you need to use trjcat afterwards. But since you haven't told us what the initial mdrun command was, there's no way to say what's going on for sure. -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 with the MDS extended trajectory in GROMACS 5.0.4
Soumadwip Thank you very much for your response. So you are suggesting that 'gmx mdrun -s final_monomer.tpr -v -deffnm md_0_1 -cpi md_0_1.cpt -append' instead of 'gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append' (which I have used for the extended simulation) can solve my problem. I will surely try this one. Thanks and RegardsPaulami On Thursday, 9 July 2015 6:54 PM, soumadwip ghosh soumadwipgh...@gmail.com wrote: Hi, Say your initial mdrun command for 30 ns were as follow grompp_mpi -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o md_0_1.tpr and mdrun_mpi -deffnm md_0_1 Then you should get the files such as md_0_1.xtc, md_0_1.log, md_0_1.edr, md_0_1.cpt, md_0_1.trr and so on Then you obtain a new tpr file say new_100ns.tpr using tpbconv or gmx convert with appropriate flags. . Now, if you want to extend your simulation by a certain amount of time and want all your previous files appended the exact command should be something like mdrun_mpi -s new_100ns.tpr -v -deffnm md_0_1 -cpi md_0_1.cpt -append I did it once and coordinates were saved from 0ns all the way to 100ns and the same md_0_1.xtc, md_0_1.edr etc files were apeended without any difficulty. I am not quite sure but there's no harm in trying. Cheers, Soumadwip -- 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] Problem with the MDS extended trajectory in Gromacs 5.04
On 7/9/15 3:09 PM, PAULAMI CHATTERJEE wrote: I have used the following commands for the initial mdrun gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr gmx mdrun -deffnm md_0_1 Can you please suggest now what went wrong? So you have a trajectory named md_0_1.xtc - that should contain the first part of the run. Then somehow you say you've got traj_comp.xtc (though none of the commands you've shown would produce a file with that name), so if that's the case: gmx trjcat -f md_0_1.xtc traj_comp.xtc -o full.xtc That will have the whole thing. -Justin Paulami On Thursday, 9 July 2015 5:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 4:15 AM, PAULAMI CHATTERJEE wrote: Dear All, I have a 30 ns trajectory which I would like to extend up to 100 ns. For that I gave the following commands gmx convert-tpr -s md_0_1.tpr -extend 7 -o final_monomer.tpr gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append After completion of the extension two new trajectory files were generated- 'traj.trr' and 'traj_comp.xtc' . When I tried to check the length of the trajectory with gmxcheck -f traj_comp.xtc the output is Checking file traj_comp.xtc Reading frame 0 time 3.000 # Atoms 16867 Precision 0.001 (nm) Last frame 35000 time 10.000 This trajectory file contains coordinate values from 30ns to 100ns. I tried to calculate the rmsd with this file (both the trr and xtc file) but the graph abruptly starts from 30ns (instead of 0) and continues upto 100ns.For the calculation I need the total trajectory from time 0 to time 100ns.I think I am missing something. Indeed, you're missing your first trajectory. You specified -append but if you're changing file names then that won't happen and you need to use trjcat afterwards. But since you haven't told us what the initial mdrun command was, there's no way to say what's going on for sure. -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 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 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] maintaining stability when uncoupling ion pairs
Hello, I want to calculate the free energy difference associated with decoupling a NaCl pair from aqueous solution, but am running into a strange error. I believe the issue is in how I define the molecule type in the topology file, since the simulation is stable when removing individual ions, or during regular production runs with the same mdp settings. I get the following error soon after submitting the job (5000 steps in): A list of missing interactions: LJC Pairs NB of 1 missing 1 exclusions of 16669 missing 1 Molecule type 'tNC' the first 10 missing interactions, except for exclusions: LJC Pairs NB atoms12 global 3 4 --- Program mdrun, VERSION 5.0.4 Source code file: /nv/blue/amb4ht/downloads/gromacs-5.0.4/src/gromacs/mdlib/domdec_top.c, line: 394 Fatal error: 2 of the 19448 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.74968 nm) or the two-body cut-off distance (1.74968 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I have modified my topology file with the following lines: [ moleculetype ] ; molnamenrexcl tNC 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 Na 1NA NA1 1.0 2 Cl 1CL CL2 -1.0 [ bonds ] [ angles ] And my mdp file is: ; Run control integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 500 ; 10 ns ; Output control nstxout = 2500 nstvout = 2500 nstfout = 0 nstlog = 2500 nstenergy= 2500 nstxout-compressed = 0 Bond parameters constraint_algorithm= lincs; holonomic constraints ;constraints= h-bonds ; all bonds (even heavy atom-H bonds) constrained ;MRS: use h-bonds lincs_iter = 2; accuracy of LINCS lincs_order = 12 ; also related to accuracy lincs_warnangle = 30 continuation = yes ; Neighborsearching and short-range nonbonded interactions ; Neighborsearching cutoff-scheme = Group; Group works with free energy rlist = 1.2 ; cut-off distance for the short-range neighbor list ns_type = grid ; search neighboring grid cells nstlist = 10 ; Electrostatics coulombtype = PME rcoulomb = 1.2 ; van der Waals vdw-type = Cutoff vdw-modifier = Potential-switch rvdw-switch = 0.90 rvdw = 0.95 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.10 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 ; Temperature coupling tc-grps = System tau_t = 2.0 ; time constant, in ps ref_t = 298 ; reference temperature in K ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman tau_p= 2.0 compressibility = 4.5e-05 ref_p= 1.0 ;### Free energy control stuff ## free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1; only immediate neighboring windows ; Vectors of lambda specified here ; Each combination is an index that is retrieved from init_lambda_state for each simulation ; init_lambda_state012345678 910 11 12 13 14 15 16 17 18 19 20 vdw_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ; We are not transforming any bonded or restrained interactions bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Masses are not changing (particle identities are the same at lambda = 0 and lambda = 1) mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Not doing simulated temperting here
Re: [gmx-users] after extending simulation
On 7/9/15 2:16 PM, Andrea Spinelli wrote: I don’t obtain a .gro file after each extension. What is wrong? No idea, only you can see your files and their time stamps. Pro tip: use -deffnm to always get different file names. I never append using mdrun and this is foolproof (e.g. extending as you are, but with slightly different names): gmx mdrun -deffnm md_1_2.tpr -cpi md_0_1.tpr The nomenclature makes it trivial to loop in a bash script to let the run go as long as you like without manual intervention. -Justin On Jul 9, 2015, at 8:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 2:10 PM, Andrea Spinelli wrote: So, I’m ok! I can read the only one .gro file created at the first simulation as the final .gro file after all extensions. That’s right? No, you should get a .gro file at the end of each run. But that's missing out on most of the information; loading the trajectory is of course more informative than any single snapshot. -Justin On Jul 9, 2015, at 7:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:49 PM, Andrea Spinelli wrote: I’m sorry, I miss something with cut and paste command. On terminal I wrote: gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt There is no gromacs coordinate file in VMD, I have to convert a md_0_2.tpr into try or try file? The contents of md_0_1.tpr and md_0_2.tpr are identical except that the latter contains a different number of steps. When providing mdrun with a .cpt file, it carries out the run from that point, so the starting point of the run (time = 0) is always the same. The final coordinates are always written to a .gro file unless you specify a different format (which your above command does not). Whatever that file is called depends on the first run (md_0_1), because the file names are stored in the .cpt file; they will be appended to by default. The final .gro file has an appended name rather than being overwritten, IIRC. -Justin On Jul 9, 2015, at 7:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:25 PM, Andrea Spinelli wrote: Dear all, I extend a simulation (GROMACS 5.0.5) with these command lines: convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr mdrun -s md_0_2.tpr -cpi md_0_1.cpt And now? Well, the above sequence of commands won't do anything because (1) it's gmx convert-tpr not just convert-tpr and (2) if you create next.tpr and try to run md_0_2.tpr then mdrun will exit. What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation? Load it like any coordinate file. -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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- == 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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- == 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
[gmx-users] echo 15 y 1 1 ...... failed for gmx pdb2gmx with -merge
Dear GROMACS researchers, I was trying to assign the protonation status in one go by the following: echo 15 y 1 1 1 .. | gmx pdb2gmx -f HC_A227E.pdb -o HC_A227E_processed.gro -water spce -inter -ignh -merge interactive In the commandline above, the .. means the protonation status for different chargeable residues. Because I have an inter-chain disulfide bond in my two-chain protein, I have to use -merge to keep this inter-chain disulfide bond. The second interactive prompt is to ask if I want to merge these two chains. So my answer is y. However, it seems that the echo command could not be recognised if y is used and I got the following error message: Merge chain ending with residue CYS214 (chain id 'L', atom 3258 SG) and chain starting with residue GLU215 (chain id 'H', atom 3263 N) into a single moleculetype (keeping termini)? [n/y] --- Program gmx, VERSION 5.0.4 Source code file: /home/lanselibai/Cheng/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 1571 Fatal error: Error reading from stdin For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- So can I ask how to use echo to merge chains so that I can assign protonation status in one go? Thank you very much. Yours sincerely Cheng -- 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] Free energy change with harmonic restraints
Dear Natalie, What I can say is that e.g Thermodynamic Integration should give the free energy difference of this transformation. If you are interested in the free energy of binding the link provided to you by Hannes Loeffler may be useful. Also, for such a k value in case you will need analytic equations it will be better to use the exact equations (the equations in this link are approximate). I'll supply an exact equation if you'll need for the free energy of a dihedral harmonic term. I hope to have more time next week and give more details (the weekend starts here). Best regards, Asaf I hope to have more time next week and to try Quoting Natalie Nguyen nguy...@wittenberg.edu: Dear Asaf, Thank you again for putting in the time to respond to me so quickly. What I have been trying to do was start from a system that is not restrained and grow the restraints onto the ligand, measuring the change in free energy of this. The harmonic restraints used are that of the umbrella pull code with a force constant of k= 1000 kJ/mol*nm^2. It is mentioned In the Gromacs manual for mdp options that the pull code can be controlled with restraint-lambdas, but there is not much detail other than this. I imagine that lambda =0 would represent a nonexistent potential with k= 0 and at lambda = 1 a full strength potential would be imposed. Please feel free to ask me to add more detail! Warm regards, Natalie From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of asaffa...@post.tau.ac.il asaffa...@post.tau.ac.il Sent: Thursday, July 09, 2015 10:38 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Free energy change with harmonic restraints Dear Natalie, You are welcome. Could you please explain in more detail so maybe I can help? Do you want to change the strength of the restraints and measure the free energy difference associated with this change? Thanks. p.s there is also http://arxiv.org/pdf/1307.1620v7.pdf with the same equations. Best regards, Asaf Quoting Natalie Nguyen nguy...@wittenberg.edu: Dear Asaf, Thank you for the quick reply! I was wondering if it was possible to use thermodynamic integration to represent growing harmonic restraints aside from using an analytical method. I will cite this article most definitely! Natalie Nguyen From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of asaffa...@post.tau.ac.il asaffa...@post.tau.ac.il Sent: Thursday, July 09, 2015 7:45 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Free energy change with harmonic restraints Dear Natalie, You have in http://xxx.tau.ac.il/pdf/1502.07196v3.pdf exact free energy of harmonic covalent bond and bond angle terms (or restrains). See Eqs. (2) and (3). There are also previous studies in the references there. For the dihedral term I assume it can also be calculated exactly (I might upload it). There is also to think if there are other contributions. If you are using it please cite. Best regards, Asaf Quoting Natalie Nguyen nguy...@wittenberg.edu: Dear all, I am trying to measure the free energy change associated with adding/removing harmonic restraints imposed on a ligand that is attached to a protein. Is there any way to set this up? Thank you ahead of time! Natalie Nguyen -- 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. -- Gromacs Users mailing list
