Re: [gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites?
Hi Bjorn (and others interested in virtual sites for non-protein molecules), We have an article in press where we describe our new tool Mkvsites, which is a great help when you want virtual sites for a new residue, ligand, etc. I will announce the article once it is available, but I might as well provide the tool already now: https://github.com/ErikMarklund/mkvsites In short: Use topinspect.py to identify any atomtypes and interactions in your itp/top file that need to be added to the force field (not needed for some things, like nucleic acids already present in the force field, but for which no vsite parameters exist). topinspect.py optionally produces an rtp file, which is very helpful because it enables you to use pdb2gmx to place all dummy masses etc at a later stage. Then use Mkvsites.py to generate the required vsite parameters, including angle constraints for -OH groups. Put that in your force field, then prepare your system with pdb2gmx etc like you would for a vanilla protein system. Look at the examples provided and get in touch if you need help. I am sure there are things we can do to improve the usability, so input is welcome. We have NOT automated the actual modification of force field files, since we have noticed that some of the input we have used for testing need human interpretation (e.g. to decide element type for new atom types). While we could implement some logic for that, it is difficult to foresee all possible flavours of input, and that strategy risk causing silent errors in the simulations. Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4562 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 27 Mar 2020, at 17:14, Bjorn Wesen mailto:bjorn.we...@gmail.com>> wrote: Hi list, I have a working sim of the solvated SARS-CoV-2 main protease dimer from https://www.rcsb.org/structure/6Y84 using amber99sb-ildn and pdb2gmx-generated vsites for speed, and wanted to proceed by adding some of the various proposed inhibitor ligands to the sim for further workflow testing, for example, this one: "COCCOc1cc(C(=O)N=c2[nH][nH]c(C)c2-c2ccc(Cl)cc2)ccn1". So I made a pdb of this and generated a .gro and .itp through one of the online Acpype servers (the one at http://bio2byte.be/acpype ), but there is no option to generate gmx vsites for getting rid of the hydrogen bond-angles so I simply assume the result will blow up when running with the longer timesteps the rest of the sim now uses. I found a 5 year old post on this list with the same problem, with this advice from Justin: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-October/101732.html "At present, the simplest way forward is to take the information you have in your ligand topology from acpype and create an .rtp entry, then allow pdb2gmx to process the whole thing and build the virtual sites on the ligand." I was wondering, is this still the recommended method? I'm not super-knowledgeable in the details of how to port something from the ITP to the RTP formats. Should I just give up on doing it this way or is it an "opportunity to learn the details" ;) Or is there a better way. Maybe some other gmx tool to build the vsites for a ligand without having to go all the way by creating the rtp stuff. Also, yes, I could simply give up the vsites and run everything slower. This is the fallback. Maybe some of these ligands simply won't work well with these constructions at any rate. Regards /Bjorn -- 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. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -- 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] Force field for urea and urea-TMAO mixture
Dear Ishrat, I recommend this article and references therein for TMAO + urea parameters: http://dx.doi.org/10.1021/jacs.7b11695. Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4562 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 5 Mar 2020, at 10:05, Alessandra Villa mailto:alessandra.villa.bio...@gmail.com>> wrote: Hi, The urea model of Lorna Smith ( https://pubs.acs.org/doi/abs/10.1021/jp030534x ) should be compatible with GROMOS force field. Best regards Alessandra On Wed, Mar 4, 2020 at 7:00 AM ISHRAT JAHAN wrote: Dear all, I want to do MD simulation of protein in urea and urea-TMAO mixture. Can you suggest me which force field would be better for urea and urea tmao mixture? Is Kast-2016 TMAO model is compatible with gromos54a5 force field as I have done the simulation of protein with this force field. Any suggestions regarding this will be highly appreciated. Thank you Regards -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- 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. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -- 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] Fourier dihedrals
Dear all, I am looking in the manual at how the Fourier dihedrals are defined, and there appears to be a discrepancy between section 5.5 and the table of topology directives in 5.14. 5.5 shows an equation with four coefficients (F1, F2, F3, F4), whereas the table shows 5 coefficients for the Fourier-type dihedrals (C1,C2,C3,C4,C5). How does gromacs actually handle this? With 4 or 5 parameters? Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4562 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -- 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] Tpr version check
Hi, Thanks Mark. See https://redmine.gromacs.org/issues/2924. Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4562 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 11 Apr 2019, at 08:42, Mark Abraham mailto:mark.j.abra...@gmail.com>> wrote: Hi, The old behavior of a graceful rejection of the file with a new version number is still expected. The most likely explanation for your observations is that they old version of gmx is linking somehow to newer versions of things (which also shouldn't happen ...), and the chimera can't work. If you can share a tpr on Redmine we can see if there is an issue we can fix. Mark On Wed., 10 Apr. 2019, 23:05 Erik Marklund, mailto:erik.markl...@kemi.uu.se>> wrote: Hi users, I accidentally used an older version (2016.3) to run trjconv on some trajectories. Some conversions worked, seemingly depending on pbc options etc, whereas others stopped with the following output: Back Off! I just backed up mol.xtc to ./#mol.xtc.1# -> frame 0 time0.000 --- Program: gmx trjconv, version 2016.3 Source file: src/gromacs/pbcutil/pbc.cpp (line 94) Fatal error: Unknown ePBC=1051770189 in ePBC2npbcdim Call me a hopeless nostalgic, but I remember a time when such mistakes rendered an error saying that I am using an older version of gmx than the version used to generate the tpr file. Is that not a thing anymore, and this is the expected behaviour? Seems problematic if gmx tools try to read nonsense data (from the viewpoint of the gromacs version used). Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4562 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se> När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -- 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<mailto: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<mailto: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] Tpr version check
Hi users, I accidentally used an older version (2016.3) to run trjconv on some trajectories. Some conversions worked, seemingly depending on pbc options etc, whereas others stopped with the following output: Back Off! I just backed up mol.xtc to ./#mol.xtc.1# -> frame 0 time0.000 --- Program: gmx trjconv, version 2016.3 Source file: src/gromacs/pbcutil/pbc.cpp (line 94) Fatal error: Unknown ePBC=1051770189 in ePBC2npbcdim Call me a hopeless nostalgic, but I remember a time when such mistakes rendered an error saying that I am using an older version of gmx than the version used to generate the tpr file. Is that not a thing anymore, and this is the expected behaviour? Seems problematic if gmx tools try to read nonsense data (from the viewpoint of the gromacs version used). Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4562 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -- 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] NVT equilibration in vacuum
Additionally, be aware of the tumbling ice cube effect and set comm-mode to angular to avoid it. Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4562 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 27 Mar 2019, at 00:53, Justin Lemkul mailto:jalem...@vt.edu>> wrote: On 3/26/19 5:43 PM, Neena Susan Eappen wrote: Hello gromacs users, I am using gromacs to simulate a peptide in vacuum. I was wondering for the NVT equilibration step, are there any particular parameters to be changed for vacuum conditions as there is no position restraining on solvent molecules? Preparing a vacuum system is not like a condensed-phase system. To do a simulation in vacuum, turn off PBC and set all cutoffs to zero (rlist, rvdw, rcoulomb). -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu<mailto:jalem...@vt.edu> | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -- 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] Different models of TMAO
Dear Dilip, Perhaps you are aware of these publications http://dx.doi.org/10.1021/jacs.7b11695, https://doi.org/10.1103/PhysRevLett.119.108102. Unless someone provides parameter files for you, you will need to learn how the gromacs topology and force field files work. That is a good thing to know long-term anyway if you plan on doing MD in the future. Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4562 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 20 Mar 2019, at 16:24, Dilip.H.N mailto:cy16f01.di...@nitk.edu.in>> wrote: Hello all, I have run a simulation with TMAO using Charmm36 FF and i want to see whether different models of TMAO ie., Kast, Netz and Garcia models do solvate/behave in the same way. So, can anybody share the relevant parameter files as .rtp, .itp etc., of the above mentioned three different TMAO models required to run the simulations... How can i include the epsilon and LJ parameters in it...? Any suggestions are appreciated. Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> 20/03/19, 20:54:23 -- 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<mailto:gmx-users-requ...@gromacs.org>. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -- 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] Vanishing cofactors
Hm. Issue largely resolved itself. The chain labels disappear with 2019.1, which is why I might have misinterpreted the output pdb. Still an issue, but minor. Redmine issue updated. Kind regards, Erik > On 20 Mar 2019, at 14:45, Erik Marklund wrote: > > Sorry. Wrong link. Here is the correct one > http://redmine.gromacs.org/issues/2900 > ______ > Erik Marklund, PhD, Associate Professor of Biochemistry > Associate Senior Lecturer in Computational Biochemistry > Department of Chemistry – BMC, Uppsala University > +46 (0)18 471 4562 > erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> > > On 20 Mar 2019, at 14:41, Erik Marklund > mailto:erik.markl...@kemi.uu.se>> wrote: > > Dear dynamicists, > > When I use a pdb file coming directly from pdb2gmx as input for editconf, my > protein’s two cofactor vanish mysteriously. This is using 2019.1. With 2016.3 > I get no such issues. Is this a known issue? Has anyone experienced similar > problems? > > I could not fine anything similar in redline, so I created an issue > http://redmine.gromacs.org/projects/gromacs/issues/new?issue%5Btracker_id%5D=1<http://redmine.gromacs.org/projects/gromacs/issues/new?issue[tracker_id]=1> > > Kind regards, > Erik > __ > Erik Marklund, PhD, Associate Professor of Biochemistry > Associate Senior Lecturer in Computational Biochemistry > Department of Chemistry – BMC, Uppsala University > +46 (0)18 471 4562 > erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär det > att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan > du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal data. > For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > -- > 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] Vanishing cofactors
Sorry. Wrong link. Here is the correct one http://redmine.gromacs.org/issues/2900 __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4562 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 20 Mar 2019, at 14:41, Erik Marklund mailto:erik.markl...@kemi.uu.se>> wrote: Dear dynamicists, When I use a pdb file coming directly from pdb2gmx as input for editconf, my protein’s two cofactor vanish mysteriously. This is using 2019.1. With 2016.3 I get no such issues. Is this a known issue? Has anyone experienced similar problems? I could not fine anything similar in redline, so I created an issue http://redmine.gromacs.org/projects/gromacs/issues/new?issue%5Btracker_id%5D=1<http://redmine.gromacs.org/projects/gromacs/issues/new?issue[tracker_id]=1> Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4562 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -- 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] Vanishing cofactors
Dear dynamicists, When I use a pdb file coming directly from pdb2gmx as input for editconf, my protein’s two cofactor vanish mysteriously. This is using 2019.1. With 2016.3 I get no such issues. Is this a known issue? Has anyone experienced similar problems? I could not fine anything similar in redline, so I created an issue http://redmine.gromacs.org/projects/gromacs/issues/new?issue%5Btracker_id%5D=1<http://redmine.gromacs.org/projects/gromacs/issues/new?issue[tracker_id]=1> Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4562 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -- 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] protein dna pulling
Hi, Not necessarily. The COM still moves if one strand moves away. Your results however suggest that the DNA’s interaction with the protein is stronger than the interaction between strands. I will leave it up to you to decide whether that makes sense or not, or if there is something wrong with your setup. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4542 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 27 Aug 2018, at 20:11, abhisek Mondal mailto:abhisek.m...@gmail.com>> wrote: Hi, I have been trying to pull a double stranded DNA from protein's binding surface. But I am facing an issue. After defining the pull vector when I apply the pull force the DNA's one stand got pulled completely while other strand partially remain attached ( https://drive.google.com/drive/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU ). Shouldn't the both strands be moving together (as the COM was determined using residues from both strand of DNA) ? Some suggestions in this regard would be highly appreciated. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Protein Crystallography Group* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *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. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/om-uu/dataskydd-personuppgifter/ -- 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] Speed up simulations with GROMACS with virtual interaction sites
Hi, We are working on a tool for automatic vsite parameter generation, which works with most force fields including CHARMM. Stay tuned. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 6 Apr 2018, at 13:11, Anthony Nash mailto:anthony.n...@dpag.ox.ac.uk>> wrote: Hi Stephane, I hope it is useful. I am afraid I have very little charmm experience. I used the approach posted for an amber ff. I hope someone can help with the charmm aspect. Kind regards Anthony Nash PhD MRSC Department of Physiology, Anatomy, and Genetics University of Oxford From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se<mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se<mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se>] on behalf of ABEL Stephane [stephane.a...@cea.fr<mailto:stephane.a...@cea.fr>] Sent: 06 April 2018 11:20 To: gromacs.org_gmx-users@maillist.sys.kth.se<mailto:gromacs.org_gmx-users@maillist.sys.kth.se> Subject: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites Many thanks Anthony I will read your post blog. I have another quick question: Does the approach work by defaults (w/o modifications) for other biomolecules such as surfactants or it is necessary to construct a virtual site table as we can found for protein in the charmm*.ff distribution ? Stéphane -- Message: 3 Date: Fri, 6 Apr 2018 09:33:46 + From: Anthony Nash mailto:anthony.n...@dpag.ox.ac.uk>> To: "gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>" mailto:gmx-us...@gromacs.org>> Subject: Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites Message-ID: <84462751076e544cbb9e12bcca3e2d49389...@mbx12.ad.oak.ox.ac.uk<mailto:84462751076e544cbb9e12bcca3e2d49389...@mbx12.ad.oak.ox.ac.uk>> Content-Type: text/plain; charset="iso-8859-1" Hi, I tried something like this about a year ago and I put an instructional blog post together. Warning: it was pulled together from a paper I found and not my own efforts although I did get it to work. Any questions I might not be able to respond, I'm on vacation! https://distributedscience.wordpress.com/2017/06/19/speeding-up-md-simulations-in-explicit-solvent/ Kind regards Anthony Nash PhD MRSC Department of Physiology, Anatomy, and Genetics University of Oxford From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of ABEL Stephane [stephane.a...@cea.fr] Sent: 06 April 2018 08:51 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites Hi gmx users, I know that it is possible to speed up the simulations by a factor 2 (by using a larger timestep) in GROMACS with virtual interaction sites. By I do not find a clear procedure on the web in particular if I use CHARMM. Do you have any pointers or procedures and examples of mdp files to share with me Thanks St?phane -- 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. End of gromacs.org_gmx-users Digest, Vol 168, Issue 24 ** -- 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-use
Re: [gmx-users] Regarding calculation of Hydrogen-Bond
A shortcut would be to only look at the C-O distance, which can be done with gmx hbond without modification. Kind regards, Erik > On 13 Mar 2018, at 15:01, Jeremy T First wrote: > > Hi Dilip, > > There is quite a bit of literature, especially recently, that considers the > alpha carbon as a hydrogen bond donor. How well this is represented in your > simulation will depend on your force field. > > You will likely need to develop your own gromacs tool to calculate this, > but it should be quite easy. We recently wrote a tool that does something > very similar, but you would need to edit it for your own purposes. If you > are interested in using our code as a template, feel free to contact me off > list. > > Good luck! > Jeremy > > > > > Jeremy Todd First > Webb Research Group > University of Texas at Austin > jeremy_fi...@utexas.edu > (443) 243-1187 > > On Tue, Mar 13, 2018 at 7:25 AM, Erik Marklund > wrote: > >> The point is that Calpha don’t form hydrogen bonds. >> >> Erik >> __ >> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow >> Department of Chemistry – BMC, Uppsala University >> +46 (0)18 471 4539 >> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> >> >> On 13 Mar 2018, at 13:20, Dilip H N > cy16f01.di...@nitk.edu.in>> wrote: >> >> Then how can i calculate the hydrogen bonding between C-alpha and Oxygen >> atom of water molecules..?? >> What are the other possible ways..?? >> >> >> >> <https://mailtrack.io/> Sent with Mailtrack >> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign= >> signaturevirality&<https://mailtrack.io/?utm_source= >> gmail&utm_medium=signature&utm_campaign=signaturevirality&>> >> >> On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund > mailto:erik.markl...@kemi.uu.se>> >> wrote: >> >> Dear Dilip, >> >> The Calpha is not considered a hbond donor. >> >> Kind regards, >> Erik >> __ >> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow >> Department of Chemistry – BMC, Uppsala University >> +46 (0)18 471 4539 >> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>> erik.markl...@kemi.uu.se> >> >> On 13 Mar 2018, at 11:03, Dilip H N > cy16f01.di...@nitk.edu.in>> cy16f01.di...@nitk.edu.in<mailto:cy16f01.di...@nitk.edu.in>>> wrote: >> >> Hello, >> I want to calculate Hydrogen bonding between C-alpha of glycine and the >> oxygen atom of water molecules. >> So, i gave the command as:- >> >> gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg >> >> but i got the error as: >> Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms) >> Found 0 donors and 511 acceptors >> No Donors found >> --- >> Program: gmx hbond, version 2016.2 >> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732) >> Fatal error: >> Nothing to be done >> >> So, how can i solve this issue..?? Is there no any Hydrogen bonding between >> this..?? (I think there is some hydrogen bonding present ...) >> >> Any suggestions are appreciated. >> >> Thank you. >> >> -- >> With Best Regards, >> >> DILIP.H.N >> PhD Student >> >> >> >> >> <https://mailtrack.io/> Sent with Mailtrack >> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign= >> signaturevirality&> >> -- >> 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<mailto:gmx-users-request@ >> gromacs.org><mailto:gmx-users-request@ >> gromacs.org<http://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.
Re: [gmx-users] Regarding calculation of Hydrogen-Bond
The point is that Calpha don’t form hydrogen bonds. Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 13 Mar 2018, at 13:20, Dilip H N mailto:cy16f01.di...@nitk.edu.in>> wrote: Then how can i calculate the hydrogen bonding between C-alpha and Oxygen atom of water molecules..?? What are the other possible ways..?? <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality&;<https://mailtrack.io/?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality&;>> On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund mailto:erik.markl...@kemi.uu.se>> wrote: Dear Dilip, The Calpha is not considered a hbond donor. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se> On 13 Mar 2018, at 11:03, Dilip H N mailto:cy16f01.di...@nitk.edu.in>mailto:cy16f01.di...@nitk.edu.in>>> wrote: Hello, I want to calculate Hydrogen bonding between C-alpha of glycine and the oxygen atom of water molecules. So, i gave the command as:- gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg but i got the error as: Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms) Found 0 donors and 511 acceptors No Donors found --- Program: gmx hbond, version 2016.2 Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732) Fatal error: Nothing to be done So, how can i solve this issue..?? Is there no any Hydrogen bonding between this..?? (I think there is some hydrogen bonding present ...) Any suggestions are appreciated. Thank you. -- With Best Regards, DILIP.H.N PhD Student <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign= signaturevirality&> -- 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<mailto:gmx-users-requ...@gromacs.org><mailto:gmx-users-request@ gromacs.org<http://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<mailto:gmx-users-requ...@gromacs.org>. -- With Best Regards, DILIP.H.N Ph.D Student -- 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<mailto: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] Regarding calculation of Hydrogen-Bond
Dear Dilip, The Calpha is not considered a hbond donor. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 13 Mar 2018, at 11:03, Dilip H N mailto:cy16f01.di...@nitk.edu.in>> wrote: Hello, I want to calculate Hydrogen bonding between C-alpha of glycine and the oxygen atom of water molecules. So, i gave the command as:- gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg but i got the error as: Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms) Found 0 donors and 511 acceptors No Donors found --- Program: gmx hbond, version 2016.2 Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732) Fatal error: Nothing to be done So, how can i solve this issue..?? Is there no any Hydrogen bonding between this..?? (I think there is some hydrogen bonding present ...) Any suggestions are appreciated. Thank you. -- With Best Regards, DILIP.H.N PhD Student <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality&;> -- 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<mailto: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] Calculation of potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling in gromacs
Hi, Just out of curiosity, what is the point of REMD for such a simple system? Is the enhanced sampling really worth the overhead? Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 9 Mar 2018, at 18:43, Marc Hoemberger mailto:hoemb...@brandeis.edu>> wrote: You could compile Gromacs with PLUMED (http://www.plumed.org/) and use that to run your umbrella sampling with replica exchange. -Marc On Thu, Mar 8, 2018 at 11:32 AM, Mayank Dixit mailto:dixit.maya...@gmail.com>> wrote: Dear Gromacs Users, I would like to calculate the potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling method in gromacs. Please let me know the details of replica exchange umbrella sampling in gromacs. Thanks and kind regards Mayank *Dr. Mayank Dixit * Post-doctoral fellow Department of Chemistry The city college of New York Marshak Science Building 160 convent avenue 138th street. New York, NY-10031 Cell no: 16465894905 -- 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<mailto:gmx-users-requ...@gromacs.org>. -- Marc Hoemberger Ph.D. Candidate, Biochemistry and Biophysics, Laboratory of Dorothee Kern MS-009, 415 South St. Brandeis University Waltham, MA, 02453 -- 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<mailto: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] Potential energy coming out to be zero but not negative
Dear Shayantani, The output you quote show a negative potential energy. Is that not for the run you refer to? (With regards to “Hello Sir”, may I suggest a more gender inclusive greeting.) Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 23 Feb 2018, at 19:32, SHYANTANI MAITI mailto:shyantani.ma...@gmail.com>> wrote: Hello Sir, When I go for energy minimization for a protein complex containing 3 proteins, I obtain potential energy being minimized upto zero from positive. The potential energy is not becoming negative even after running for many steps as viewed in potential.xvg obtained after energy minimzation. Energy Average Err.Est. RMSD Tot-Drift --- Potential-6.06412e+061.2e+06 5.5e+07 -7.26522e+06 (kJ/mol) Is the energy minimization considerable for further equilibration or do I need to obtain only negative energy and after that only should I start my equilibration? Does the value of potential energy obtained after minimization need to be negative in all cases? Can I continue my equilibration with this result? Thanking you -- Best regards, *Shyantani Maiti* -- 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<mailto: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] Why the '5-Helix' randomly displayed in the scount.xvg after running do_dssp?
Dear Cheng, Gromacs is open source. Implement this at your own will. If there is a sufficient interest in such a feature it might even have a place in the official release at some point. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 22 Feb 2018, at 18:19, ZHANG Cheng <272699...@qq.com<mailto:272699...@qq.com>> wrote: Dear Gromacs, The scount.xvg file was obtained after running echo 1 | gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns The secondary structures listed are: 'Structure','Coil','B-Sheet','B-Bridge','Bend','Turn','A-Helix','3-Helix','5-Helix' I ran the command for different proteins. It surprised me that the last '5-Helix' randomly displayed in the scount.xvg. Maybe some proteins did not have the '5-Helix', but why not just show them as 0? Can this be improved? Because I am using a script to read the scount.xvg files, so I want all the files have the same format. Thank you. 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<mailto: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] gmx hbond
Hi Negar, Correct, the -dist option doesn’t do what you want it to. I cannot come up with a recipe for how to do this, but I suspect multiple rounds of gmx select and gmx hbond might do the trick. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 5 Feb 2018, at 15:49, negar habibzadeh mailto:negar...@gmail.com>> wrote: Hi I want to calculate *number of hydrogen bond* by *distance from center of bilayer*. i use gmx hbonds -dist but it doesn't give me the proper result.is<http://result.is> it true? which options should i implement to get the best result? best regads -negar -- 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<mailto: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 set hetrodimer for MD Simulation
Dear Rana, a) We are not (necessarily) Amber users. This is a gromacs mailing list. b) If the separate structures are correctly positioned relative to each other, you basically just need to cut-and-paste the ATOM records from one pdb file into the other one. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 22 Nov 2017, at 22:15, Rana Rehan Khalid mailto:rrkha...@umich.edu>> wrote: Dear Amber users My protein system consist of two subunit chains alpha and beta each chain consist four domains. I predicted the structure of both subunit chains now i want to combine both structure subunits models, How i can combine them in one pdb file. so that i can run the simulation on complete structure. Kindly guide me. Regards -- 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<mailto: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] autocorrelation function and residence time
Dear Tsaneem, Negative values don’t signify lack of correlation, but anticorrelation. Also, by omitting negative values you introduce a slight bias in your fit towards longer half-life. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 22 Sep 2017, at 06:18, Tasneem Kausar mailto:tasneemkausa...@gmail.com>> wrote: Thank you for reply I read the references and I know that one of the columns of g_hbond output is without subtraction and the value ranges between 0 to 1. The only help I need is that can I fit the curve of the first column (which has negative value) and neglect the range of curve of negative part while fitting to get the exponential parameters of the curve. This seems to me reasonable only for getting information parameter as negative ACF value mean no correlation parameter. Any help will be appreciated. Thanks in Advance. On Thu, Sep 21, 2017 at 2:54 PM, Erik Marklund mailto:erik.markl...@kemi.uu.se>> wrote: Dear Tasneem, Quite often ACF calculations involve subtraction of the average signal, and this normally renders some negative values in the ACF. It’s been a bit too long since I dealt with the gmx hbond code, but I suspect that is what is going on here. I suggest reading the references that gmx hbond mentions, where the four quantities in the output are defined. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se> On 21 Sep 2017, at 11:12, Tasneem Kausar mailto:tasneemkausa...@gmail.com>< mailto:tasneemkausa...@gmail.com>> wrote: Still waiting for suggestions. On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar mailto:tasneemkausa...@gmail.com> <mailto:tasneemkausa...@gmail.com>> wrote: Dear all I want to calculate residence time of interface water molecules at protein interface. I am using Gromacs-4.6.4. I am using using following command g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac protein_ac.xvg -contact In the index file there are protein interface residues and 8 water molecule that are present at the protein interface. I have selected protein interface and 8 water for calculation. In the output of autocorrelation there are four y axis columns. I came through reply of Erik. He mentioned the effect of periodic boundary condition on the output. In my case first y axis has several negative values. I want to do an exponential fit with function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the negative values of the output file? If yes what is the reason to do that. If I am wrong please suggest me to do the right way to obtain residence time. Thanks in Advance Tasneem Kausar -- 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<mailto:gmx-users-requ...@gromacs.org><mailto:gmx-users-request@ gromacs.org<http://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<mailto: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<mailto: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] autocorrelation function and residence time
Dear Tasneem, Quite often ACF calculations involve subtraction of the average signal, and this normally renders some negative values in the ACF. It’s been a bit too long since I dealt with the gmx hbond code, but I suspect that is what is going on here. I suggest reading the references that gmx hbond mentions, where the four quantities in the output are defined. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 21 Sep 2017, at 11:12, Tasneem Kausar mailto:tasneemkausa...@gmail.com>> wrote: Still waiting for suggestions. On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar mailto:tasneemkausa...@gmail.com>> wrote: Dear all I want to calculate residence time of interface water molecules at protein interface. I am using Gromacs-4.6.4. I am using using following command g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac protein_ac.xvg -contact In the index file there are protein interface residues and 8 water molecule that are present at the protein interface. I have selected protein interface and 8 water for calculation. In the output of autocorrelation there are four y axis columns. I came through reply of Erik. He mentioned the effect of periodic boundary condition on the output. In my case first y axis has several negative values. I want to do an exponential fit with function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the negative values of the output file? If yes what is the reason to do that. If I am wrong please suggest me to do the right way to obtain residence time. Thanks in Advance Tasneem Kausar -- 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<mailto: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] Regarding calculation of Lennard-Jones potential
Dear Dilip, The LJ parameters are present in the topology file and the force-field files included within. So no need to calculate anything, just to locate them in said files. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 18 Sep 2017, at 05:42, Dilip H N mailto:cy16f01.di...@nitk.edu.in>> wrote: Hello, I have a simulation mixture of aminoacid (eg., glycine) with water and cosolvent. I want to calculate Lennard-Jones Parameters of the all atom types. How can i calculate it...?? Can it be done with commands, or any other method..?? Any suggestions are appreciated... Thank you.. -- With Best Regards, DILIP.H.N Ph.D Student <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> -- 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<mailto: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] regarding hydrogen bond correlation function for Cdd for TIP4P/2005 water model
Dear Abhinav, This is a bit tricky. We implemented the geminate recombination model some time ago, but have taken it our of the gmx hbond tool because it complicates the code quite a lot. That said, if you want to use that old code you first need to "pbc-unwrap” your trajectory using trjconv -nojump. Try that and see if you get more reasonable output. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 13 Sep 2017, at 06:16, Abhinav Srivastava (P14CHM002) mailto:srivastav...@iitj.ac.in>> wrote: Dear Gromacs Users, Kindly consider this as my query mail as in the last mail, subject line was not complete. I apologize for the same . I am trying to calculate hydrogen bond correlation function Cdd(t) for bulk water (TIP4P/2005 water) using reversible geminate recombination as mentioned in Markovitch et al., J. Chem. Phys.,129,084505(2008). Following is the command which I have used : g_hbond -f NVT.xtc -s NVT.tpr -n bulk-water.ndx -b 0 -e 100 -P 1 -temp 308 -geminate dd -ac Cdd-bulk-water.xvg I have simulated two systems viz. smaller system consisting of 851 water molecules and a bigger system consisting of 1944 water molecules. I am not able to get t^-3/2 scaling in hydrogen bond correlation function for Cdd case in both these systems. It would be nice if you can please help me. Thanks in advance. -- *Abhinav Srivastava* *Research Scholar* Indian Institute of Technology, Jodhpur Rajasthan -- 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<mailto: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] Difference in hydrogen bond lifetimes with and without pbc
Dear Apramita, What version are you using? There might have been some PBC-related bugs that were fixed if memory serves me right. Kind regards Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 29 Aug 2017, at 15:26, Apramita Chand mailto:apramita.ch...@gmail.com>> wrote: Dear Eric and other Gromacs users, Thanks for clarifying about how different timescale of trajectories can affect lifetimes But the case with and without pbc have same length of trajectories (100 ns). Then why the difference in lifetimes ( 1793ps with pbc and 2345 without pbc) Which can be regarded as more accurate? Yours sincerely, Apramita -- 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<mailto: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] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc
Dear Apramita, Right. Still, the same still applies with regards to the -666. It could be a matter of statistics, why you get sensible values for the longer trajectory chunk. Also, note that the trajectory length limits the possible timescales that the model can tease out. If I understand correctly, your trajectories with and without pic have different length, so I’m not surprised that the kinetic constants that you get out are different. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 29 Aug 2017, at 14:02, Apramita Chand mailto:apramita.ch...@gmail.com>> wrote: Dear Eric, Its actually the DG(kj/mol) value which is -666. The time is coming to be-126 ps. But the g_hbond is failing to fit the kinetic model to the data for the last 60ns as you have implied. Any reasons why this could have happened, while for the entire trajectory, I am getting positive values? But for the entire trajectory, with and without pbc(1793ps and 2345ps respectively) , I have two separate values for lifetime. Which one should I take? I would be appreciative of any suggestions Looking forward to your help, yours sincerely Apramita *Message:( 2 Date: Tue, 29 Aug 2017 08:09:32 +0000 From: Erik Marklund mailto:erik.markl...@kemi.uu.se> mailto:erik.markl...@kemi.uu.se>>> To: "gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> mailto:gmx-us...@gromacs.org>>" mailto:gmx-us...@gromacs.org> mailto:gmx-us...@gromacs.org>>> Subject: Re: [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc Message-ID: mailto:e2a33c50-036b-4dc7-9f79-bc136147f...@kemi.uu.se> mailto:e2a33c50-036b-4dc7-9f79-bc136147f...@kemi.uu.se>>> Content-Type: text/plain; charset="utf-8" Dear Apramita, IIRC, the time is set to.-666 when gmx hbond fails to fit the kinetic model to the data. Not the most informative way of indicating an error perhaps. Kind regards, Erik __* * Erik Marklund, PhD, Marie Sk?odowska Curie INCA Fellow Department of Chemistry ? BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> mailto:erik.markl...@kemi.uu.se>><* *mailto:erik.markl...@kemi.uu.se mailto:erik.markl...@kemi.uu.se>>> On 29 Aug 2017, at 07:20, Apramita Chand mailto:apramita.ch...@gmail.com> mailto:apramita.ch...@gmail.com>><* *mailto:apramita.ch...@gmail.com mailto:apramita.ch...@gmail.com>>>> wrote: Dear All, I've carried out a 100ns simulation of protein in water and want to calculate hydrogen bond (forward) lifetime between Protein-Water. Initially, I thought it would be better to analyse hydrogen bonds in last 60ns of simulation, so I truncated the trajectory using g_trjconv using -b 4 -e 10 as options. The results came as *ACF 10628/10628Normalization for c(t) = 0.0621737 for gh(t) = 2.07246e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.1#Hydrogen bond thermodynamics at T = 300 KFitting parameters chi^2 = 2.8733Q = 0-* *-Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2Forward-0.008 -126.851-666.000 2.8733* (This came for both with and without pbc). I also tried to do it from the g_hbond command itself by giving starting time as 40ns and ending as 100ns, but again it came negative lifetime. Next, I tried g_trjconv with application of -pbc mol -ur compact options on untruncated(100ns) trajectory. The results came as: *ACF 11303/11303Normalization for c(t) = 0.0615891 for gh(t) = 1.23179e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.2#Hydrogen bond thermodynamics at T = 300 KFitting parameters chi^2 =3.03095Q = 0-* *-Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2Forward 0.001 1793.775 23.259 3.03095* When I tried the same with the original unconverted trajectory(without g_trjconv ,without pbc options), I got a lifetime of *2345.890ps*. *My question is ,1) why do the truncated trajectories give negative values for my simulation?* *2)If I take the whole 100ns for analysis of hydrogen bond lifetime, which value should I take, since application of pbc gives a different value than that of the original trajectory value of lifetime.* I would be very grateful for your help. Looking forward to your suggestions Yours sincerely Apramita Chand* -- 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_List
Re: [gmx-users] gmx analyze Luzar analysis
Dear Valerio, Have a glance at the paper by Luzar and Chandler. Btw: your data doesn’t fit with the kinetic model very well, hence the -666 for the integral. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 29 Aug 2017, at 13:52, Valerio Ferrario mailto:valerio.ferra...@gmail.com>> wrote: Dear all, I am trying to obtain parameters for h-bonds. I used the tool gmx hbonds with -ac option but resulted in segmentation fault. Therefore from the normal gmx hbond output I used gmx analyze to obtain the autocorrelation function. Therefore, using again gmx analyze with -luzar options and the autorrelated xvg as input I want to calculate the hbonds parameters. I have an output like this: Hydrogen bond thermodynamics at T = 300 K One-way 0.006156.395 17.174 Integral -0.076- 13.220-666.000 Relaxation 1.0380.963 4.478 So my question is: what are the different values? I do not understand what those values indicate since no "legend" is provide. I guess that 2 of the 3 values for relaxation might be k and k´ (rate constant for breaking and reforming hbonds), but I am not sure... Can anyone help me in interpreting those numbers? -- 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<mailto: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] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc
Dear Apramita, IIRC, the time is set to.-666 when gmx hbond fails to fit the kinetic model to the data. Not the most informative way of indicating an error perhaps. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 29 Aug 2017, at 07:20, Apramita Chand mailto:apramita.ch...@gmail.com>> wrote: Dear All, I've carried out a 100ns simulation of protein in water and want to calculate hydrogen bond (forward) lifetime between Protein-Water. Initially, I thought it would be better to analyse hydrogen bonds in last 60ns of simulation, so I truncated the trajectory using g_trjconv using -b 4 -e 10 as options. The results came as *ACF 10628/10628Normalization for c(t) = 0.0621737 for gh(t) = 2.07246e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.1#Hydrogen bond thermodynamics at T = 300 KFitting parameters chi^2 = 2.8733Q = 0--Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2Forward-0.008 -126.851-666.000 2.8733* (This came for both with and without pbc). I also tried to do it from the g_hbond command itself by giving starting time as 40ns and ending as 100ns, but again it came negative lifetime. Next, I tried g_trjconv with application of -pbc mol -ur compact options on untruncated(100ns) trajectory. The results came as: *ACF 11303/11303Normalization for c(t) = 0.0615891 for gh(t) = 1.23179e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.2#Hydrogen bond thermodynamics at T = 300 KFitting parameters chi^2 =3.03095Q = 0--Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2Forward 0.001 1793.775 23.259 3.03095* When I tried the same with the original unconverted trajectory(without g_trjconv ,without pbc options), I got a lifetime of *2345.890ps*. *My question is ,1) why do the truncated trajectories give negative values for my simulation?* *2)If I take the whole 100ns for analysis of hydrogen bond lifetime, which value should I take, since application of pbc gives a different value than that of the original trajectory value of lifetime.* I would be very grateful for your help. Looking forward to your suggestions Yours sincerely Apramita Chand -- 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<mailto: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_cluster
Dear Nikolai, Group 1. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 24 Aug 2017, at 00:07, Smolin, Nikolai mailto:nikolai.smo...@gmail.com>> wrote: Dear All, I am using g_cluster. I am wondering what two groups used for? group 1 for fit and RMSD calculation group 2 for output is g_cluster use RMSD values for clustering based on group 1 or group 2? Any suggestions? Thanks Nikolai -- 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<mailto: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_hbonds calculation on GPU
Dear Rraj, Nope. No-one has made GPU support for gmx hbond (or any other analysis tool as far as I know). Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 9 Aug 2017, at 14:16, Rituraj Purohit mailto:riturajpuro...@gmail.com>> wrote: Hi Everyone, I would like to run g_hbons calculation on GPU boards. I could only find --nthreads option to fasten my calculations, Is it possible to use GPU boards for this like mdrun. reg Rraj -- 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<mailto: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] Regarding indexing to calculate hydrogen bond autocorrelation function
On 26 Jul 2017, at 19:04, Dilip H N mailto:cy16f01.di...@nitk.edu.in>> wrote: but i dont have any OH or NH groups in glycine,water mixture... Your water is packed with OH, and glycine has both NH and OH. Kind regards, Erik -- 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] ForceField for Zn
…here: https://kamerlinlab.com/ On 24 Jul 2017, at 14:14, Erik Marklund mailto:erik.markl...@kemi.uu.se>> wrote: Hi, Metal ions are tricky, and Zn is particularly beasty. Check out Kammerlin’s work in this area. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se> On 24 Jul 2017, at 13:24, Anjali Patel mailto:anjalipatel60...@gmail.com><mailto:anjalipatel60...@gmail.com>> wrote: Hello to all In my pdb structure their are two ion of Zn; Can anyone suggest which forcefield is appropriate for that. With regards Anjali Patel Research Scholar Department of Physics The M S University of Baroda, Vadodara-390002 -- 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<mailto:gmx-users-requ...@gromacs.org><mailto: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<mailto: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] ForceField for Zn
Hi, Metal ions are tricky, and Zn is particularly beasty. Check out Kammerlin’s work in this area. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 24 Jul 2017, at 13:24, Anjali Patel mailto:anjalipatel60...@gmail.com>> wrote: Hello to all In my pdb structure their are two ion of Zn; Can anyone suggest which forcefield is appropriate for that. With regards Anjali Patel Research Scholar Department of Physics The M S University of Baroda, Vadodara-390002 -- 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<mailto: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] Third column of the " hbnum.xvg " file?...What is it meant for ?
Hi Mark, Exactly. But we want to phrase it such that it is legible in the legend if the file is plotted. Erik On 1 Jun 2017, at 16:51, Mark Abraham mailto:mark.j.abra...@gmail.com>> wrote: Hi, "Pairs within 0.35" has misled David, Justin and I, and doubtless others... without clarification, it is normal to assume that if a hydrogen bond is "pairs within 0.35 nm and a suitable angle," then "pairs within 0.35" would be a superset of the former. But the field is actually "pairs within 0.35 that do not satisfy the angle requirement." Mark On Thu, Jun 1, 2017 at 3:47 PM Erik Marklund mailto:erik.markl...@kemi.uu.se>> wrote: Yes. The sets have no overlap. But for some reason putting that in a short description seems difficult :-) On 1 Jun 2017, at 15:31, Mark Abraham mailto:mark.j.abra...@gmail.com>> wrote: Hi, I still don't understand your description. Is the third column *additional* pairs within 0.35 that do not satisfy the angle criterion? Mark On Sat, May 27, 2017 at 4:36 PM Erik Marklund mailto:erik.markl...@kemi.uu.se>> wrote: On 26 May 2017, at 22:12, David van der Spoel mailto:sp...@xray.bmc.uu.se> <mailto:sp...@xray.bmc.uu.se>> wrote: On 26/05/17 22:05, Erik Marklund wrote: “Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which is why they are sometimes fewer than the hbonds. Therefore I would assume they are more instead. They sometimes are, but not necessarily. I pointed it out because sometimes people ask if g_hbond is buggy when they see that there are occasionally lower numbers in the third column, assuming that it contains all pairs within 3.5 Å regardless of angle which should more numeorus than the pairs that also fullfil the angle criterion. That’s not the meaning of the third column however. Kind regards, Erik On 26 May 2017, at 19:38, Adarsh V. K. mailto:adarsh_p13008...@nitc.ac.in> <mailto:adarsh_p13008...@nitc.ac.in>> wrote: Dear all, The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg " I would like to edit the file before viewing in 'Xmgrace' I opened the hbnum.xvg using 'gedit'. It shows following details (see below) Can you please tell me what is there in the third column of the file? - # gmx hbond is part of G R O M A C S: # # GROtesk MACabre and Sinister # @title "Hydrogen Bonds" @xaxis label "Time (ps)" @yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" 02 7 10 2 5 20 4 3 30 3 2 40 3 3 50 5 1 60 3 6 70 3 6 80 2 3 90 5 1 100 3 3 -- 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<mailto:gmx-users-requ...@gromacs.org>mailto:gmx-users-requ...@gromacs.org>>. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205 <018-471%2042%2005> <018-471%2042%2005> . http://www.icm.uu.se<http://www.icm.uu.se/> -- 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<mailto:gmx-users-requ...@gromacs.org&g
Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?
Yes. The sets have no overlap. But for some reason putting that in a short description seems difficult :-) > On 1 Jun 2017, at 15:31, Mark Abraham wrote: > > Hi, > > I still don't understand your description. Is the third column *additional* > pairs within 0.35 that do not satisfy the angle criterion? > > Mark > > On Sat, May 27, 2017 at 4:36 PM Erik Marklund > wrote: > >> >> >> On 26 May 2017, at 22:12, David van der Spoel > <mailto:sp...@xray.bmc.uu.se>> wrote: >> >> On 26/05/17 22:05, Erik Marklund wrote: >> “Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which >> is why they are sometimes fewer than the hbonds. >> >> Therefore I would assume they are more instead. >> >> >> They sometimes are, but not necessarily. I pointed it out because >> sometimes people ask if g_hbond is buggy when they see that there are >> occasionally lower numbers in the third column, assuming that it contains >> all pairs within 3.5 Å regardless of angle which should more numeorus than >> the pairs that also fullfil the angle criterion. That’s not the meaning of >> the third column however. >> >> Kind regards, >> Erik >> >> On 26 May 2017, at 19:38, Adarsh V. K. > <mailto:adarsh_p13008...@nitc.ac.in>> wrote: >> >> Dear all, >> >> The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg " >> >> I would like to edit the file before viewing in 'Xmgrace' >> >> I opened the hbnum.xvg using 'gedit'. It shows following details (see >> below) >> >> Can you please tell me what is there in the third column of the file? >> >> - >> # gmx hbond is part of G R O M A C S: >> # >> # GROtesk MACabre and Sinister >> # >> @title "Hydrogen Bonds" >> @xaxis label "Time (ps)" >> @yaxis label "Number" >> @TYPE xy >> @ view 0.15, 0.15, 0.75, 0.85 >> @ legend on >> @ legend box on >> @ legend loctype view >> @ legend 0.78, 0.8 >> @ legend length 2 >> @ s0 legend "Hydrogen bonds" >> @ s1 legend "Pairs within 0.35 nm" >> 02 7 >> 10 2 5 >> 20 4 3 >> 30 3 2 >> 40 3 3 >> 50 5 1 >> 60 3 6 >> 70 3 6 >> 80 2 3 >> 90 5 1 >> 100 3 3 >> -- >> 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-requ...@gromacs.org>. >> >> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Head of Department, Cell & Molecular Biology, Uppsala University. >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205 <018-471%2042%2005> >> . >> http://www.icm.uu.se<http://www.icm.uu.se/> >> -- >> 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-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] Third column of the " hbnum.xvg " file?...What is it meant for ?
Hi Mark, Thinking out loud: “Non-Hbonding pairs within 3.5 Å”. Kind regards, Erik > On 27 May 2017, at 17:56, Mark Abraham wrote: > > Hi, > > So what should we document in the help text as the meaning, so we don't > keep having emails about this? > > Mark > > On Sat, May 27, 2017 at 4:36 PM Erik Marklund > wrote: > >> >> >> On 26 May 2017, at 22:12, David van der Spoel > <mailto:sp...@xray.bmc.uu.se>> wrote: >> >> On 26/05/17 22:05, Erik Marklund wrote: >> “Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which >> is why they are sometimes fewer than the hbonds. >> >> Therefore I would assume they are more instead. >> >> >> They sometimes are, but not necessarily. I pointed it out because >> sometimes people ask if g_hbond is buggy when they see that there are >> occasionally lower numbers in the third column, assuming that it contains >> all pairs within 3.5 Å regardless of angle which should more numeorus than >> the pairs that also fullfil the angle criterion. That’s not the meaning of >> the third column however. >> >> Kind regards, >> Erik >> >> On 26 May 2017, at 19:38, Adarsh V. K. > <mailto:adarsh_p13008...@nitc.ac.in>> wrote: >> >> Dear all, >> >> The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg " >> >> I would like to edit the file before viewing in 'Xmgrace' >> >> I opened the hbnum.xvg using 'gedit'. It shows following details (see >> below) >> >> Can you please tell me what is there in the third column of the file? >> >> - >> # gmx hbond is part of G R O M A C S: >> # >> # GROtesk MACabre and Sinister >> # >> @title "Hydrogen Bonds" >> @xaxis label "Time (ps)" >> @yaxis label "Number" >> @TYPE xy >> @ view 0.15, 0.15, 0.75, 0.85 >> @ legend on >> @ legend box on >> @ legend loctype view >> @ legend 0.78, 0.8 >> @ legend length 2 >> @ s0 legend "Hydrogen bonds" >> @ s1 legend "Pairs within 0.35 nm" >> 02 7 >> 10 2 5 >> 20 4 3 >> 30 3 2 >> 40 3 3 >> 50 5 1 >> 60 3 6 >> 70 3 6 >> 80 2 3 >> 90 5 1 >> 100 3 3 >> -- >> 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-requ...@gromacs.org>. >> >> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Head of Department, Cell & Molecular Biology, Uppsala University. >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205 <018-471%2042%2005> >> . >> http://www.icm.uu.se<http://www.icm.uu.se/> >> -- >> 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-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] Third column of the " hbnum.xvg " file?...What is it meant for ?
On 26 May 2017, at 22:12, David van der Spoel mailto:sp...@xray.bmc.uu.se>> wrote: On 26/05/17 22:05, Erik Marklund wrote: “Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which is why they are sometimes fewer than the hbonds. Therefore I would assume they are more instead. They sometimes are, but not necessarily. I pointed it out because sometimes people ask if g_hbond is buggy when they see that there are occasionally lower numbers in the third column, assuming that it contains all pairs within 3.5 Å regardless of angle which should more numeorus than the pairs that also fullfil the angle criterion. That’s not the meaning of the third column however. Kind regards, Erik On 26 May 2017, at 19:38, Adarsh V. K. mailto:adarsh_p13008...@nitc.ac.in>> wrote: Dear all, The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg " I would like to edit the file before viewing in 'Xmgrace' I opened the hbnum.xvg using 'gedit'. It shows following details (see below) Can you please tell me what is there in the third column of the file? - # gmx hbond is part of G R O M A C S: # # GROtesk MACabre and Sinister # @title "Hydrogen Bonds" @xaxis label "Time (ps)" @yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" 02 7 10 2 5 20 4 3 30 3 2 40 3 3 50 5 1 60 3 6 70 3 6 80 2 3 90 5 1 100 3 3 -- 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<mailto:gmx-users-requ...@gromacs.org>. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se<http://www.icm.uu.se/> -- 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<mailto: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] Third column of the " hbnum.xvg " file?...What is it meant for ?
“Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which is why they are sometimes fewer than the hbonds. Kind regards, Erik > On 26 May 2017, at 19:38, Adarsh V. K. wrote: > > Dear all, > > The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg " > > I would like to edit the file before viewing in 'Xmgrace' > > I opened the hbnum.xvg using 'gedit'. It shows following details (see below) > > Can you please tell me what is there in the third column of the file? > > - > # gmx hbond is part of G R O M A C S: > # > # GROtesk MACabre and Sinister > # > @title "Hydrogen Bonds" > @xaxis label "Time (ps)" > @yaxis label "Number" > @TYPE xy > @ view 0.15, 0.15, 0.75, 0.85 > @ legend on > @ legend box on > @ legend loctype view > @ legend 0.78, 0.8 > @ legend length 2 > @ s0 legend "Hydrogen bonds" > @ s1 legend "Pairs within 0.35 nm" > 02 7 >10 2 5 >20 4 3 >30 3 2 >40 3 3 >50 5 1 >60 3 6 >70 3 6 >80 2 3 >90 5 1 > 100 3 3 > -- > 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] gmx hbond
Dear Moshen, I doubt the difference in versions will cause any problems in this case. The second column is ill-described. It contains the number of pairs within 0.3 nm that don’t fulfil the angle criterion. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 14 Apr 2017, at 03:20, Mohsen Ramezanpour mailto:ramezanpour.moh...@gmail.com>> wrote: Hi Gromacs users, I have a question regarding the output file from g_hbond: First:I have done my simulations with version 4.6.7 and doing the analysis with version 2016.2 Will this cause any hidden problem in analysis? the analysis is working fine but I am asking about the correctness of results because of this change. Second and the main question: When I use this command: gmx hbond -f md.xtc -n index.ndx -s file.tpr -num hbond.xvg -g test.log -r 0.30 I get this: ... @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.3 nm" 400 0 * 40.1 1 0* 40.2 1 3 40.3 2 2 40.4 0 2 40.5 1 1 * 40.6 2 0* ... the first column is time frame the second is number of h-bonds the third is "Pairs within 0.3 nm" by -r 0.30 I wanted to change the cut-off for h-bond definition. i.e. report a h-bond if and only if the D...A distance is less or equal to 0.30 ns, AND, the angle of H..D...A is less or equal than 35 (this angle is default in 2016.2 version). Regarding the highlighted lines: How it is possible that the there is not any pair in this distance but we still have hbond? If they are not in this cut-off, thy should not be recognized as hbond either. I assume the pair means the D...A pair because I did NOT use -noda option. Also, it does not give any test.log file, and other problems :-) Please let me know your opinion about this results. Thanks in advance for your reply Cheers Mohsen -- *Rewards work better than punishment ...* -- 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<mailto: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] Md simulation by Gromacs
Dear Maria, Let’s keep this to the user list. I am first of all not a private tutor. Secondly, the answers you get (below) might be relevant for others. > On 6 Apr 2017, at 16:04, maria khan wrote: > > Good evening Dear sir Erik Marklund.. > > I am very Thankful for your attention ..Actually i even dont know the basics > and one of the NAMD expert user told me so that gromacs use united atom ff > thats why gromacs is fast and NAMD use all atom thats why it is slow. > That is incorrect. Gromacs can do both all-atom and united-atom. Gromacs can also make use of virtual sites, which allows for a longer time step, hence more simulated ns per hour. You can also choose not to. And then there are on top of that a number of reasons why gromacs is really fast without cutting (important) corners. > Now my problems are : is there any option for considering hydrogen atom to > process its calculation in MD run as last time when i did simulation i > applied the command of ignoring hydrogen atom ,,secondly what is the > difference Between ignoring h- atoms and considering it in MD running.I mean > would it effect the result of calculation after MD run..and if there is > option for taking h- atom as part of amino acid then why there is an option > for ignoring it.. > Please be specific. Are you referring to pdb2gmx -ignh? That just tells pdb2gmx to derive hydrogen positions and occupancies based on hydrogen bonding patterns and force-field-related information. It doesn’t normally produce topologies without hydrogens, and the hydrogens are thus part of the subsequent simulations. See the user-list archives. I know this has been discussed before. And you can also inspect the output files to see what they contain. > Furthermore i dont know about forming parameters for my ligand thats is > alkaloid so im confuse how to form its parameter and if some one has > published its parameters then how i can find..i just need a stepwise protocol > for MD simulation,,most of the manuals are not understandable my majors are > pure biochemistry and mostly the explanations there are mathematica basedl. > Well, parametrisation is not really for beginners. I also think others are more experienced in that area than I am. > And yes i have studied the old version of manuals not updated one. > > IF u have simplist form of manuals or any other stuff, kindly send me that i > very thankful. Last time u shared a paper of ur self but it was not my > research related. > -- 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] Fast energy evaluation
Dear Andras, Concatenate all structures into one trajectory and issue gmx mdrun -rerun. That will evaluate the energies for all conformations. You will of course need a tpr file too. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 6 Apr 2017, at 12:39, András Ferenc WACHA mailto:wacha.and...@ttk.mta.hu>> wrote: Dear Gromacs Users, does someone know a way to quickly evaluate the energy of a few structures? In more detail: I have several conformations of the same peptide, stored in PDB format. In principle, they have the same topology. I want to optimize various force field parameters, which involves the need to calculate the energy multiple times, each time with different bond/angle/dihedral parameters. Currently I use a single-step mdrun (integrator = steep) and "gmx_energy" to extract the energy terms, but the overhead of calling grompp, mdrun and energy in each case for each structure is too much. In charmm you can write a script for this job: is there an equivalent in gromacs without the overheads? Thank you in advance. Best regards, András Wacha -- András Ferenc Wacha, PhD research fellow, CREDO instrument responsible Biological Nanochemistry Research Group Institute of Materials and Environmental Chemistry Research Centre for Natural Sciences Hungarian Academy of Sciences (RCNS HAS) Magyar tudósok körútja 2. H-1117 Budapest, Hungary Phone: +36-1-382-6427 Web: http://bionano.ttk.mta.hu, CREDO SAXS instrument: http://credo.ttk.mta.hu -- 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<mailto: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] (no subject)
Dear Maria, Are you confusing gromos and gromacs? In the manual, under the Force fields heading: "GROMACS 2016 includes several force fields, and additional ones are available on the website. If you do not know which one to select we recommend GROMOS-96 for united-atom setups and OPLS-AA/L for all-atom parameters. That said, we describe the available options in some detail.” (The comment about OPLS-AA/L is probably very old and in need of revision.) Then follows subsections describing a range of supported force fields, most of which are all-atom. The phrase “united-atom” occurs only once in the manual, in the sentence quoted above. What made you think gromacs is united-atom only? Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 5 Apr 2017, at 12:00, maria khan mailto:mariabiochemi...@gmail.com>> wrote: Dear Erik.. I have studied the manuals of gromacs and from that i came to know that gromacs use united atom ff thats why i asked and in manuals many things has been explained by quantum basis,,which is not understandable for me. How can i find ff parameters for my ligand of interest?? also if ff parameters are not in published form then it means i will not be able to use that ligand for MD run?? My ligand of interest is alkaloid. and i dont know how can i make the parameters for it. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org<mailto: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] Hydrogen bond occupancy
Dear Neha, What fraction of the time the ligand hydrogen bonds to whatever it interacts with. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 5 Apr 2017, at 10:00, Neha Gupta mailto:nehaphysic...@gmail.com>> wrote: Hi gromacs users, What is meant by Hydrogen bond occupancy in protein ligand simulations? What information do we extract from % of hydrogen bond occupancy? Thanks, Neha -- 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<mailto: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] Charmm ff compatibility with Gromacs
Dear Maria, Please see below. Kind regards, Erik > On 5 Apr 2017, at 09:08, maria khan wrote: > > Hello Gromacs users.. > > Charmm 37 ff is for charmm and Namd which is all atom ff using codes,,and > gromacs is united atom so how can its results will be reliable as these are > different things??.My protein of interest is having DNA.. > This does not make sense. What do you mean by “using codes”? And while gromacs can do united atom, all-atom force fields are routinely used with gromacs. > Secondly how can i find ff parameters for my ligand of interest?? also if > ff parameters are not in published form then it means i will not be able to > use that ligand for MD run?? > > Regards.. > -- > 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] vsites with CHARMM force fields
On 31 Mar 2017, at 10:51, Ramon Crehuet Simon mailto:ramon.creh...@iqac.csic.es>> wrote: In that case, does it make sense to use virtual sites to allow 4fs time step? In other words, if vsites remove the fastest degrees of freedom, but we do not constrain bond distances, will a 4 fs time-step be stable? No. Kind regards, Erik Marklund -- 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] solvate with hexagonal box
Done! https://redmine.gromacs.org/issues/2148 On 28 Mar 2017, at 10:24, Erik Marklund mailto:erik.markl...@kemi.uu.se>> wrote: Hi Mark, Thanks. I will do so once my collaborators confirm that it’s ok that I upload the structure files. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se> On 27 Mar 2017, at 20:20, Mark Abraham mailto:mark.j.abra...@gmail.com><mailto:mark.j.abra...@gmail.com>> wrote: Hi, Sounds like there is something worth improving, although I can't answer your questions right now. Please open an issue on https://redmine.gromacs.org and attach a tarball of suitable inputs for the two(?) cases. Mark On Mon, 27 Mar 2017 13:54 Erik Marklund mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se>> wrote: Dear gmx-users, We are trying to merge a box containing a peripheral membrane protein with another box generated with memgen. Both boxes are hexagonal and exactly the same size,Naively, we thought that gmx solvate -cp protein.gro -cs membrane_and_water.gro would do the trick. Unfortunately, this causes gmx solvate to crash: Generating solvent configuration Will generate new solvent configuration of 1x2x1 boxes Solvent box contains 99373 atoms in 28208 residues Removed 12253 solvent atoms due to solvent-solvent overlap Removed 5122 solvent atoms due to solute-solvent overlap Sorting configuration Found 2 different molecule types: POPE ( 52 atoms): 233 residues SOL ( 3 atoms): 23294 residues gmx(16892,0x7fffaa24f3c0) malloc: *** error for object 0x7fe36d0008f0: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug Abort trap: 6 So we then tried to remove the membrane, keeping only the water, and use that system as the argument for -cs. Gmx solvate doesn’t crash now, but the output file has strange gaps of some size in the water parts, which cannot be explained by the removed lipids. Can gmx solvate not handle non-orthogonal boxes as arguments for -cs? The whole point in doing it this way was to avoid water molecules being inserted in the membrane. Perhaps overkill, but I am quite surprised at how bad things went with gmx solvate. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se> -- 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<mailto:gmx-users-requ...@gromacs.org><mailto: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<mailto:gmx-users-requ...@gromacs.org><mailto: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<mailto: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] Bond energy difference between CHARMM and GROMACS
Dear Yvon, Are you sure you ‘re not constraining, say, H-bonds in one and not the other? Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 28 Mar 2017, at 07:55, Yvon Wong mailto:wong.y...@gmail.com>> wrote: I try to compare the energy in CHARMM and GROMACS. After running 4 systems I found the dihedral energies are the same, but the bond energies are different. Can somebody help me to solve this problem? (1)Only one residue: MET Bond: 0.44*4.18 = 1.839 (CHARMM) > 2.587 (GROMACS) (different) Dihedral: 3.687* 4.18 = 15.4116 (CHRAMM) > 15.4448 (GROMACS) (the same) (2)Only one residue: GLY BONDS: 0.34243*4.18= 1.431 ===> 1.209 Dihedrals 1.77911*4.18 = 7.436 ===> 7.447 (3)5 -residue: ASN GLY PHE TRP THR BONS: 4.82777* 4.18=20.1800 > 22.58 DIHE: 37.82747*4.18 = 158.1188 > 158.504 (4)20- residue: GLY LYS MET PHE SER TRP TYR VAL ALA ARG CYS VAL PRO TRP MET SER SER LYS LYS MET BONDS 17.48049 * 4.18 =73.068 ===> 78.64 DIHE 185.71* 4.18 = 776.26 ===> 777.32 -- 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<mailto: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] solvate with hexagonal box
Hi Mark, Thanks. I will do so once my collaborators confirm that it’s ok that I upload the structure files. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 27 Mar 2017, at 20:20, Mark Abraham mailto:mark.j.abra...@gmail.com>> wrote: Hi, Sounds like there is something worth improving, although I can't answer your questions right now. Please open an issue on https://redmine.gromacs.org and attach a tarball of suitable inputs for the two(?) cases. Mark On Mon, 27 Mar 2017 13:54 Erik Marklund mailto:erik.markl...@kemi.uu.se>> wrote: Dear gmx-users, We are trying to merge a box containing a peripheral membrane protein with another box generated with memgen. Both boxes are hexagonal and exactly the same size,Naively, we thought that gmx solvate -cp protein.gro -cs membrane_and_water.gro would do the trick. Unfortunately, this causes gmx solvate to crash: Generating solvent configuration Will generate new solvent configuration of 1x2x1 boxes Solvent box contains 99373 atoms in 28208 residues Removed 12253 solvent atoms due to solvent-solvent overlap Removed 5122 solvent atoms due to solute-solvent overlap Sorting configuration Found 2 different molecule types: POPE ( 52 atoms): 233 residues SOL ( 3 atoms): 23294 residues gmx(16892,0x7fffaa24f3c0) malloc: *** error for object 0x7fe36d0008f0: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug Abort trap: 6 So we then tried to remove the membrane, keeping only the water, and use that system as the argument for -cs. Gmx solvate doesn’t crash now, but the output file has strange gaps of some size in the water parts, which cannot be explained by the removed lipids. Can gmx solvate not handle non-orthogonal boxes as arguments for -cs? The whole point in doing it this way was to avoid water molecules being inserted in the membrane. Perhaps overkill, but I am quite surprised at how bad things went with gmx solvate. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se> -- 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<mailto: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<mailto: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] solvate with hexagonal box
Dear gmx-users, We are trying to merge a box containing a peripheral membrane protein with another box generated with memgen. Both boxes are hexagonal and exactly the same size,Naively, we thought that gmx solvate -cp protein.gro -cs membrane_and_water.gro would do the trick. Unfortunately, this causes gmx solvate to crash: Generating solvent configuration Will generate new solvent configuration of 1x2x1 boxes Solvent box contains 99373 atoms in 28208 residues Removed 12253 solvent atoms due to solvent-solvent overlap Removed 5122 solvent atoms due to solute-solvent overlap Sorting configuration Found 2 different molecule types: POPE ( 52 atoms): 233 residues SOL ( 3 atoms): 23294 residues gmx(16892,0x7fffaa24f3c0) malloc: *** error for object 0x7fe36d0008f0: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug Abort trap: 6 So we then tried to remove the membrane, keeping only the water, and use that system as the argument for -cs. Gmx solvate doesn’t crash now, but the output file has strange gaps of some size in the water parts, which cannot be explained by the removed lipids. Can gmx solvate not handle non-orthogonal boxes as arguments for -cs? The whole point in doing it this way was to avoid water molecules being inserted in the membrane. Perhaps overkill, but I am quite surprised at how bad things went with gmx solvate. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> -- 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] COMMAND IN HBOND
Dear Neha, Gromacs doesn’t offer that much in terms of viewing. This sounds more like a PyMol/VMD/Other question. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 24 Mar 2017, at 14:33, Neha Gupta mailto:nehaphysic...@gmail.com>> wrote: Hi gromacs users, What is the command to view the residues of protein and atoms of ligand involved in hydrogen bond? Thanks, Neha -- 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<mailto: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] Failed to execute command: Try specifying your dssp version with the -ver option.
Dear Atila, Have you confirmed that your dssp is working? Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 28 Feb 2017, at 07:11, Andrew Bostick mailto:andrew.bosti...@gmail.com>> wrote: Dear Gromacs users, I did MD simulation of my peptide on Gromacs 5.1.3. I want to do do_dssp analysis. After using following command: gmx_mpi do_dssp -f *.xtc -s *.tpr -n index.ndx -o -sc Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. According to the manuall for gmx do_dssp, I used following command: gmx_mpi do_dssp -f *.xtc -s *.tpr -n index.ndx -o -sc -ver 2 But, again: Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How to fix it? Any help will highly be appreciated. Best, Atila -- 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<mailto: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] run parameters
Dear Nikhil, It depends, but generally no electrostatic cut-offs since there is no dielectric medium, making the effective range of electrostatics very long. And no pbc. If you are doing NVE with constraints you might want to increase lincs-iter and -order from their default values. Kind regards, __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 10 Feb 2017, at 13:06, NIKHIL JOSHI mailto:nikhil.joshi...@gmail.com>> wrote: hii What will be the best mdp file options for production run for polymer in vacuum simulation.? -- 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<mailto: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] Hydrogen bond problem
Dera Tasneem, First thing to check is if you have read the -hbn or -hbm output upside down. This is a common mistake. Seriously. Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 8 Feb 2017, at 06:06, Tasneem Kausar mailto:tasneemkausa...@gmail.com>> wrote: Dear all I am calculating hydrogen bond between protein and drug molecule using gmx hbond tool. I am using default value for hydrogen bond radius. Here is the command: gmx hbond -f protein_drug.xtc -s protein+drug.tpr -hbn hbond.ndx -hbm hbond.ndx I am selecting group 1 and 13. It shows many hydrogen bonds. Then I have calculated the percentage of hydrogen bond using perl script. There are there hydrogen bonds that show a significant existence. I wrote the snapshots of trajectories having all three hydrogen bonds. In every snapshot, when visulaized with a visulaization sofware such as chimera and LIGPLUS hydrogen bond of serin does not exist though it shows hydrophobic interaction with drug molecule. LIGPLUS gives a provision to show the missing hydrogen bond. When I have plotted by taking consideration serin hydrogen bond, it shows a bond length of 4.26 angstrom and like that in almost every extracted snapshot. In existence map serin is showing 92% abundance of hydrogen bond. This problem is occurring with serin only. Why is this happening? Is there a cut off problem with the visualization tools or something else? Is there an method to write the hydrogen bond and there distance simultaneously. Thanks in Advance Tasneem -- 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<mailto: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] ignoring -h atoms
Dear Maria, I’m not saying that it never makes a difference for the topology generation, but it depends on the quality of your input structure. Justin and I both gave examples of why you might want to use it. When you do, -ignh ignores the hydrogens in the input pdb and uses the rtp to model new ones. I don’t understand why you say that the “ff its ignore it”. As for what is most reliable, that again depends on the quality of the input structure. Pdb2gmx -ignh normally does a good job. Kind regards, Erik > On 8 Feb 2017, at 07:20, maria khan wrote: > > Dear ERIK.. > > """..No. -ignh ignores the hydrogen atoms in the input structure, but uses > the rtp file(s) to generate new hydrogens. This is useful, for example, > when some hydrogens are missing in the pdb file. The structure and topology > will therefore contain hydrogens in the end also with -ignh.""".. > > > now i have confusion if the ff ist ignore it and then in rtp files consider > it..so why it at ist it ignores..there is no need to do so.after all h-atom > will be same if it is in input file or when later form by rtp file. > > secondly what will be the consequences,,if in case it is ignored or not > ignored..would it make difference to results in both cases.and if there > would difference in results,,what kind of results are more reliable.??? > > regards.. > -- > 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] Ignoring H-atoms.
> On 7 Feb 2017, at 08:35, Amir Zeb wrote: > > Hello Maria, > > f igoring h-atom command is applied ,,then forcefield will ignore all the > added h-atoms > > What I know about -ignh flag, it does not mean to remove the h-atoms, > alternatively means that during the topology generation, the force field is > considering the h-atoms as the light atoms and does not pay much attention > to consider their parameters so accurately. No. -ignh ignores the hydrogen atoms in the input structure, but uses the rtp file(s) to generate new hydrogens. This is useful, for example, when some hydrogens are missing in the pdb file. The structure and topology will therefore contain hydrogens in the end also with -ignh. Kind regards, Erik > > it would be a vaccum simulation if > the h-atom will be ignored > > Also, in case of vacuum simulation, I think there is no water addition, > while here we are gonna adding the water during the salvation step of the > procedure. So, I think you don't need to worry about it. > > At the end, I would like to appraise in deep the explanation of other users. > > Cheers! > > Amir > > On Mon, Feb 6, 2017 at 10:12 PM, maria khan > wrote: > >> Dear Gromacs users,, >> >> if igoring h-atom command is applied ,,then forcefield will ignore all the >> added h-atoms,,,so my question is then it would be a vaccum simulation if >> the h-atom will be ignored,,secondly the results will be also differnt then >> when h-atoms are considered. >> >> Regards.. >> -- >> 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] INDEX
Dear Subashini, You forgot to provide trjconv with the index file you created. Try gmx trjconv -n your_index_file.ndx … Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 6 Feb 2017, at 13:06, Subashini .K mailto:subashi...@hotmail.com>> wrote: Hi gromacs users, I want to visualize the results of simulations using the command gmx trjconv -s em.gro -f eq.xtc -e 1000.0 -o movie.pdb Wish to see Protein and ligand simulations together in the pdb file. But, when the command is given, we can either select protein group or ligand group Before this was done, The following commands were given (1) gmx make_ndx -f em.gro In this step, group No 22 was created namely Protein-ligand (2)genrestr -f em.gro -n index.ndx -fc 500 500 500 (3) gmx grompp -f nvt.mdp -c em.gro -p complex_GMX.top -n index.ndx -o nvt.tpr (4) gmx mdrun -deffnm nvt However, despite typing make_ndx 1|13 (Protein-ligand), it is not reflected in the movie.pdb file. What to do? Can someone help? Thanks, Subashini.K -- 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<mailto: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] Installing DSSP
Dear Soumadwip, This is not a problem with do_dssp, but with your deep installation. My guess is that you have not completed the installation of dssp. Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 3 Feb 2017, at 07:51, soumadwip ghosh mailto:soumadwipgh...@gmail.com>> wrote: Hello all, I am trying to install dssp in centos 7 for determining the secondary structure of a protein in combination with do_dssp. These are the steps I followed: 1. installation directory : /opt/apps/dssp/dssp-2.2.1/ 2. but there is no dssp executable in the dssp-2.2.1 directory 3. however there was a dssp.o file in the obj directory of dssp-2.2.1 4. we renamed the dssp.o file to dssp and moved it to dssp-2.2.1 directory 5. ln -s /opt/apps/dssp/dssp2.2.1/dssp /usr/local/bin/ 6. export dssp=/usr/local/bin/dssp but inspite of executing the above steps, when we run the do_dssp command we get the following error : Fatal error: DSSP executable (usr/local/bin/dssp/dssp) does not exist (use setenv DSSP) PS. we are using bash I have read various threads on the errors related to do_dssp but could not find a solution. Any kind of help would be appreciated. Best, Soumadwip Ghosh Research Associate Indian Institute of Technology Bombay India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org<mailto: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] posre.itp for dimer protein
Hi, Check your top-file. It will include all relevant posre.itp files if the POSRE preprocessor macro is defined, assuming you created your topology with pdb2gmx. Add -DPOSRE to the definitions in your mdp-file and everything will be taken care of. Kind regards, Erik > On 1 Feb 2017, at 23:11, chemocev marker wrote: > > Hi > I am running a simulation of a dimer protein and I did not included the > posre.itp comments in my topology.top file and protein is moving out of the > box. But I find that gromacs has produced the separate posre.itp for each > chain. Should I include the posre.itp for both chain ? or there is some way > to make only one posre.itp for the complete dimer protein. > > > thanks > > J Vitali > -- > 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] (no subject)
Dear Mahbodeh, No. You need to restart your simulations. If the beginning of the trajectories can be recovered, then you can make a continuation from the intact part, but that continuation will not be exact. Kind regards, Erik > On 31 Jan 2017, at 06:51, Mahboobeh Eslami wrote: > > Hi dear GROMACS usersI hope you are well > I performed a md simulation. When simulation was finished, I moved our files > to another place. Unfortunately, trajectory files (.trr and .xtc files) were > damaged. Can I produce new trajectory files form checkpoint file > (.cpt)?Please guide meThank you so muchBest > -- > 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] Dynamics
Dear Rahul, I really don’t think you understand the concept of pbc in molecular simulations. Please read up on the concept in appropriate literature. Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 26 Jan 2017, at 09:25, RAHUL SURESH mailto:drrahulsur...@gmail.com>> wrote: Thank you But if I am extending my simulation with protein outside the box, then there will not be any effect of water molecules right.? On Thu, 26 Jan 2017 at 1:25 PM, mailto:jkrie...@mrc-lmb.cam.ac.uk>> wrote: Hi Rahul, The protein being out of the box is not a problem except for visualisation and some analysis (e.g. RMSD). For continuing the simulation, it is a completely normal consequence of having periodic boundaries and you shouldn't worry about it. You can then fIx the protein for visualisation and analysis separately to running. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions To continue the simulation just use mdrun as normal but with the -cpi flag. If you want more time than you originally set the mdp to ask for then use tpbconv (gmx convert_tpr in gromacs 5 and later). See http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Best wishes James Hi mark I want to extend it for another 50ns. At 100ns protein is out of the box. Now is t possible to apply boundary conditions and extend.? On Wed, 25 Jan 2017 at 11:12 PM, Mark Abraham wrote: Hi, On Wed, 25 Jan 2017 18:00 RAHUL SURESH wrote: from production output of a monomer for 100ns, there s a instability in the structure from 83ns to 100ns. Many things could be going on here... Also .gro file shows, the protein is out of the cube. Mdrun doesn't care. There's infinitely many equivalent representations of a periodic system. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions gmx make_ndx -f md.gro -o index.ndx trjconv -f md.xtc -s md.tpr -n index.ndx -pbc mol -ur compact -center -o outputfile.xtc I used the above commands to bring the protein to the center of the box. gmx trjconv -f outputfile.xtc -s md.tpr -o newmd.trr And using the above command, extracted a trr file. Now can I extend this job with this trr file as it is or should i give any periodic boundary conditions or should take the conformer structure at 80ns and run for another 50ns? None of this is needed. See http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Whether it makes sense to try to repeat or extend or go back to the start and try to fix something depends on what the "instability" is, and what is causing it. Mark waiting for your valuable note. -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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.o
Re: [gmx-users] Farideh Khamseh shared "profileNH2.xlsx" with you
That ACF looks very strange. How did you calculate it? Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 25 Jan 2017, at 19:51, Farideh Khamseh (via Dropbox) mailto:no-re...@dropbox.com>> wrote: Hi there, Farideh Khamseh (farideh.kham...@gmail.com<mailto:farideh.kham...@gmail.com>) invited you to view the file " profileNH2.xlsx " on Dropbox. View file[1] Enjoy! The Dropbox team [1]: https://www.dropbox.com/l/scl/AADR0hVYXtrYU5y-yFnAEf-3KbNwewzJnMo -- 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<mailto: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] simulation of ternary complex
Dera Maria, Yes that is possible. Be sure to make a good choice of forcefield, so that you have decent parameters for all molecule types in your simulation. Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 24 Jan 2017, at 11:25, maria khan mailto:mariabiochemi...@gmail.com>> wrote: Dear gromacs Users.. I want to simulate ternary complex of protein -DNA -ligand..Is it possible to simulate it combinely? secondly..Gromacs has no graphical interface to visualize results..how can we resolve this issue..Using VMD i have some issues regarding trajectories.. Regards.. Maria khan. ICS,,university of peshawar.. -- 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<mailto: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 concatenate tpr files?
Dear Leila, The RMSD is, by default, calculated with respect to the coordinates in the tpr file, which is why you get different results with different tprs. Which one to choose depends on exactly what you want to measure. Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 23 Jan 2017, at 17:10, leila karami mailto:karami.lei...@gmail.com>> wrote: Dear gromacs users, About the concatenation trajectory files, I have a question. I did 10 MD simulations (each section 10 ns). Now, I want to concatenate all of the trajectories and determine RMSD on whole trajectory. To do this, I used the following command: gmx trjcat -f md1.trr md2.trr md3.trr md4.trr md5.trr md6.trr md7.trr md8.trr md9.trr md10.trr -o all_md.xtc –settime The whole trajectory file made correctly. To determined RMSD, I used the following command. gmx rms -f all_md.xtc -s *.tpr -n index.ndx -o rmsd.xvg -tu ns I want to know, which tpr file must be used? tpr1 or tpr2 or tpr3 or …? I tried this command with md1.tpr and md10.tpr and in each time, RMSD had the different values. So, should I concatenate the tpr files and use the complete tpr file. How can I concatenate the tpr files? Best -- 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<mailto: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 autocorrelation of Rg
I can reproduce your result, and if I change the value of a single datapoint by, say 5% or so, I get a non-zero acf. It could be that cmx analyze is too insensitive for numeric reasons, or it could also be that your data is too sparsely sampled to contain any trace of “memory” in the system. Have you tried calculating the act by other means, xmgrace for instance? Does that yield a similar result? Kind regards, Erik > On 23 Jan 2017, at 12:08, faride badalkhani wrote: > > Kindly find the Rg plot in the following link: > > https://www.dropbox.com/s/8yqkrr0hym6c899/Rg9-polymer%2BLigand.xlsx?dl=0 > > Let me know if you need any other files or information. > > Regards, > F. > > On Mon, Jan 23, 2017 at 2:07 PM, Erik Marklund > wrote: > >> Hi, >> >> Thanks. And the file Rg.xvg looks sound? >> >> Kind regards, >> Erik >> >>> On 23 Jan 2017, at 11:33, faride badalkhani >> wrote: >>> >>> Hi, >>> >>> Thanks for the answer. I used the autocorrelation function of the squared >>> radius of gyration cross-correlation of time course of Rg with itself >> with >>> the following command >>> gmx analyze -f Rg.xvg -ac >>> >>> and the autocorrelation is exactly zero. >>> >>> it is worth mentioning that I have performed the same PMF calculations >> on a >>> polymer-drug system and I did not have any problem in that case. The only >>> difference of that system with this one was in the terminal groups of >>> polymer. The first polymer has protonated surface groups (NH3+) but the >>> second one is neutral (acetylene). >>> >>> Best, >>> F. >>> >>> On Mon, Jan 23, 2017 at 1:42 PM, Erik Marklund >> >>> wrote: >>> >>>> Dear Farideh, >>>> >>>> Can you please inform us about how you calculated the ac? Hard to help >>>> otherwise. Also, is it exactly zero or just very small numbers? >>>> >>>> Kind regards, >>>> Erik >>>> >>>>> On 23 Jan 2017, at 10:50, faride badalkhani >> >>>> wrote: >>>>> >>>>> Dear GROMACS users, >>>>> >>>>> I am performing umbrella sampling on a polymer-ligand system and I >>>> generate >>>>> configurations successfully but the problem is that when I plot the >>>>> autocorrelation function of Rg for each window it is zero for the whole >>>>> time of simulation. I changed the run time for each window but nothing >>>>> changed. Moreover, the initial polymer-ligand structure is equilibrated >>>>> well. >>>>> Any comment or suggestion will be greatly appreciated. >>>>> >>>>> Best, >>>>> Farideh >>>>> -- >>>>> 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] Problem with the autocorrelation of Rg
Hi, Thanks. And the file Rg.xvg looks sound? Kind regards, Erik > On 23 Jan 2017, at 11:33, faride badalkhani wrote: > > Hi, > > Thanks for the answer. I used the autocorrelation function of the squared > radius of gyration cross-correlation of time course of Rg with itself with > the following command > gmx analyze -f Rg.xvg -ac > > and the autocorrelation is exactly zero. > > it is worth mentioning that I have performed the same PMF calculations on a > polymer-drug system and I did not have any problem in that case. The only > difference of that system with this one was in the terminal groups of > polymer. The first polymer has protonated surface groups (NH3+) but the > second one is neutral (acetylene). > > Best, > F. > > On Mon, Jan 23, 2017 at 1:42 PM, Erik Marklund > wrote: > >> Dear Farideh, >> >> Can you please inform us about how you calculated the ac? Hard to help >> otherwise. Also, is it exactly zero or just very small numbers? >> >> Kind regards, >> Erik >> >>> On 23 Jan 2017, at 10:50, faride badalkhani >> wrote: >>> >>> Dear GROMACS users, >>> >>> I am performing umbrella sampling on a polymer-ligand system and I >> generate >>> configurations successfully but the problem is that when I plot the >>> autocorrelation function of Rg for each window it is zero for the whole >>> time of simulation. I changed the run time for each window but nothing >>> changed. Moreover, the initial polymer-ligand structure is equilibrated >>> well. >>> Any comment or suggestion will be greatly appreciated. >>> >>> Best, >>> Farideh >>> -- >>> 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] Problem with the autocorrelation of Rg
Dear Farideh, Can you please inform us about how you calculated the ac? Hard to help otherwise. Also, is it exactly zero or just very small numbers? Kind regards, Erik > On 23 Jan 2017, at 10:50, faride badalkhani wrote: > > Dear GROMACS users, > > I am performing umbrella sampling on a polymer-ligand system and I generate > configurations successfully but the problem is that when I plot the > autocorrelation function of Rg for each window it is zero for the whole > time of simulation. I changed the run time for each window but nothing > changed. Moreover, the initial polymer-ligand structure is equilibrated > well. > Any comment or suggestion will be greatly appreciated. > > Best, > Farideh > -- > 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] Simulation in vacuum
Dear Mijiddorj, We have had good energy conservation with bond constraints and a 1 fs time step under double precision, using a setup similar to yours. We did not remove rotation however, because we wanted to honour the rotational temperature of the system. Whether that is an important choice or not is for you to decide, but do note that the spinning ice cube effect is an artefact arising from the thermostat, which is turned off in your setup. Whether bonds should be constrained or not is related to what your scientific questions are, and the time step depends on what bonds are constrained, if any. I can’t remember what LINCS parameters we used, but be prepared to increase the order and/or iter. Consult the manual for details. Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 20 Jan 2017, at 11:01, Мижээ Батсайхан mailto:b.mijidd...@gmail.com>> wrote: Dear gmx users, I would like to get experience of simulation in vacuum. Please suggest me tutorials, and advice me. I read about following comments which written on Shourjiya Sanyal tutorial. Can you discuss about it? In vacuum simulation, integration should be reduced compared to solvent phase simulation. Periodic boundary conditions, non-bonded interaction cutoffs, temperature coupling and pressure coupling were all turned off. Center of mass translation and rotation around the center of mass are to be removed to avoid the fast spin of the protein. One should also constrain the hydrogen bond using algorithms like SHAKE/LINCS. http://www.shourjya.thinkbiosolution.com/md-simulation-in-gas-phasevacuum-with-gromacs/ Best regards, Mijiddorj -- 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] Creating a temperature gradient in water
Dear Ibrahim, Do you use pbc? If so, how does that work with your gradient? Kind regards, Erik > On 10 Jan 2017, at 15:00, ibrahim khalil > wrote: > > Dear gromacs users, > > I have a simulation box containing nothing but water (TIP3P). I want to > create a temperature gradient within water (ie. 300K in the left side and > 500K in the right side of the simulation box). > > I have successfully applied different temperatures to different groups in > my other simulations (for example, different temperatures for water and > proteins). > > How can apply different temperatures within the same group of liquids (in > my case, water)? > > Thanks in advance. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] generation of ions additional to solvent molecules
Dear Raag, Where would those extra ions go? If you need a higher number density of ions than the solvent (assuming the box is full of water, plus the protein) you will most likely raise the pressure of the system to bizarre levels. What ion concentration are you aiming for? Is that a reasonable concentration? Kind regards, Erik > On 6 Jan 2017, at 07:05, Raag Saluja wrote: > > Hi! > > I wanted to study the impact of certain ions on a particular protein. > Earlier, I used to simply replace the solvent molecules with the ions. > However, in the current case I need to add a very large number of ions, > which exceeds the number of solvent molecules.So its giving me an error. > > The command I used was: > > genion -s ions.tpr -o PDB_solv_ions.gro -p topol.top -pname K -nname CL -np > 84300 > > Is there a way to add ions additional to the solvent molecules, instead of > replacing them? > > Thank you and regards, > > Raag Saluja > -- > 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] correction of pmf profile due to entropic decrease
Dear Alex, No. First of all, this is taken care of by gmx wham if I remember correctly. And it does so by looking at the dimensionality of your umbrella sampling setup. Secondly, there are cases where you don’t want that correction at all. The manual mentions one such example. In such cases the entropic contribution must be removed. Kind regards, Erik > On 7 Dec 2016, at 19:33, Alex wrote: > > Any suggestion please? > Thank you. > > > On Tue, Dec 6, 2016 at 1:16 PM, Alex wrote: > >> >> Hello gmx user, >> >> Do we need always correct the PMF profile from US by the >> "$k_{B}T*log[4π(\epsilon)^2]$" factor in which epsilon is reaction >> coordinate in order to removes the entropic decrease? as been mentioned >> here: >> >> 10.1021/ct100494z >> >> Hub, J. S.; de Groot, B. L.; van der Spoel, D.J. Chem. Theory >> Comput.2010,6, 3713-3720 >> >> Best regards, >> Alex >> >> > -- > 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] trjconv
Dear Apramita, Unfortunately, the short answer is that you need to think it through. What is being calculated, and how is the trajectory information affected by trjconv? If you for instance apply trjconv -fit rot+trans prior to RDF calculations, you might influence the results. Kind regards, Erik > On 29 Nov 2016, at 07:36, Apramita Chand wrote: > > Dear Justin,Gregory and Erik, > I'd asked earlier whether trjconv might change calculation of > properties.For diffusion probably, I could avoid applying trjconv before > analysis. For RDF, I checked before and after trjconv, there is a slight > difference in the RDFs. For instance , I'm studying a peptide-water-urea > system . On increasing concentration of urea, before I apply trjconv , the > interaction decreases . After applying trjconv , it increases slightly. > But how do I know for sure whether I should apply it or not? > Say I calculate properties like RDF,RMSD, etc after applying trjconv and > properties like diffusion,lifetimes without trjconv ; would that be right? > My peptide isn't broken or anything . It just seems to be partially out of > the box. > > Please advise. > > > Regards, > Apramita > -- > 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] Regarding trjconv
Dear Aparamita, trjconv can enable or preclude subsequent analysis of trajectories, depending on what you want to do. For example, by fitting chosen groups to a reference structure. By centering your protein, you effectively remove all lateral diffusion, so it’s not surprising that a very low diffusion coefficient is reported for the processed trajectory. Kind regards, Erik > On 17 Nov 2016, at 08:53, Apramita Chand wrote: > > Dear All, > I had one doubt regarding g_trjconv which I used to center my protein after > simulation. I got different diffusion values when I used the .xtc file > before and after applying trjconv. Which one should be used? Is trjconv > just for visualisation or is necessary for analysis too? Does it change the > values or interactions in any way? > For example, the diffusion values that I got were > Before trjconv After Trjconv > Urea - 1.6628 2.089 > Protein -0.09270.000108 > Water 2.513 2.59 > > Please advise. Which values should be taken? > > Regards > Apramita > -- > 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] Molecular dynamic simulations of Protein-DNA complex
Dear Khadija, Whether this is a real problem or not is not clear from what you have told us. It could be that what you see in the simulation is real, or it could be that the physical model is inadequate. Or you might even be reporting a visualisation artefact. Can you please elaborate what you mean by “deformations”? Kind regards, Erik > On 24 Oct 2016, at 10:06, Khadija Amine wrote: > > Dear Gromacs users, > > I have run 20ns of MD simulations of my protein-DNA complex. > > All my trajectory files have been combined in a same final file. > > I have visualized that trajectory file using pymol software. Unfortunately, > the DNA structure and some parts of the complexed protein structure show > deformations. > > How can I prevent this issue and obtain correct structure, movement of my > complex? > > This is the first time I perform MD for the protein - DNA complex. > > Thank you > > *Khadija AMINE* > > > *Computational Biology* > *Postdoctoral Research Associate* > *Carnegie Mellon University* > -- > 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] gromacs 2016 vs 5.1.4
Dear Nikhil, Use gmx2016. The 5.1.X versions only get bug fixes and a few backports now as far as I know. Kind regards, Erik > On 11 Oct 2016, at 07:19, Nikhil Maroli wrote: > > Dear all > > We have Workstation with GTX 1070 Cards, Which Gromacs I should install > Gromacs 2016 or 5.1.4 .. ? , I have seen 2016 is much better but later > there was an updated version of v5 ,Would like to get it confirmed. > > -- > Regards, > Nikhil Maroli > -- > 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] Center-of-Mass motion removal setting for Membrane system with multiple peptides.
Hi, I don’t simulate membranes much, so perhaps someone else’s input might be more valuable. But unless the relative motion of the membrane with respect to the rest is artificial and not just diffusion, I would still recommend COM-motion removal of the whole system. Kind regards, Erik > On 28 Sep 2016, at 16:39, Abhi Acharya wrote: > > Thank you Eric for your clarification. However, I have seen that in > membrane simulations, its is suggested to couple membrane, and solvent and > solute to two different COM groups. The argument is that in case of > membrane systems, there is an inherent tendency of lateral drift of > membranes; with a single COM for the whole system, even though the COM > would remain essentially unchanged, there may be appreciable drift of the > membrane relative to the rest of the system. Could you possibly shed some > light on this? > > Following the above argument, probably for my system I should assign > membrane to one COM group and the rest of the system (including solute > solvent and the peprides ) to other. What do you think? > > Thank you. > > Regards, > Abhishek Acharya > -- > 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] Center-of-Mass motion removal setting for Membrane system with multiple peptides.
Periodic systems should be translation invariant, and diffusion across periodic boundaries normally is not a concern. There are occasional exceptions to this, mostly (only?) because of technical implementation details. Unless your system warrants special treatment (and from what you’ve told us so far I don’t think that’s the case) I’d say that separate coupling of COM removal would only add artefacts. Take the extreme example of separate COM-motion removal of a single Na+ and a single CL-. They would be locked in place throughout the simulation. The same effect would come into play also for a group of Na+ and a group of Cl- with separate COM-motion removal, albeit in a more subtle way. What you suggest is similar. Kind regards, Erik > On 27 Sep 2016, at 11:33, Abhi Acharya wrote: > > Actually, I am really not sure whether diffusion out of the box will affect > the results or not. As long as the system is able to correctly simulate the > intended biological phenomenon i.e. interaction of peptides with membrane, > it is fine. Intuitively, one may say that for a semi-isotropic membrane > system diffusion along XY direction should be fine; but any diffusion along > Z would not be acceptable. Not sure, how this can be correctly handled. > > There have been studies like this with other peptides, but none of them > have commented on the above aspect. > > On Tue, Sep 27, 2016 at 2:36 PM, Erik Marklund > wrote: > >> Hi Abhi, >> >> No, restricting the COM motion of the entire system is perfectly fine in >> most cases. From the conservation of momentum, the COM should not change >> its velocity at all. One reason the COM motion needs to be kept at bay >> explicitly is because the accumulation of numerical error during the >> simulation. If you separately remove the COM motion of separate groups you >> will however affect the diffusion of one group relative to the other, for >> example. Is diffusion out of the simulation box really a concern in your >> case? >> >> Erik >> >>> On 27 Sep 2016, at 10:40, Abhi Acharya wrote: >>> >>> Another thing which I don't understand is in case of the peptide group, >>> which I expect to diffuse freely, would COM motion removal be non >> physical? >>> The starting system has 16 peptides added to one side of the membrane. >> Now >>> to allow the peptides to diffuse freely and interact with the membrane, I >>> would assume that translational, rotational and conformational freedom >>> would be required. Wouldn't restricting the COM restrict its dof? >>> >>> Thanks. >>> >>> On Tue, Sep 27, 2016 at 1:59 PM, Abhi Acharya >>> wrote: >>> >>>> What I meant to ask was a way to ensure that the peptides and membrane >> COM >>>> don't drift out of the simulation box, but the peptides should be free >> to >>>> move ( relative to the membrane) within the box. Basically, the best >> way to >>>> simulate the diffusion and subsequent interaction of the peptides with >> the >>>> lipid membrane. >>>> >>>> What I can surmise from previous similar studies is that creating >> separate >>>> comm groups for Membrane, solute and ion and the peptide should be the >>>> correct way. Also, I wanted to know how different nstcomm values would >>>> effect the result especially in the context of complex systems such as >>>> this. >>>> >>>> Just wanted to be sure, before I start the production runs. >>>> >>>> >>>> >>>> On Tue, Sep 27, 2016 at 1:01 PM, Erik Marklund < >> erik.markl...@kemi.uu.se> >>>> wrote: >>>> >>>>> >>>>>> On 27 Sep 2016, at 06:26, Abhi Acharya >>>>> wrote: >>>>>> >>>>>> Dear Gromacs users, >>>>>> >>>>>> I am trying to perform a simulations of different concentration of >>>>> peptides >>>>>> in a box with lipid bilayer. In this context, I had a query regarding >>>>> the >>>>>> correct Center-of-Mass removal settings; what would be the correct way >>>>> to >>>>>> ensure that the Membrane is stationary during long simulations while >> the >>>>>> peptides, solutes etc freely diffuse in the box. Based on my >>>>> understanding, >>>>>> I am using the following settings in the parameter file: >>>>>> >>>>>> nstco
Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.
Hi Abhi, No, restricting the COM motion of the entire system is perfectly fine in most cases. From the conservation of momentum, the COM should not change its velocity at all. One reason the COM motion needs to be kept at bay explicitly is because the accumulation of numerical error during the simulation. If you separately remove the COM motion of separate groups you will however affect the diffusion of one group relative to the other, for example. Is diffusion out of the simulation box really a concern in your case? Erik > On 27 Sep 2016, at 10:40, Abhi Acharya wrote: > > Another thing which I don't understand is in case of the peptide group, > which I expect to diffuse freely, would COM motion removal be non physical? > The starting system has 16 peptides added to one side of the membrane. Now > to allow the peptides to diffuse freely and interact with the membrane, I > would assume that translational, rotational and conformational freedom > would be required. Wouldn't restricting the COM restrict its dof? > > Thanks. > > On Tue, Sep 27, 2016 at 1:59 PM, Abhi Acharya > wrote: > >> What I meant to ask was a way to ensure that the peptides and membrane COM >> don't drift out of the simulation box, but the peptides should be free to >> move ( relative to the membrane) within the box. Basically, the best way to >> simulate the diffusion and subsequent interaction of the peptides with the >> lipid membrane. >> >> What I can surmise from previous similar studies is that creating separate >> comm groups for Membrane, solute and ion and the peptide should be the >> correct way. Also, I wanted to know how different nstcomm values would >> effect the result especially in the context of complex systems such as >> this. >> >> Just wanted to be sure, before I start the production runs. >> >> >> >> On Tue, Sep 27, 2016 at 1:01 PM, Erik Marklund >> wrote: >> >>> >>>> On 27 Sep 2016, at 06:26, Abhi Acharya >>> wrote: >>>> >>>> Dear Gromacs users, >>>> >>>> I am trying to perform a simulations of different concentration of >>> peptides >>>> in a box with lipid bilayer. In this context, I had a query regarding >>> the >>>> correct Center-of-Mass removal settings; what would be the correct way >>> to >>>> ensure that the Membrane is stationary during long simulations while the >>>> peptides, solutes etc freely diffuse in the box. Based on my >>> understanding, >>>> I am using the following settings in the parameter file: >>>> >>>> nstcomm = 100 >>>> comm_mode = linear >>>> comm_grps = MEMB SOL_ION Peptide >>>> >>>> Here the Peptide group includes a total of say 16 peptides. Would this >>> be >>>> the correct way to perform the simulation? >>>> >>>> Is is possible to set individual nstcomm values for each group so as to >>>> ensure that the peptides diffuse freely while the membrane stays >>> stationary? >>> >>> Why do you want that in the first place? Membranes aren’t stationary. >>> >>> Kind regards, >>> Erik >>> >>>> >>>> The full mdp settings I intend to use is provided in the following link: >>>> >>>> https://drive.google.com/file/d/0B9VrCGta6IxES3NHU3lRbGJ4d00 >>> /view?usp=sharing >>>> >>>> Please advise of what would be the best settings to perform the >>> simulation. >>>> >>>> Best Regards, >>>> Abhishek Acharya >>>> C-CAMP >>>> Bangalore. >>>> -- >>>> 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] Center-of-Mass motion removal setting for Membrane system with multiple peptides.
> On 27 Sep 2016, at 06:26, Abhi Acharya wrote: > > Dear Gromacs users, > > I am trying to perform a simulations of different concentration of peptides > in a box with lipid bilayer. In this context, I had a query regarding the > correct Center-of-Mass removal settings; what would be the correct way to > ensure that the Membrane is stationary during long simulations while the > peptides, solutes etc freely diffuse in the box. Based on my understanding, > I am using the following settings in the parameter file: > > nstcomm = 100 > comm_mode = linear > comm_grps = MEMB SOL_ION Peptide > > Here the Peptide group includes a total of say 16 peptides. Would this be > the correct way to perform the simulation? > > Is is possible to set individual nstcomm values for each group so as to > ensure that the peptides diffuse freely while the membrane stays stationary? Why do you want that in the first place? Membranes aren’t stationary. Kind regards, Erik > > The full mdp settings I intend to use is provided in the following link: > > https://drive.google.com/file/d/0B9VrCGta6IxES3NHU3lRbGJ4d00/view?usp=sharing > > Please advise of what would be the best settings to perform the simulation. > > Best Regards, > Abhishek Acharya > C-CAMP > Bangalore. > -- > 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] Interest of c alpha atoms for least square fitting?
Yes > On 22 Sep 2016, at 06:45, Seera Suryanarayana wrote: > > Dear gromacs users, > > Can I give my interest of c alpha atoms for least square fitting in gmx rms > for RMSD calculation? > > Thanks in advance > Surya > Graduate student > India. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Large (600k particle) semi-isotropic lipid bilayer system transformed into vacuum-separated coordinates by grompp and mdrun
Dear George, Is this not just a visualisation issue because of periodic boundary conditions? Are you sure that the vacuum was not present in the input coordinate file? Kind regards, Erik > On 7 Sep 2016, at 23:58, George Pantelopulos wrote: > > Dear all, > > I have been trying to equilibrate a very large lipid bilayer system for the > past few days, but I have not been able to move past a very curious error > that happens when producing a tpr file and running miminization or MD. > > The system ends up being split in to 8 quadrants, leaving sizeable vacuums > between each quadrant, and the coordinates of the system are transposed. > I've tried to resolve this via various combinations of minimization and > equilibration schemes but have had no success. At this point, I think I may > only turn to the mailing list for advice. > > Does anyone have an idea of what might be going on and how I could resolve > this? > Thank you for the help, > George Pantelopulos > -- > 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] forced conformational change by MD
Dear Pappu, You could use position restraints for the two conformations and switch between them by gradually shifting the lambda parameter from zero to one. Kind regards, Erik > On 1 Sep 2016, at 12:47, Pappu Kumar wrote: > > I want to run MD to simulate conformational change from one protein structure > to another. But I am not sure how do that in gromacs. It would be like doing > morphing through MD and see what kind of changed take place around the > protein. Thank you. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to run MD simulation remotely
Dear Charles, Is mdrun_mpi available on the node side? Nothing in the script suggests it is, but sometimes part of the environment is inherited from the session where sub was run. Do you get any output files at all? I would expect the stdout and stderr to provide some error message. Kind regards, Erik > On 9 Jul 2016, at 10:55, charles k.davis wrote: > > Dear all, > > My name is Charles, PhD student at National Institute of Technology, > Calicut, India. > > I'm facing problem in giving Gromacs MD simulation job remotely (via ssh > command) in a Hybrid Cluster system. The system administrator told me to > copy paste the following script > > *#! /bin/bash * > *#PBS - q small * > *#PBS -e errorfile.err * > *#PBS -o logfile.log * > *#PBS -l select=2:ncpus=16 * > *tpdir=`echo $PBS_JOBID | cut -f 1 -d .` * > *tempdir=/scratch/job$tpdir * > *mkdir -p $tempdir * > *cd $tempdir * > *cp -R $PBS_O_WORKDIR/* . * > *mpirun -np 32 -hostfile $PBS_NODEFILE mdrun_mpi -v -s input.tpr -c > output.gro* > *mv ../job$tpdir $PBS_O_WORKDIR/.* > > > in a text document and save it as* script.sh* and to submit the job run the > following command in terminal, > > > > *qsub script.sh* > This method is not working for us. It will show that the job has been taken > up but soon it will vanish. > > In our lab workstation (which we control directly, not remotely) we use the > following commands lines, > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *pdb2gmx -f Protein.pdb -o Protein.gro -p Protein.top -water spc > -ignhgenrestr -f UNK.gro -o posre_UNK.itp -fc 1000 1000 1000grompp -v -f > minim.mdp -c Protein.gro -p Protein.top -o Protein-EM-vacuum.tprmdrun -v > -deffnm Protein-EM-vacuum -c Protein_minimized.gro -nt 1editconf -f > Protein_minimized.gro -o Protein_minimized_box.gro -d 1.1 -bt cubicgenbox > -cp Protein_minimized_box.gro -cs spc216.gro -p Protein.top -o > Protein-water.grogrompp -v -f minim_water.mdp -c Protein-water.gro -p > Protein.top -o Protein-water.tprgenion -s Protein-water.tpr -o > Protein-water-ions.gro -p Protein.top -conc 0.15 -neutral -pname NA -nname > CLgrompp -v -f minim_water.mdp -c Protein-water-ions.gro -p Protein.top -o > Protein-EM-solvated.tprmdrun -v -deffnm Protein-EM-solvated -o > Protein_minim_traj_water.trr -c Protein_minimized_water.gro -e > minim_ener_water.edrmake_ndx -f Protein_minimized_water.gro -o > index.ndxgrompp -v -f nvt.mdp -c Protein_minimized_water.gro -p Protein.top > -o nvt.tprmdrun -v -deffnm nvtgrompp -f npt.mdp -c nvt.gro -t nvt.cpt -p > Protein.top -o npt.tpr -n index.ndx mdrun -v -deffnm nptgrompp -f md.mdp -c > npt.gro -t npt.cpt -p Protein.top -o Protein_md_1.tpr -n index.ndx mdrun -v > -deffnm Protein_md_1* > > to do the simulation and keeping the files md.mdp, minim.mdp, > minim_water.mdp, npt.mdp and nvt.mdp in the work directory. We also keep > protein file as Protein.pdb and ligand file as UNK.pdb, UNK.gro and UNK.itp. > > Can someone help me sort out this problem. > > Many thanks, > > Regards, > > Charles K Davis > PhD Student > School of Biotechnology, > National Institute of Technology, > Calicut, Kerala, India-673 601 > Cell Phone: +91 9495595458 > -- > 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] Hbond occupancy
gmx hbond > On 8 Jul 2016, at 12:24, Amali Guruge wrote: > > Dear All, > > Can anyone know how to calculate H bond occupancy with Gromacs? > > Thank you > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] charge of aminoacids in an special pH
Hi, In addition, if you only wish to alter the protonation states of, say, aspartates, you can use the -asp flag so that you don’t have to go through all possible titratable residues. See vmx pdb2gmx for more residue-specific options. Erik > On 28 Jun 2016, at 09:34, Marlon Sidore wrote: > > You can change the protonation state of amino acids with pdb2gmx -inter > option. > It will ask you the protonation state of every AA. You could also start > with a tool like propka in order to know which ones are protonated. > > Best regards, > > Marlon Sidore > > > PhD Student > Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) > CNRS - UMR7255 > 31, Chemin Joseph Aiguier > 13402 cedex 20 Marseille > France > > > 2016-06-28 9:18 GMT+02:00 Atila Petrosian : > >> Dear Gromacs users, >> >> I want to study MD simulation of my protein in an special pH (2). >> >> I want to investigate partially unfolding in this protein. >> >> How to set charge of aminoacids in pdb file, prior to start MD? >> >> Any help will highly appreciated. >> >> Best >> -- >> 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] Number of H bonds formed between ligand and amino acid residues
Hi Amali, gmx hbond identifies typical acceptor and donor groups by default. In fact, analysing non-standard donors/acceptors is a bit underdeveloped. What the program basically does, if memory serves me right, is to identify N and O with H bound to them, or optionally without H in case of acceptors. If you wish to analyse the hbonds separated by residue number you may wan to either run vmx bond multiple times with one group being a single residue and the other the ligand, or you can run it once with the -hbm and -hbn options and extract the information from the resulting matrix. Kind regards, Erik > On 28 Jun 2016, at 08:59, Amali Guruge wrote: > > Thank you very much for the answer. How we identify residues involving in H > bonds? In index file do we have to specify them? > > On Tue, Jun 28, 2016 at 11:45 AM, Subhomoi Borkotoky > wrote: > >> Hello, >> >> Please use the "hbond" utility in gromacs. >> >> gmx hbond [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n >> [<.ndx>]][-num [<.xvg>] >> >> >> On Tue, Jun 28, 2016 at 11:24 AM, Amali Guruge >> wrote: >> >>> Dear Gromacs users, >>> >>> I carried out 20 ns long MD simulation for my receptor-ligand complex >> using >>> Gromacs software. Now I want to calculate number of hydrogen bonds formed >>> in the ligand and receptor corresponding to the residue number. Can >> anyone >>> help me? >>> >>> >>> Thank you. >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >> >> >> >> -- >> Yours Sincerely, >> -- >> SUBHOMOI BORKOTOKY, >> Centre for Bioinformatics >> Pondicherry University >> Pondicherry,INDIA. >> >> Alternate Email: subho...@mails.bicpu.edu.in >> -- >> 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] selection of start or end terminus
Dear Alex, A single amino acid is not a peptide sine it has no peptide bonds. Kind regards, Erik > On 22 Jun 2016, at 20:19, Alexander Alexander > wrote: > > Thanks for your response. > > And then why does "1" go wrong for a single amino acid in zwitterions > form, as well? Isn't a single amino acid is a kind of peptide with only one > residue? > > Thanks. > Regards, > Alex > > On Wed, Jun 22, 2016 at 8:05 PM, Justin Lemkul wrote: > >> >> >> On 6/22/16 12:53 PM, Alexander Alexander wrote: >> >>> Dear Gromacs user, >>> >>> In the selection of start or end terminus type for peptide in OPLS_AA >>> force >>> field, what is the diffeece between option 0 and 1 in below list? I am >>> interested in the Zwitterion form, but the option 0 is Zwitterion form if >>> I >>> am not wrong! >>> >>> >>> Select start terminus type for >>> 0: NH3+ >>> 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one >>> residue) >>> 2: NH2 >>> 3: None >>> >>> And why choosing 1 introduces a tiny amount of charge (0.010 e) in the >>> system and then the whole system in not neutral anymore but 0 is fine. It >>> is clear below the differences and origination of the extra charge in >>> \alpha-C, but how can I fix this if I want to choose 1? Can I simply edit >>> the topol file by replacing the opls_299 to opls_283 ... .? >>> >>> >>> Choosing 0. :-) >>> >>> ; residue 1 LEU rtp LEU q +1.0 >>> 5 opls_293B 1LEU CA 10.25 12.011 >>> >>> ;residue 7 GLU rtp GLU q -2.0 >>> 112 opls_283 7GLU CA 37 0.04 12.011 >>> >>> >>> Choosing 1. :-( >>> >>> ;residue 1 LEU rtp LEU q +0.9 >>> 5 opls_299 1LEU CA 1 0.15 12.011 >>> >>> ;residue 7 GLU rtp GLU q -1.9 >>> 112 opls_299 7GLU CA 37 0.15 12.011 >>> >>> >> pdb2gmx tells you what to do: >> >> "only use with zwitterions containing exactly one residue" >> >> Do you have more than one residue? If yes, this is a wrong choice. >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> == >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Calculating Eccentricity
Dear Sanket, Removing periodicity is difficult if SDS molecules transiently leave the micelle and return after having moved one or more unit cells. You might want to try using gmx clustsize to generate snapshots along the trajectory and use trjconv on them to put all molecules in the same unit cell. Have never used those tools for that purpose so I can’t guarantee that it will work. Kind regards, Erik > On 15 Jun 2016, at 07:28, Sanket Ghawali wrote: > > Dear gmx user > > I am performing a MD simulation of peptides in sds for 100ns. After the > completion of my production I am unable to remove the periodic boundary > condition. > I wanted to Calculate the eccentricity of the SDS micelle after 100ns, does > the periodic boundary condition affect my eccentricity result ? > Is it necessary first to remove the pbc effect and then calculate > Eccentricity. > Also does the high eccentricity value obtained after 100ns tell me that the > micelle is distorted and the peptide has some activity? > > Thank you. > Sanket > -- > 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] Open-closed transition in a dimeric enzyme, WTM simulations
Dear Tarak, My guess is that your reaction coordinate is ill-chosen and that it fails to capture some significant transitions in orthogonal directions. This can be difficult to know beforehand unfortunately. Kind regards, Erik > On 10 Jun 2016, at 19:09, tarak karmakar wrote: > > Dear All, > I am studying an enzyme where the closing of a loop should happen upon > ligand binding to the active site. In unbiased simulations, even after 300 > ns of simulation time the loop does not close the reaction center. Thus, we > realized that the open-closed conformational change may have a high free > energy barrier, inaccessible by the unbiased trajectory. Thus, we performed > well-tempered metadynamics (WTM) simulations to study that event. > > In WTM simulations, we see the opening and closing of the loop almost five > to six times within 300 ns time span. The free energy associated with this > event has barriers of only few kJ/mol (almost flat surface). Now, given > these low values of the free energy barriers, I would expect to observe the > open-closed transitions in the unbiased simulations. However, we do not see > that transition in the unbiased trajectories. > > So, my questions are, > 1) Are the collective variables used here inappropriate? (Although I see > the open-closed > transition a many times in the metadynamics trajectory.) > > 2) Is the free energy not converged? (plotting hills heights a function of > time, decays close to zero after 200-250 ns) > > 3) How would I make sure that the free energy is converged? (block averages > using -stride in plumed) How would I decide the blocks from the COLVAR plot? > > Any suggestions would be highly appreciated. > > -- > Regards, > Tarak > -- > 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] gmx hbond - specify precise atom names involved
Hi, Not as of yet I’m afraid. Erik > On 3 May 2016, at 08:16, Nash, Anthony wrote: > > > Hi all, > > Can gmx hbond accept user specified atoms for the donors (default OH and > NH) and acceptor (default O and N)? I don¹t seem to find any mention of > this in the -help text. > > I have a post-trans modified protein from a rather bulk cross-linked > peptide chain. I defined unique atom times but I have used a unique set of > atom names. > > Thanks > Anthony > > > > >> > > -- > 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] a suitable forcefield for ions
Hi, Which ions? The monovalent ions commonly used with Amber have a tendency to cluster in unrealistic ways at moderate concentrations if memory serves me right. Kind regards, Erik > On 25 May 2016, at 10:41, mah maz wrote: > > Hi all, > > i need forcefield parameters for ions. can anyone tell me which forcefield > contains ions? can i do ion simulations with amber ff? > > Thank you > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] query
To clarify: Your gromacs appears to be compiled for different hardware, most likely on a different machine. I strongly recommend to build on the same machine you will be running on. Kind regards, Erik > On 18 May 2016, at 11:28, Nikhil Maroli wrote: > > This is the problem with installation. try installing it again > 1.gromacs from source > 2.correct g_mmpbsa from source/binary you have to check with binary first > -sometimes it will work from binary > > -- > 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] water model
Dear Mahdiyeh, For water molecules the constraints can be solved analytically with SETTLE, so no need to invoke SHAKE. SETTLE is used by default so just simulate as normal and you will have rigid water. Kind regards, Erik > On 9 May 2016, at 09:04, mahdiyeh poorsargol wrote: > > Dear all > I am a beginner in gromacs. I want to use water in my system. I choose the > SPC/E water model in the topol.top file by: > > ; Include water topology > #include "spce.itp" > > My question is, is rigid water molecule in the SPC/E model or should use > the SHAKE algorithm for water in order to fix the length of bonds and > angles? > I would be more than pleased if someone could guide me. > Thank You in advance > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs fftw installation
Dear Neha, with -DGMX_BUILD_OWN_FFTW=ON you tell gromacs to download and build its own fftw. Turn this option off. Kind regards, Erik > On 6 May 2016, at 09:05, Neha Gandhi wrote: > > Dear List, > > I am trying to install gromacs on a machine which is not allowed to connect > to the internet. > I have installed fftw in a directory /home/gandhin/fftw using --enable-float > > I am trying to install gromacs but it always tries to download fftw and > therefore the installation ends up in error. > > I am using following command > CMAKE_PREFIX_PATH=/home/gandhin/fftw-3.3.3/ cmake .. > -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=on -DGMX_GPU=on -DGMX_SIMD=NONE > -DCMAKE_C_COMPILER=${MPICCDIR}mpicc -DCMAKE_CXX_COMPILER=${MPICCDIR}mpicxx > -DCMAKE_INSTALL_PREFIX=/home/gandhin/gromacs-5.0.7 > > Any suggestion would be helpful. > > > -- > Regards, > Dr. Neha S. Gandhi, > Vice Chancellor's Research Fellow, > Queensland University of Technology, > 2 George Street, Brisbane, QLD 4000 > Australia > LinkedIn > Research Gate > -- > 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] distance restraint between 2 molecules
Hi, Or use the pull code. Kind regards, Erik > On 27 Apr 2016, at 08:09, Catarina A. Carvalheda dos Santos > wrote: > > Hi Hong, > > You have (at least) two options: > > 1) Edit the specbond.dat file so that the pdb2gmx creates a covalent bond > between the ligand and the protein (the bonded terms for this interaction > have to be present in the force field files); > > 2) Use position restrains on these two atoms instead. > > Chose whatever makes more sense for your system. > > Hope this helps. > > Regards, > > -- > > Catarina A. Carvalheda > PhD Student > Computational Biology Division > SLS & SSE > University of Dundee > DD1 5EH, Dundee, Scotland, UK > Hi Gromacs users, > I want to assign a distance restraint between 2 atom, one belongs to > protein and one belongs to ligand. I have a .top file for protein and > include .itp of ligand. However, it seem Gromacs only perform distance > restraint between 2 atom within same molecule. > except the merging two molecules into a single moleculetype, is there any > option that i can keep protein and ligand itp files seperately? > > Thank you so much. > Hongtham > -- > 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. > > The University of Dundee is a registered Scottish Charity, No: SC015096 > -- > 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] Protein is Jumping from water Box
Dear Abid, I wouldn’t call it an issue nor an error. Your protein is still interacting with some periodic copy of the solvent molecules. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. Kind regards, Erik On 27 Apr 2016, at 05:23, Abid Channa mailto:abid_chann...@yahoo.com>> wrote: Dear Gromacs users, I have run 40 ns simulation , after 20 ns simulation my protein is continuously jumping from water Box. Is there any periodic boundary conditions issue with my system or an other error is that . Kindly give your valuable remarks. Thanks, Regards, Abid Ali Channa, Junior Research Fellow, Lab No. P-133, Computational Chemistry Unit, Dr .Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi-75270.Karachi-Pakistan.UAN # (92-21) 111-222-292 Ext. (309) Cell # +923013553051. http://www.iccs.edu/ -- 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: range checking error
Hi, Strange. Do you get the same error with 5.1.2? If so, can you please file a redmine issue (http://redmine.gromacs.org/) and upload the input files that generate this error? Assign the issue to me. Kind regards Erik Marklund On 26 Apr 2016, at 12:01, Shubhangi Gupta mailto:ignahbuhs.gup...@gmail.com>> wrote: Hi all, I want to calculate the number of hydrogen bonds between protein and solvent. I am using g_hbond (gromacs 5.0.2) with the two groups - protein and SOL. When i run the command, I get a *Range Checking error* *Variable gx has value -3. It should have been within [0 ..19]* However when i do the same and choose the two groups as protein and protein, the command goes through. Any help is greatly appreciated. Thanks Regards, Shubhangi Gupta PhD Research Scholar (YUS lab) Dept of Chemistry Indian Institute of Technology Bombay Powai, Mumbai-400076. e-mail ID: ignahbuhs.gup...@gmail.com<mailto:ignahbuhs.gup...@gmail.com> 144033...@iitb.ac.in<mailto:144033...@iitb.ac.in> -- 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<mailto: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] Flat-bottom potential SEGFAULT
Hi, >From what I have observed so far this appears to be a cluster configuration >issue rather than a gromacs error. Thanks for your input. Kind regards, Erik On 29 Mar 2016, at 15:14, Erik Marklund mailto:erik.markl...@chem.ox.ac.uk>> wrote: On 28 Mar 2016, at 01:52, Justin Lemkul mailto:jalem...@vt.edu>> wrote: On 3/26/16 12:47 PM, Erik Marklund wrote: Dear dynamicists, I am using flat bottom potentials to prevent water molecules from evaporating from a droplet in vacuum. The manual suggests this is pretty straightforward, but we run into a segfault with our approach. Having never used flat-bottom potentials before, chances are we are doing something wrong without realising it. Let me describe what we do and perhaps you can tell me where things go wrong. We make our own copy of tip3p.itp, in which we put a [ position_restraints ] directive for the OW1, HW2, and HW3 atoms: [ position_restraints ] ; id func_typeg r k 121 10 1000 221 10 1000 321 10 1000 We then create a new gro-file, where we move all water atoms in the middle of the box. This is to be used for reference coordinates in the next step. We run grompp, where we provide the new gro file using the -r flag. We launch mdrun, which segfaults. If we prepare the system without the -r flag in the previous step everything runs fins, but the reference point for the flat-bottom potential is presumably wrong. Where might the error be? I just did this with a toy system of a single water molecule and it worked quite well. What version of GROMACS are you using? Does a simple test like I did work? -Justin Hi, Forgot to mention the version. It is 5.1.1. Will run some simple tests like yours and get back with more info. Kind regards, Erik -- == 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 == -- 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<mailto: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 in implementing do_dssp
Dear Rishikesh, No, you misunderstand. We don’t suggest to issue “do_dssp”, but to run dssp, which you say is located in /usr/local/bin, to make sure it works the way it should. Kind regards, Erik > On 6 Apr 2016, at 18:08, Rishikesh Parulekar > wrote: > > while running directly it shows do_dssp command not found. > > > On Wed, Apr 6, 2016 at 10:29 PM, Justin Lemkul wrote: > >> >> >> On 4/6/16 12:57 PM, Rishikesh Parulekar wrote: >> >>> Hi ErikMarklund, >>>Ya I have tested dssp as it shows all flags options with gmx_mpi >>> do_dssp -h that means executable is locatable but it is not giving output >>> after selecting group protein ends with fatal error : failed to execute >>> command. Try specifying your dssp version with the -ver option >>> >>> >> Executing gmx do_dssp is not a valid test of whether or not your dssp >> works. That just means your gmx binary is capable of displaying help >> information. Please do as Erik and I both suggested and try to run the dssp >> binary directly, not via gmx do_dssp. >> >> -Justin >> >> >> On Wed, Apr 6, 2016 at 10:14 PM, Rishikesh Parulekar < >>> rishi05parule...@gmail.com> wrote: >>> >>> Hi Justin Lemkul, >>>> It works with gmx binary complied with mpi as u can see this is my >>>> command >>>> : gmx_mpi do_dssp -f md.trr -s md.tpr -o ss.xpm -sc protein.xvg -ver 2 . >>>> After executing command I am able to select group for dssp calculation >>>> but >>>> it ends with fatal error : failed to execute command. Try specifying your >>>> dssp version with the -ver option >>>> >>>> On Wed, Apr 6, 2016 at 9:52 PM, Erik Marklund < >>>> erik.markl...@chem.ox.ac.uk >>>> >>>>> wrote: >>>>> >>>> >>>> Dear Rishikesh, >>>>> >>>>> And you have tested that your dssp runs properly on your computer? Do >>>>> you >>>>> run do_dssp from a script? If so, can you please show the script and >>>>> maybe >>>>> someone spots something? >>>>> >>>>> Kind regards, >>>>> Erik >>>>> >>>>> On 6 Apr 2016, at 17:03, Rishikesh Parulekar < >>>>>> >>>>> rishi05parule...@gmail.com> wrote: >>>>> >>>>>> >>>>>> Hi all, >>>>>> Is there any possible solution for my mentioned problem of do_dssp >>>>>> implementation fatal error. >>>>>> >>>>>> regards >>>>>> >>>>>> On Wed, Apr 6, 2016 at 6:36 PM, Rishikesh Parulekar < >>>>>> rishi05parule...@gmail.com> wrote: >>>>>> >>>>>> my error is not regarding the mismatch of name for the software. It has >>>>>>> recognised the software at usr/local/bin but it is showing fatal error >>>>>>> >>>>>> : failed >>>>> >>>>>> to execute command. Try specifying your dssp version with the -ver >>>>>>> >>>>>> option. >>>>> >>>>>> If the problem is with path of software the error of setenv have >>>>>>> >>>>>> occured. >>>>> >>>>>> Hence I have mentioned the ver in the command : gmx_mpi do_dssp -f >>>>>>> >>>>>> md.trr >>>>> >>>>>> -s md.tpr -o ss.xpm -sc protein.xvg -ver 2 but still the same error. >>>>>>> >>>>>>> On Wed, Apr 6, 2016 at 6:32 PM, Rishikesh Parulekar < >>>>>>> rishi05parule...@gmail.com> wrote: >>>>>>> >>>>>>> dssp executable is directly downloaded from the >>>>>>>> ftp://ftp.cmbi.ru.nl/pub/software/dssp site and it has ready to use >>>>>>>> executable file for version 2.0.4. So this is the case and it has >>>>>>>> >>>>>>> been kept >>>>> >>>>>> under path /usr/local/bin with dssp name. >>>>>>>> >>>>>>>> On Wed, Apr 6, 2016 at 6:17 PM, Sarath Chandra < >>>>>>>> sarathchandrada...@gmail.com> wrote: >>>>>>>> >>>>>>>> dssp executable generally gets installed as
Re: [gmx-users] Problem in implementing do_dssp
Dear Rishikesh, And you have tested that your dssp runs properly on your computer? Do you run do_dssp from a script? If so, can you please show the script and maybe someone spots something? Kind regards, Erik > On 6 Apr 2016, at 17:03, Rishikesh Parulekar > wrote: > > Hi all, > Is there any possible solution for my mentioned problem of do_dssp > implementation fatal error. > > regards > > On Wed, Apr 6, 2016 at 6:36 PM, Rishikesh Parulekar < > rishi05parule...@gmail.com> wrote: > >> my error is not regarding the mismatch of name for the software. It has >> recognised the software at usr/local/bin but it is showing fatal error : >> failed >> to execute command. Try specifying your dssp version with the -ver option. >> If the problem is with path of software the error of setenv have occured. >> Hence I have mentioned the ver in the command : gmx_mpi do_dssp -f md.trr >> -s md.tpr -o ss.xpm -sc protein.xvg -ver 2 but still the same error. >> >> On Wed, Apr 6, 2016 at 6:32 PM, Rishikesh Parulekar < >> rishi05parule...@gmail.com> wrote: >> >>> dssp executable is directly downloaded from the >>> ftp://ftp.cmbi.ru.nl/pub/software/dssp site and it has ready to use >>> executable file for version 2.0.4. So this is the case and it has been kept >>> under path /usr/local/bin with dssp name. >>> >>> On Wed, Apr 6, 2016 at 6:17 PM, Sarath Chandra < >>> sarathchandrada...@gmail.com> wrote: >>> dssp executable generally gets installed as mkdssp. Check if this is the case. Regards, Sarath -- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Powai Mumbai, 400-076, India On 6 April 2016 at 18:00, Rishikesh Parulekar < rishi05parule...@gmail.com> wrote: > I have named dssp executable with proper name in usr/local/bin but still > the error persists. I have also shown the path for the dssp with export. > > On Wed, Apr 6, 2016 at 2:27 PM, Sarath Chandra < > sarathchandrada...@gmail.com >> wrote: > >> do_dssp is looking for /usr/local/bin/dssp and if your dssp executable > has >> some other name do_dssp will fail. >> >> Before you run do_dssp you need to set the DSSP variable. >> >> for bash environment do this: >> >> export DSSP=`which dssp-2.0.4-linux-amd64` >> >> Regards, >> >> Sarath >> >> >> -- >> Sarath Chandra Dantu, PhD, ELS >> Room No. 606, New BSBE Building >> Department of Biosciences and Bioengineering >> Indian Institute of Technology Bombay >> Powai Mumbai, 400-076, India >> >> >> On 6 April 2016 at 13:16, Rishikesh Parulekar < > rishi05parule...@gmail.com> >> wrote: >> >>> Hi dear all, >>> >>> I am trying to analyse the secondary structure of my protein by >> using >>> do_dssp on gromacs-5.1.2. However it consistently showing the fatal >> error: >>> failed to execute command. Try specifying your dssp version with the > -ver >>> option. >>> I am using dssp executable file i.e dssp-2.0.4-linux-amd64 and it has >> been >>> properly placed in /usr/local/bin and also command with -ver option has >>> also been executed >>> gmx_mpi do_dssp -f md.trr -s md.tpr -o ss.xpm -sc protein.xvg -ver 2 > but >>> the fatal error still persists. I am actually not getting the valid >>> solution after many executions. >>> >>> Thanks in advance, >>> >>> Rishikesh S. Parulekar >>> Research scholar, >>> Department of Microbiology, >>> Shivaji University,Kolhapur >>> 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 > > * Fo
Re: [gmx-users] on -dt of trjcat and trjconv
Dear Brett, MOD refers to the modulus operator. For example, trjconv -f infile.xvg -s infile.tpr -dt 1000 -o outfile.xvg will downsample a trajectory and save only the frames at multiples of 1000 ps (0 ps, 1000 ps, 2000 ps, …), assuming that infile.xvg starts at 0 ps. Kind regards, Erik > On 4 Apr 2016, at 05:21, Brett wrote: > > Dear All, > > For both trjcat and trjconv, there was an option "-dt", which the on-line > GROMACS material explained as following, "Only write frame when t MOD dt = > first time (ps) ". > > Will you please explain to me what is the meaning of "Only write frame when t > MOD dt = first time (ps)", by a detailed example with command? > > Brett > -- > 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.