Re: [gmx-users] Implicit solvent improvement in Gromacs 5.1.2
Hi, There's been no active work since 4.5 and no plans I've heard of. I hear AMBER is pretty good at it on GPUs :-) Mark On Wed, Nov 9, 2016 at 12:04 AM Christian Bope Domilongo < christianb...@aims.ac.za> wrote: > Dear all, > > There is any improvement of GB implicit solvent in Gromacs package 5.1.2? > > 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.
[gmx-users] Implicit solvent improvement in Gromacs 5.1.2
Dear all, There is any improvement of GB implicit solvent in Gromacs package 5.1.2? 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.
[gmx-users] sn-2 splitting
Dear Justin Lemkul,In "kalp in dppc tutorial", why can not seen the splitting of the order parameter at the second carbon of sn-2 chain? Many thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] sn-2 splitting
Dear Justin Lemkul,In "kalp in dppc" tutorial, why can not see the splitting of the order parameter at the secondcarbon of sn-2 chain?Many thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Md simulation error
Dear justin lemkul,, Thanks alot..i like the way u answer my stupid questions..actually i dont have anyone to guide me except u.thats why i ask even stupid questions.dont mind please.i want to work under your supervision because i have passion for simulation on gromacs. Now coming to the point,,my problem was concerned with his residue of atom HD1.I just went to pdb file and rename that HD1 to H3.then two files formed that are " "posre _protein chain_A.itp and topol_protein_chain _A.itp"" .while topol.top remained empty.now it gives me another error that is " " Residue 'IS A' not found in residue topology database"". im using version 5.1.2 actually. i 'll encourage and wellcome even live discussion with you.I studied your papers on simulation. Regards. GOD bless you. Maria khan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] REMD ensemble of states
Yes On Tue, 8 Nov 2016 18:43 Abramyan, Tigran wrote: > Hi Mark, > > Thanks a lot for your prompt response. So demux.pl creates continuous > trajectories, *_trajout.xtc, but the ensemble of states (lowest energy > ensemble, typically of interest in the analysis of REMD results) is saved > in the original 0.xtc file produced during REMD before using demux.pl? > > Thank you, > Tigran > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > Abraham > Sent: Tuesday, November 8, 2016 5:53 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] REMD ensemble of states > > Hi, > > Mdrun wrote that. You made the trajectories contiguous with the demux. > > Mark > > On Tue, 8 Nov 2016 04:55 Abramyan, Tigran wrote: > > > Hi, > > > > > > I conducted REMD, and extracted the trajectories via > > trjcat -f *.trr -demux replica_index.xvg > > And now I was wondering which *.xtc file is the ensemble of states at the > > baseline replica (lowest temperature replica). Intuitively my guess is > that > > the numbers in the names of *_trajout.xtc files correspond to the replica > > numbers starting from the baseline, and hence 0_trajout.xtc is the > ensemble > > of states at the baseline replica, but I may be wrong. > > > > > > Please suggest. > > > > > > Thank you, > > > > Tigran > > > > > > -- > > Tigran M. Abramyan, Ph.D. > > Postdoctoral Fellow, Computational Biophysics & Molecular Design > > Center for Integrative Chemical Biology and Drug Discovery > > Eshelman School of Pharmacy > > University of North Carolina at Chapel Hill > > Chapel Hill, NC 27599-7363 > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)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] qm/mm LA not found
Hi, I could reproduce your problem and may know the reason. I had not realised you were using Gromos force field. Normally one uses the gb_XX defines after each pair of bonded atoms to inform grompp of the values the bond parameters. See for example how it is done in your topol.top. Without information (i.e. bond distance and force constant) in the topology file, grompp cannot proceed. You wrote it worked for 'pure' MM. I suppose that in that .itp file there are defines (gb_XX) or explicitly included values for bond length and force constant? Best, Gerrit That's strange indeed. You showed a copy from the bonded section. Which was line 133? bond 24-23? The linkatom is defined as a virtual site and has no mass? I can only guess, but perhaps if I can see the input files, I may understand quicker what goes wrong here. Best, gerrit Hi Gerrit, yes, grompp complains only about bond type 1. It gives only error for lines where the bond types are described, nothing about angle or torsion types. I was able to run normal MM, as well as QM/MM if I get the whole cofactor in QM region, meaning if all bond types in cofactor are type 5 it runs without problems. Greetings Sylwia On 07.11.2016 14:50, Groenhof, Gerrit wrote: > Hi, > > Do I understand correctly that the grompp complains about a bond that is > still bond type 1? > > If so, then the error message suggests that grompp cannot access a ff*bin.itp > with the parameters for the atom pair. > > Usually you'd also get additional errors for missing angle and torsion types. > Do you get those? > > Can you run without QM/MM, i.e. a 'normal' MM simulations with this topology? > > Gerrit > > > Hi Gerrit, > > thank you for your hint. There was no LA entry in the ff*nb.it file. I > have added it there. > But now I get a new error. I have a protein with cofactor. Part of the > cofactor is in QM part > and the rest in MM. For the cofactor I have a separate *itp file as for > the rest of protein. > By preparing the calculation I get and error for all MM atoms: > > ERROR 1 [file DRGGMX_groups_v3_QMMM.itp, line 133]: > No default Bond types > > example from *itp file > > [ bonds ] > ; ai aj fuc0, c1, ... > ... > 21 22 5 ; C9A N10 > 22 23 5 ; N10 C1' ;' > 24 23 1 ; C2' C1' > 24 25 1 ; C2' O2' > > There is no error for atoms with bond type 5, but for all with bond type 1. > > Greetings > Sylwia > > > On 11/05/2016 03:40 PM, Groenhof, Gerrit wrote: >> Is the LA also defined for the force field you're using? Can you check >> whether there is a LA entry in the ff*nb.it of the force field? If not, add >> it there manually. >> >> Best, >> gerrit >> >> Message: 2 >> Date: Fri, 4 Nov 2016 16:10:03 +0100 >> From: Sylwia Kacprzak >> To: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: [gmx-users] qm/mm LA not found >> Message-ID: <581ca4cb.2050...@physchem.uni-freiburg.de> >> Content-Type: text/plain; charset=utf-8; format=flowed >> >> Dear all, >> >> I have set qm/mm calculations with Gromacs 5.1.4 and Orca. >> I treat first the full cofactor on a QM level. However when I cut the >> bond to take only part of it for QM and >> introduce link atom according to the manual with link atom (LA) I get >> following error. >> >> --- >> Program gmx grompp, VERSION 5.1.4 >> Source code file: >> /home/widu/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line: 1345 >> >> Fatal error: >> Atomtype LA not found >> >> Any ideas? >> >> Greetings >> Sylwia >> >> >> > > > -- > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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 151, Issue 22 > ** -- Message: 5 Date: Mon, 7 Nov 2016 18:06:34 + (UTC) From: m g To: "gromacs.org_gmx-users@maillist.sys.kth.se" Subject: [gmx-users] convergence Message-ID: <951804911.2088266.1478541994...@mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 Dear Justin Lemkul,what must be done for checking of convergence of the umbrella sampling simulations? which kind of parameter must be calculated? Many thanks -- Message: 6 Date: Mon, 7 Nov 2016 23:03:06 +0100 From: Szil?rd P?ll To: Discussion list for GROMACS users Subject: Re: [gmx-users] Can't locate AMD SDK opencl, among else, during compile Message-ID: Content-Type: text/plain; charset=UTF-8 Jacob, Not sure where did things go wrong; please provide full cmake invocation and it would help to see the contents of CMakeCache.txt (
Re: [gmx-users] REMD ensemble of states
Hi Mark, Thanks a lot for your prompt response. So demux.pl creates continuous trajectories, *_trajout.xtc, but the ensemble of states (lowest energy ensemble, typically of interest in the analysis of REMD results) is saved in the original 0.xtc file produced during REMD before using demux.pl? Thank you, Tigran From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Tuesday, November 8, 2016 5:53 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] REMD ensemble of states Hi, Mdrun wrote that. You made the trajectories contiguous with the demux. Mark On Tue, 8 Nov 2016 04:55 Abramyan, Tigran wrote: > Hi, > > > I conducted REMD, and extracted the trajectories via > trjcat -f *.trr -demux replica_index.xvg > And now I was wondering which *.xtc file is the ensemble of states at the > baseline replica (lowest temperature replica). Intuitively my guess is that > the numbers in the names of *_trajout.xtc files correspond to the replica > numbers starting from the baseline, and hence 0_trajout.xtc is the ensemble > of states at the baseline replica, but I may be wrong. > > > Please suggest. > > > Thank you, > > Tigran > > > -- > Tigran M. Abramyan, Ph.D. > Postdoctoral Fellow, Computational Biophysics & Molecular Design > Center for Integrative Chemical Biology and Drug Discovery > Eshelman School of Pharmacy > University of North Carolina at Chapel Hill > Chapel Hill, NC 27599-7363 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] oplsaa HISE is charged in gmx 5.1.4 and 2016
Thanks Mark and Justin, I'll have a go at 2016.1 then. Cheers, Jon Mark Abraham skrev Hi, Actually http://manual.gromacs.org/documentation/5.1.4/ReleaseNotes/release-notes.html#fixed-opls-aa-l-charges-for-hisd-and-hise refers to David's first fix of https://redmine.gromacs.org/issues/2013, which was indeed incorrect in this aspect. Justin has since fixed that, but after 5.1.4 was released. That fix will be in 5.1.5 if/when we make one. However, you can feel quite comfortable about taking the 2016.1 share/top/oplsaa.ff directory and using it with 5.1.x. Mark On Tue, Nov 8, 2016 at 4:03 PM Justin Lemkul wrote: > > > On 11/8/16 9:54 AM, Jon Kapla wrote: > > Hi everyone, > > > > I’m trying to setup topologies for OPLS-aa simulations with GPCRs. When > running pdb2gmx in gromacs 5.1.4 (and gromacs 2016) the total charge of a > specific GPCR ends up at 2.435e. Running gromacs 4.6.7 results in the same > protonation, but a more reasonable integer charge of 3e. > > > > I have investigated the issue, and it seems that the difference is > stemming from differing atom charges in the HISE residue in aminoacids.rtp. > If I sum up the atom charges in HISE (5.1.4) I find that it actually is > charged by -0.113e, which exatly corresponds to the difference in the > reported charge from pdb2gmx (5 HISE * -0.113). > > > > Is this a known problem? > > > > This should have been fixed for 5.1.4 (and the release notes say it was), > but > clearly the files are incorrect. The charges are correct in 2016.1 so > please > use that version. > > -Justin > > > Cheers, > > Jon > > -- > > Postdoc, Carlsson lab > > Dept. of Cell and Molecular Biology, Computational Biology and > Bioinformatics > > > > Uppsala Biomedicinska Centrum BMC, Husarg. 3 > > Box 596 > > S-751 24, Uppsala > > > > E-mail: jon.ka...@icm.uu.se > > Phone: +46 70 3041989 <070-304%2019%2089> > > > > -- > == > > 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] binding free energy with gromacs2016
On 11/8/16 11:00 AM, Qasim Pars wrote: Dear users, Hope someone will answer the questions in my previous mail. Thanks in advance, On 6 Nov 2016, at 23:48, Qasim Pars wrote: Dear users, I will try to do binding free energy calculation using GROMACS2016 but I am confused a little bit about the preparation of the input files. I have a few questions: 1) There are below lines to apply a harmonic distance restraint in the mdp files of the binding free energy tutorial http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = no pull_init1 = 0.654 pull_ngroups = 1 pull_group0= a_1391 pull_group1= a_2615 pull_k1= 0.0 ; kJ*mol^(-1)*nm^(-2) pull_kB1 = 4184 ; kJ*mol^(-1)*nm^(-2) Question 1: Instead of those lines I would like to use the [ intermolecular_interactions ] section in the topology file with GROMACS2016. Could you please tell me what to write the [ intermolecular_interactions ] section? Why? The pull code is modulated in a lambda-dependent fashion, which is probably part of the tutorial and computed free energy. 2) complex.top file of the tutorial is as follows: ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" [ atomtypes ] ;name bond_type masscharge ptype sigma epsilon c3c3 0. 0. A 3.39967e-01 4.57730e-01 dc3 c3 0. 0. A 0.0e+00 0.0e+00 Question 2: Why all values (sigma and epsilon) of dc3 are zero? This is effectively a dummy atom, used in transforming the ligand. [ nonbond_params ] ; i jfunc sigma epsilon c3 c31 3.3996700e-01 4.5773000e-01 dc3 dc3 1 3.3996700e-01 4.5773000e-01 Question 3: Why all values of dc3 aren't zero? These are pair-specific interactions. [ angle_restraints ] ; ai ajakaltype thA kA multA thB kB multB 1393 1391 2615 1391 188.8 0.00 1 88.8 41.84 1 1391 2615 2614 2615 132.9 0.00 1 32.9 41.84 1 [ dihedral_restraints ] ; aiajakal type phiA dphiA kA phiB dphiB kB 1410 1393 1391 2615 1 -159.7 0.0 0.00-159.7 0.0 41.84 1393 1391 2615 2614 1 122.6 0.0 0.00 122.6 0.0 41.84 1391 2615 2614 2610 1 12.80.0 0.00 12.8 0.0 41.84 . Question 4: Do I still need to put those ligand parameters (dc3, [ angle_restraints ], [ dihedral_restraints ] ... ) into the topology file to use with GROMACS2016? There is no version-dependent difference here with respect to the topology. -Justin I read section 5.4.2 and 6.1 of the GROMACS2016 manual but I couldn't understand how to prepare the input files. -- Qasim Pars -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] oplsaa HISE is charged in gmx 5.1.4 and 2016
Hi, Actually http://manual.gromacs.org/documentation/5.1.4/ReleaseNotes/release-notes.html#fixed-opls-aa-l-charges-for-hisd-and-hise refers to David's first fix of https://redmine.gromacs.org/issues/2013, which was indeed incorrect in this aspect. Justin has since fixed that, but after 5.1.4 was released. That fix will be in 5.1.5 if/when we make one. However, you can feel quite comfortable about taking the 2016.1 share/top/oplsaa.ff directory and using it with 5.1.x. Mark On Tue, Nov 8, 2016 at 4:03 PM Justin Lemkul wrote: > > > On 11/8/16 9:54 AM, Jon Kapla wrote: > > Hi everyone, > > > > I’m trying to setup topologies for OPLS-aa simulations with GPCRs. When > running pdb2gmx in gromacs 5.1.4 (and gromacs 2016) the total charge of a > specific GPCR ends up at 2.435e. Running gromacs 4.6.7 results in the same > protonation, but a more reasonable integer charge of 3e. > > > > I have investigated the issue, and it seems that the difference is > stemming from differing atom charges in the HISE residue in aminoacids.rtp. > If I sum up the atom charges in HISE (5.1.4) I find that it actually is > charged by -0.113e, which exatly corresponds to the difference in the > reported charge from pdb2gmx (5 HISE * -0.113). > > > > Is this a known problem? > > > > This should have been fixed for 5.1.4 (and the release notes say it was), > but > clearly the files are incorrect. The charges are correct in 2016.1 so > please > use that version. > > -Justin > > > Cheers, > > Jon > > -- > > Postdoc, Carlsson lab > > Dept. of Cell and Molecular Biology, Computational Biology and > Bioinformatics > > > > Uppsala Biomedicinska Centrum BMC, Husarg. 3 > > Box 596 > > S-751 24, Uppsala > > > > E-mail: jon.ka...@icm.uu.se > > Phone: +46 70 3041989 <070-304%2019%2089> > > > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Md simulation of protein ligand error.
On 11/8/16 10:15 AM, maria khan wrote: Dear justin.. My problem of protein ligand simulation , regarding protonation states for His residue has solved..now that error exists no more.There are two things that i want to share,,one is that i didnot get how that problem solved,i just followed that manuals while i have no idea how it just solved..secondly it gives furthur another error that says that is "software inconsistancy error"can u kindly guide me please, There is nothing anyone can do to help you without an exact description of what you're doing - what version you're using, exact commands, exact screen output (everything copied and pasted from the terminal). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Md simulation of protein ligand error.
Dear justin.. My problem of protein ligand simulation , regarding protonation states for His residue has solved..now that error exists no more.There are two things that i want to share,,one is that i didnot get how that problem solved,i just followed that manuals while i have no idea how it just solved..secondly it gives furthur another error that says that is "software inconsistancy error"can u kindly guide me please, regards and thanks alot for your coperation. Maria khan. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] binding free energy with gromacs2016
Dear users, Hope someone will answer the questions in my previous mail. Thanks in advance, > On 6 Nov 2016, at 23:48, Qasim Pars wrote: > > Dear users, > > I will try to do binding free energy calculation using GROMACS2016 but I am > confused a little bit about the preparation of the input files. I have a few > questions: > > 1) There are below lines to apply a harmonic distance restraint in the mdp > files of the binding free energy tutorial > http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme > > pull = umbrella > pull_geometry = distance > pull_dim = Y Y Y > pull_start = no > pull_init1 = 0.654 > pull_ngroups = 1 > pull_group0= a_1391 > pull_group1= a_2615 > pull_k1= 0.0 ; kJ*mol^(-1)*nm^(-2) > pull_kB1 = 4184 ; kJ*mol^(-1)*nm^(-2) > > Question 1: Instead of those lines I would like to use the [ > intermolecular_interactions ] section in the topology file with GROMACS2016. > Could you please tell me what to write the [ intermolecular_interactions ] > section? > > 2) complex.top file of the tutorial is as follows: > ; Include forcefield parameters > #include "amber99sb-ildn.ff/forcefield.itp" > > [ atomtypes ] > ;name bond_type masscharge ptype sigma epsilon > c3c3 0. 0. A 3.39967e-01 4.57730e-01 > dc3 c3 0. 0. A 0.0e+00 0.0e+00 > > > Question 2: Why all values (sigma and epsilon) of dc3 are zero? > > [ nonbond_params ] > ; i jfunc sigma epsilon > c3 c31 3.3996700e-01 4.5773000e-01 > dc3 dc3 1 3.3996700e-01 4.5773000e-01 > > Question 3: Why all values of dc3 aren't zero? > > [ angle_restraints ] > ; ai ajakaltype thA kA multA thB > kB multB > 1393 1391 2615 1391 188.8 0.00 1 88.8 > 41.84 1 > 1391 2615 2614 2615 132.9 0.00 1 32.9 > 41.84 1 > > [ dihedral_restraints ] > ; aiajakal type phiA dphiA kA phiB > dphiB kB > 1410 1393 1391 2615 1 -159.7 0.0 0.00-159.7 0.0 > 41.84 > 1393 1391 2615 2614 1 122.6 0.0 0.00 122.6 0.0 > 41.84 > 1391 2615 2614 2610 1 12.80.0 0.00 12.8 0.0 > 41.84 > . > Question 4: Do I still need to put those ligand parameters (dc3, [ > angle_restraints ], [ dihedral_restraints ] ... ) into the topology file to > use with GROMACS2016? > > I read section 5.4.2 and 6.1 of the GROMACS2016 manual but I couldn't > understand how to prepare the input files. > -- > Qasim Pars -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_wham error in umbrella simulation
Dear all I am doing an umbrella simulation by using the pull code in Gromacs 4.6.5 to calculate the PMF. The pull parameters are the following: ;Pull code pull= constant_force pull_geometry = position pull_dim= N N Ypull_start = no pull_ngroups = 1pull_group0 = GRApull_group1 = UNKpull_rate1 = 0.01 pull_k1 = 1000 pull_vec1 = 0.0 0.0 1.0 When i run the WHAM with the Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal it gave me the following error: Fatal error: This is not a tpr of an umbrella simulation. Found pull type "constant-force" (ir.ePull= 3) I would be more than pleased if someone could guid 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.
Re: [gmx-users] oplsaa HISE is charged in gmx 5.1.4 and 2016
On 11/8/16 9:54 AM, Jon Kapla wrote: Hi everyone, I’m trying to setup topologies for OPLS-aa simulations with GPCRs. When running pdb2gmx in gromacs 5.1.4 (and gromacs 2016) the total charge of a specific GPCR ends up at 2.435e. Running gromacs 4.6.7 results in the same protonation, but a more reasonable integer charge of 3e. I have investigated the issue, and it seems that the difference is stemming from differing atom charges in the HISE residue in aminoacids.rtp. If I sum up the atom charges in HISE (5.1.4) I find that it actually is charged by -0.113e, which exatly corresponds to the difference in the reported charge from pdb2gmx (5 HISE * -0.113). Is this a known problem? This should have been fixed for 5.1.4 (and the release notes say it was), but clearly the files are incorrect. The charges are correct in 2016.1 so please use that version. -Justin Cheers, Jon -- Postdoc, Carlsson lab Dept. of Cell and Molecular Biology, Computational Biology and Bioinformatics Uppsala Biomedicinska Centrum BMC, Husarg. 3 Box 596 S-751 24, Uppsala E-mail: jon.ka...@icm.uu.se Phone: +46 70 3041989 -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] oplsaa HISE is charged in gmx 5.1.4 and 2016
Hi everyone, I’m trying to setup topologies for OPLS-aa simulations with GPCRs. When running pdb2gmx in gromacs 5.1.4 (and gromacs 2016) the total charge of a specific GPCR ends up at 2.435e. Running gromacs 4.6.7 results in the same protonation, but a more reasonable integer charge of 3e. I have investigated the issue, and it seems that the difference is stemming from differing atom charges in the HISE residue in aminoacids.rtp. If I sum up the atom charges in HISE (5.1.4) I find that it actually is charged by -0.113e, which exatly corresponds to the difference in the reported charge from pdb2gmx (5 HISE * -0.113). Is this a known problem? Cheers, Jon -- Postdoc, Carlsson lab Dept. of Cell and Molecular Biology, Computational Biology and Bioinformatics Uppsala Biomedicinska Centrum BMC, Husarg. 3 Box 596 S-751 24, Uppsala E-mail: jon.ka...@icm.uu.se Phone: +46 70 3041989 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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_wham error in umbrella simulation
On 11/8/16 9:50 AM, diana p wrote: Dear all I am doing an umbrella simulation by using the pull code in Gromacs 4.6.5 to calculate the PMF. The pull parameters are the following: ;Pull code pull= constant_force pull_geometry = position pull_dim= N N Ypull_start = no pull_ngroups = 1pull_group0 = GRApull_group1 = UNKpull_rate1 = 0.01 pull_k1 = 1000 pull_vec1 = 0.0 0.0 1.0 When i run the WHAM with the Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal it gave me the following error: Fatal error: This is not a tpr of an umbrella simulation. Found pull type "constant-force" (ir.ePull= 3) I would be more than pleased if someone could guid me. The error is pretty explicit - you didn't do umbrella sampling. You applied a constant biasing force. To do umbrella sampling, you need "pull = umbrella" in the .mdp file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
On 11/8/16 6:13 AM, Kingsley Theras Primus Dass . wrote: Even when I add the new atom types to aminoacid.rtp, .hdb , .atp , Still it shows the same error The error has nothing to do with atom types, and without seeing what you did, there's no possible way to solve it. An anionic sulfotyrosine residue should have the same .hdb entry as normal tyrosine. Copy it and rename the residue to whatever your .rtp specifies. -Justin Could you please suggest some solutions. Thank you in advance On 8 Nov 2016 6:59 p.m., "Justin Lemkul" wrote: On 11/7/16 10:44 PM, Kingsley Theras Primus Dass . wrote: Hello users!! I generated a Topology file for SO3- using ATB topology generator , which is compatible with GROMACS. Then I copied the .rtp file from ATB and pasted it into GROMACS aminoacid.rtp. The partial charge of aminoacid sulfated-tyrosine was -1. When I run -pdb2gmx there was error saying the atoms were missing , --- Program gmx pdb2gmx, VERSION 5.1 Source code file: /home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreproce ss/pdb2top.cpp, line: 1584 Fatal error: There were 6 missing atoms in molecule Protein_chain_D, if you want to use this incomplete topology anyhow, use the option -missing then I ran pdb2gmx -ignh -p topol.top -missing It generated the topology file. But the parital charge of sulfated tyrosine was changed to -2, coz of missing hydrogen atoms. can you please suggest some solutions , to overcome this problem. Add an .hdb entry for your residue so that pdb2gmx will build the missing atoms. In general, never use the -missing option. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support /Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
Even when I add the new atom types to aminoacid.rtp, .hdb , .atp , Still it shows the same error Could you please suggest some solutions. Thank you in advance On 8 Nov 2016 6:59 p.m., "Justin Lemkul" wrote: > > > On 11/7/16 10:44 PM, Kingsley Theras Primus Dass . wrote: > >> Hello users!! >> >> I generated a Topology file for SO3- using ATB topology generator , which >> is compatible with GROMACS. Then I copied the .rtp file from ATB and >> pasted >> it into GROMACS aminoacid.rtp. >> >> The partial charge of aminoacid sulfated-tyrosine was -1. >> When I run -pdb2gmx there was error saying the atoms were missing , >> --- >> Program gmx pdb2gmx, VERSION 5.1 >> Source code file: >> /home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreproce >> ss/pdb2top.cpp, >> line: 1584 >> >> Fatal error: >> There were 6 missing atoms in molecule Protein_chain_D, if you want to use >> this incomplete topology anyhow, use the option -missing >> >> >> then I ran pdb2gmx -ignh -p topol.top -missing >> >> It generated the topology file. But the parital charge of sulfated >> tyrosine >> was changed to -2, coz of missing hydrogen atoms. >> >> can you please suggest some solutions , to overcome this problem. >> >> > Add an .hdb entry for your residue so that pdb2gmx will build the missing > atoms. In general, never use the -missing option. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
On 11/7/16 10:44 PM, Kingsley Theras Primus Dass . wrote: Hello users!! I generated a Topology file for SO3- using ATB topology generator , which is compatible with GROMACS. Then I copied the .rtp file from ATB and pasted it into GROMACS aminoacid.rtp. The partial charge of aminoacid sulfated-tyrosine was -1. When I run -pdb2gmx there was error saying the atoms were missing , --- Program gmx pdb2gmx, VERSION 5.1 Source code file: /home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1584 Fatal error: There were 6 missing atoms in molecule Protein_chain_D, if you want to use this incomplete topology anyhow, use the option -missing then I ran pdb2gmx -ignh -p topol.top -missing It generated the topology file. But the parital charge of sulfated tyrosine was changed to -2, coz of missing hydrogen atoms. can you please suggest some solutions , to overcome this problem. Add an .hdb entry for your residue so that pdb2gmx will build the missing atoms. In general, never use the -missing option. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to restart mdrun at a specific time from checkpoint
On 11/7/16 11:37 PM, 张慧玲 wrote: But the -cpi option will restart mdrun from checkpoint at time 46840ps, I want to start from a previous time, for example 45000ps. Then you need to use the -cpi option to specify the name of the checkpoint file that contains the state at 45000 ps. -Justin Hui Message: 4 Date: Mon, 7 Nov 2016 22:14:47 -0500 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to restart mdrun at a specific time from checkpoint Message-ID: Content-Type: text/plain; charset=UTF-8; format=flowed On 11/7/16 10:01 PM, ??? wrote: Hi, my mdrun stopped at 46840ps, I want to restart the mdrun at 45000ps from checkpoint. How could I told the mdrun to do this??? Supply that checkpoint file to mdrun -cpi. http://www.gromacs.org/Documentation/How-tos/Doing_Restarts -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD ensemble of states
Hi, Mdrun wrote that. You made the trajectories contiguous with the demux. Mark On Tue, 8 Nov 2016 04:55 Abramyan, Tigran wrote: > Hi, > > > I conducted REMD, and extracted the trajectories via > trjcat -f *.trr -demux replica_index.xvg > And now I was wondering which *.xtc file is the ensemble of states at the > baseline replica (lowest temperature replica). Intuitively my guess is that > the numbers in the names of *_trajout.xtc files correspond to the replica > numbers starting from the baseline, and hence 0_trajout.xtc is the ensemble > of states at the baseline replica, but I may be wrong. > > > Please suggest. > > > Thank you, > > Tigran > > > -- > Tigran M. Abramyan, Ph.D. > Postdoctoral Fellow, Computational Biophysics & Molecular Design > Center for Integrative Chemical Biology and Drug Discovery > Eshelman School of Pharmacy > University of North Carolina at Chapel Hill > Chapel Hill, NC 27599-7363 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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 restart mdrun at a specific time from checkpoint
Hi, You can start from any cpt you have, but each file contains only one snapshot. So you can't arbitrarily restart unless you saved cpt files manually. Using mdrun -noappend is a good way to do this, but leaves you with manual work to do concatenating files for your analysis. Or archive your cpt files between runs. But be aware that you will not generally be able to repeat the same trajectory from any checkpoint, so only do this if you have an appropriate reason. Mark On Tue, 8 Nov 2016 05:45 张慧玲 wrote: > > > But the -cpi option will restart mdrun from checkpoint at time 46840ps, I > want to start from a previous time, for example 45000ps. > > > Hui > > > > Message: 4 > > Date: Mon, 7 Nov 2016 22:14:47 -0500 > > From: Justin Lemkul > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] How to restart mdrun at a specific time from > > checkpoint > > Message-ID: > > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > > > > > On 11/7/16 10:01 PM, ??? wrote: > > > Hi, > > > my mdrun stopped at 46840ps, I want to restart the mdrun at > 45000ps from checkpoint. How could I told the mdrun to do this??? > > > > Supply that checkpoint file to mdrun -cpi. > > > > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts > > > > -Justin > > > > > > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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.