Hello Jon and Justin I had a MD simulation "dyn" running for 46 ns (actually it's 30 umbrella simulations using pull code)
I did try the -cpi option and my calculation seems to have restarted correctly renaming the files dyn.part0003.... But just running gmx mdrun -cpi -noappend does not allow me to tell the number of additional steps I want in my dynamics - So right now it's running 46 more ns (the original mdp and tpr file) which is not reasonable because I have 100s of calculations to run - I want to be able to specify 5 ns more for instance Usually I use gmx convert-tpr - extend 5000 which builds a new tpr with which I can restart with -cpi And running without a checkpoint file, Justin is not what I want - I really need to restart my dynamics after 46 ns, just I don't want the trr files - (I've got all the other files all right) - There should be a trick to restart without writing to a trr file... Isn't there ? Thanks again for your help Serge Crouzy PhD HDR Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et Biologie des Métaux Département des Interfaces pour l'Energie, la Santé et l'Environnement Institut de Recherche Interdisciplinaire de Grenoble CEA Grenoble UMR CEA/CNRS/UJF 5249 17, rue des martyrs 38054 Grenoble Cedex 9 Bat. K pièce 110 Tel (33) 438782963 Fax (33) 438785487 http://big.cea.fr/drf/big/english/CBM/GMCT -----Message d'origine----- De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> De la part de gromacs.org_gmx-users-requ...@maillist.sys.kth.se Envoyé : lundi 13 mai 2019 15:23 À : gromacs.org_gmx-users@maillist.sys.kth.se Objet : gromacs.org_gmx-users Digest, Vol 181, Issue 30 Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. Gromacs error while running energy minimization step (Muneeswaran S) 2. Re: ligand in water (Bratin Kumar Das) 3. Re: water mediated Hbond (Bratin Kumar Das) 4. nmr distance restraints (Eiso AB) 5. Restart dynamics when trr files removed (CROUZY Serge 119222) 6. Re: Restart dynamics when trr files removed (John Whittaker) ---------------------------------------------------------------------- Message: 1 Date: Mon, 13 May 2019 17:36:36 +0530 From: Muneeswaran S <wmunee...@gmail.com> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Gromacs error while running energy minimization step Message-ID: <CAN=_hbdryft2ppawmbmbx7euigkysycdjfdrgeojq2+e+rb...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" I got the following error while running the gromacs *NOTE: disabling dynamic load balancing as it is only supported with dynamics, not with integrator 'steep'.Using 16 MPI threadsUsing 4 OpenMP threads per tMPI threadOn host localhost.localdomain 2 GPUs auto-selected for this run.Mapping of GPU IDs to the 16 GPU tasks in the 16 ranks on this node: PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1-------------------------------------------------------Program: gmx mdrun, version 2018.6Source file: src/gromacs/utility/filestream.cpp (line 115)Function: gmx::internal::FileStreamImpl::FileStreamImpl(const char*, const char*)MPI rank: 12 (out of 16)System I/O error:Failed to compile NBNXN kernels for GPU #Quadro P620 Could not open file '/usr/share/gromacs/opencl/nbnxn_ocl_kernels.cl <http://nbnxn_ocl_kernels.cl>' Reason: No such file or directory (call to fopen() returned error code 2)For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors <http://www.gromacs.org/Documentation/Errors>* ------------------------------ Message: 2 Date: Mon, 13 May 2019 18:15:27 +0530 From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] ligand in water Message-ID: <cam7tw5t_i0ckx64h9fk0r1x_-+-jx1fuxrg5xgmpduh+4g9...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hi The procedure you are following is not ok. Generate the co-ordinate file of ligand and the topology parameter file. Setup the box and add water to it. Lastly do energy minimisation. On Thu 9 May, 2019, 2:33 PM RAHUL SURESH, <drrahulsur...@gmail.com> wrote: > Hi Users. > > I want to simulate ligand in the water box. I prepared a water > molecule and started with pdb2gmx and then planned to follow protein-ligand > tutorial. > Unfortunately ended up with an error in gro file format. Have check > every possibility but still couldn't find any solution. > My initial pdb is water.pdb and the corresponding gro file is > water.gro. I clubbed the ligand gro file and water gro file as > complex.gro. I have uploaded the file here. can anyone help me with the > format issues>? > > -- > *Regards,* > *Rahul * > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. ------------------------------ Message: 3 Date: Mon, 13 May 2019 18:18:38 +0530 From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] water mediated Hbond Message-ID: <CAM7TW5u-KQ6tzvcawBo=VztGr1enPQj+38br5=ponfro+gj...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hi, You can make a ndx file containing the residue of interest and the SOL. In gmx h-bond command use the index file. It will give you water mediated hbond On Tue 7 May, 2019, 12:40 PM , <sp...@iacs.res.in> wrote: > Dear all > I want to determine the water mediated hydrogen between DNA bases and > small molecule. What extra flag should I use in gmx hbond command? Is > there any other option to capture the water mediated Hbonds? Please > suggest something. > Sunipa Sarkar > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > ------------------------------ Message: 4 Date: Mon, 13 May 2019 14:49:17 +0200 From: Eiso AB <eis...@gmail.com> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] nmr distance restraints Message-ID: <CAD3n-aaNenMX7g7XqmRorhmLwE8S3p_cY6qeLoZ4y=kpvjg...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hi, I've setup an mdrun with [ distance restraints ] but the restraints don't seem to have any effect on the simulation, so I'm wondering if there's anything i need to do to switch them on that I missed. gmx disre or gmx nmr doesn't give any info about restraints. and the .log file doesn't show any energy component for Distance Restraints, e.g. Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. Improper Dih. 4.14550e+03 1.13252e+04 1.29502e+04 9.20032e+01 6.00131e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 5.01723e+03 6.08476e+04 3.13964e+05 -2.12124e+06 5.15532e+03 Potential Kinetic En. Total Energy Conserved En. Temperature -1.70714e+06 2.85181e+05 -1.42196e+06 -1.34064e+06 2.99828e+02 Pressure (bar) Constr. rmsd 1.15517e+02 4.10744e-06 I have defined restraints between protein, ligand and a few waters - all in different [molecules] - so I used [ intemolecular_interactions ] followed by [ distance restraints ] my topol.top ends like this : [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_chain_A 1 lig 1 SOL 35926 NA 4 [ intermolecular_interactions ] [ distance_restraints ] ; ai aj type index type' low up1 up2 fac ; # source 465 564 1 0 1 0.2540 0.2540 0.4115 1 ; # 308 ile hd+ 216 val hg1+ 2.54 465 565 1 0 1 0.2540 0.2540 0.4115 1 ; # 465 566 1 0 1 0.2540 0.2540 0.4115 1 ; # 466 564 1 0 1 0.2540 0.2540 0.4115 1 ; # 466 565 1 0 1 0.2540 0.2540 0.4115 1 ; # 466 566 1 0 1 0.2540 0.2540 0.4115 1 ; # 467 564 1 0 1 0.2540 0.2540 0.4115 1 ; # 467 565 1 0 1 0.2540 0.2540 0.4115 1 ; # 467 566 1 0 1 0.2540 0.2540 0.4115 1 ; # [...snap...] 1607 5241 1 34 1 0.5680 0.5680 0.6384 1 ; # 170 leu hd1# 411 lig h09 5.68 1608 5241 1 34 1 0.5680 0.5680 0.6384 1 ; # 1609 5241 1 34 1 0.5680 0.5680 0.6384 1 ; # [ ..snap ... ] 2720 5571 1 52 2 0.1900 0.1900 0.2900 1 ; # 217 asp od1 501 sol hw2 1.90 2720 5569 1 53 2 0.3000 0.3000 0.4000 1 ; # 217 asp od1 501 sol ow 3.00 disre is set to simple. From the mdout.mdp []$ grep disre mdout.mdp ; Distance restraints type: No, Simple or Ensemble disre = Simple ; Force weighting of pairs in one distance restraint: Conservative or Equal disre-weighting = Conservative ; Use sqrt of the time averaged times the instantaneous violation disre-mixed = no disre-fc = 1000 disre-tau = 0 ; Output frequency for pair distances to energy file nstdisreout = 100 gmx dump shows that the run topology has the distance restraints and looks ok to me gmx dump -s md_0_10.tpr |grep -10 dis [..snap..] Reading file md_0_10.tpr, VERSION 2019-beta1 (single precision) Reading file md_0_10.tpr, VERSION 2019-beta1 (single precision) disre = Simple disre-weighting = Conservative disre-mixed = false nstdisreout = 100 0 type=1038 (DISRES) 464 563 1 type=1038 (DISRES) 464 564 2 type=1038 (DISRES) 464 565 3 type=1038 (DISRES) 465 563 4 type=1038 (DISRES) 465 564 5 type=1038 (DISRES) 465 565 [..snap ...] D.R.Viol. (nm): nr: 0 [...snap...] functype[1038]=DISRES, label= 0, type=1, low= 2.54000008e-01, up1= 2.54000008e-01, up2= 4.11500007e-01, fac= 1.00000000e+00) functype[1039]=DISRES, label= 1, type=1, low= 2.56999999e-01, up1= 2.56999999e-01, up2= 4.12600011e-01, fac= 1.00000000e+00) functype[1040]=DISRES, label= 2, type=1, low= 3.72999996e-01, up1= 3.72999996e-01, up2= 4.80199993e-01, fac= 1.00000000e+00) functype[1041]=DISRES, label= 3, type=1, low= 3.84000003e-01, up1= 3.84000003e-01, up2= 4.88200009e-01, fac= 1.00000000e+00) functype[1042]=DISRES, label= 4, type=1, low= 2.33999997e-01, up1= 2.33999997e-01, up2= 4.04900014e-01, fac= 1.00000000e+00) functype[1043]=DISRES, label= 5, type=1, low= 2.39999995e-01, up1= 2.39999995e-01, up2= 4.06699985e-01, fac= 1.00000000e+00) functype[1044]=DISRES, label= 6, type=1, low= 3.03000003e-01, up1= 3.03000003e-01, up2= 4.35000002e-01, fac= 1.00000000e+00) etc... Any suggestions about what is wrong here would be appreciated Thanks, Eiso ------------------------------ Message: 5 Date: Mon, 13 May 2019 12:20:48 +0000 From: CROUZY Serge 119222 <serge.cro...@cea.fr> To: "gromacs.org_gmx-users@maillist.sys.kth.se" <gromacs.org_gmx-users@maillist.sys.kth.se> Subject: [gmx-users] Restart dynamics when trr files removed Message-ID: <47ad30a9288c1e49bcf6c0cbb2e5bba654c28...@exdag0-a1.intra.cea.fr> Content-Type: text/plain; charset="iso-8859-1" Dear Gromacs users I ran long MD simulations ( 50ns) with nstxout=5000 resulting in very large .trr files Realizing that I did not need these files (xtc enough), I removed them hoping to regenerate necessary restart files from a new gmx grompp and corrected mdp file (with nstxout=0)... But NO - I can't restart the simulation from 50 ns on without trr files - Whatever tricks I seem to have tried to fool the controls I hope someone can tell me how I can solve my problem - Even if it is recompiling the source to remove the flag checking that the trr file is absent Thanks for your help ! Serge Crouzy PhD HDR Groupe de Mod?lisation et Chimie Th?orique Laboratoire de Chimie et Biologie des M?taux D?partement des Interfaces pour l'Energie, la Sant? et l'Environnement Institut de Recherche Interdisciplinaire de Grenoble CEA Grenoble UMR CEA/CNRS/UJF 5249 17, rue des martyrs 38054 Grenoble Cedex 9 Bat. K pi?ce 110 Tel (33) 438782963 Fax (33) 438785487 http://big.cea.fr/drf/big/english/CBM/GMCT ------------------------------ Message: 6 Date: Mon, 13 May 2019 15:22:41 +0200 From: "John Whittaker" <johnwhitt...@zedat.fu-berlin.de> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Restart dynamics when trr files removed Message-ID: <51954.160.45.109.178.1557753761.webm...@webmail.zedat.fu-berlin.de> Content-Type: text/plain;charset=utf-8 Hi, > But NO - I can't restart the simulation from 50 ns on without trr > files There should be a checkpoint file called (by default) state.cpt that was generated when your 50 ns simulation finished. You can use this file to continue your run from the final state of that simulation with: gmx mdrun -cpi state.cpt Your checkpoint file might be named something different than "state.cpt", but regardless, that procedure should do the trick. Good luck, John ------------------------------ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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 181, Issue 30 ****************************************************** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
