Re: [gmx-users] NVT equilibration in vacuum
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 | (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.
[gmx-users] NVT equilibration in vacuum
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? Thank you, Neena -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] WG: WG: Issue with CUDA and gromacs
Hi Steffi, Thanks for running the tests; yes, the patch file was meant to be applied to the unchanged GROMACS 2019 code. Please also share the log files from thr failed runs, not just the copy-paste of the fatal error -- as a result of the additional check there might have been a note printed which I was after. Regarding the regression tests, what I would like to have is the actual directories of the tests that failed, i.e. as your log indicates a few of the complex tests at least. Cheers, -- Szilárd On Tue, Mar 26, 2019 at 1:44 PM Tafelmeier, Stefanie < stefanie.tafelme...@zae-bayern.de> wrote: > Hi Szilárd, > > thanks again for your answer. > Regarding the tests: > without the new patch: > > -ntmpi 1 -ntomp 11 -pin on -pinstride 1:all ran > -ntmpi 1 -ntomp 11 -pin on -pinstride 2:all ran > -ntmpi 1 -ntomp 11 -pin on -pinstride 4:all ran > -ntmpi 1 -ntomp 11 -pin on -pinstride 8:all ran > and > -ntmpi 1 -ntomp 22 -pin on -pinstride 1:none ran* > -ntmpi 1 -ntomp 22 -pin on -pinstride 2:none ran* > -ntmpi 1 -ntomp 22 -pin on -pinstride 4:one out of 5 ran > > > With the new patch (devicebuffer.cuh had to be the original, right? The > already patched didn't work as the lines didn't fit, as far as I > understood.): > > -ntmpi 1 -ntomp 11 -pin on -pinstride 1:all ran > -ntmpi 1 -ntomp 11 -pin on -pinstride 2:all ran > -ntmpi 1 -ntomp 11 -pin on -pinstride 4:all ran > -ntmpi 1 -ntomp 11 -pin on -pinstride 8:all ran > and > -ntmpi 1 -ntomp 22 -pin on -pinstride 1:none ran* > -ntmpi 1 -ntomp 22 -pin on -pinstride 2:none ran* > -ntmpi 1 -ntomp 22 -pin on -pinstride 4:none ran* > > * Fatal error: > Asynchronous H2D copy failed: invalid argument > > > Regarding the regressiontest: > The LastTest.log is available here: > https://it-service.zae-bayern.de/Team/index.php/s/3sdki7Cf2x2CEQi > this was not given in the log: > The following tests FAILED: > 42 - regressiontests/complex (Timeout) > 46 - regressiontests/essentialdynamics (Failed) > Errors while running CTest > CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target > 'CMakeFiles/run-ctest-nophys' failed > make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 > CMakeFiles/Makefile2:1397: recipe for target > 'CMakeFiles/run-ctest-nophys.dir/all'failed > make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 > CMakeFiles/Makefile2:1177: recipe for target > 'CMakeFiles/check.dir/rule' failed > make[1]: *** [CMakeFiles/check.dir/rule] Error 2 > Makefile:626: recipe for target 'check' failed > make: *** [check] Error 2 > > Many thanks again. > Best wishes, > Steffi > > > > > > -Ursprüngliche Nachricht- > Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Szilárd > Páll > Gesendet: Montag, 25. März 2019 20:13 > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs > > Hi, > > > > -- > Szilárd > > > On Mon, Mar 18, 2019 at 2:34 PM Tafelmeier, Stefanie < > stefanie.tafelme...@zae-bayern.de> wrote: > > > Hi, > > > > Many thanks again. > > > > Regarding the tests: > > - ntmpi 1 -ntomp 22 -pin on > > >OK, so this suggests that your previously successful 22-thread runs did > > not > > turn on pinning, I assume? > > It seems so, yet it does not run successfully each time. But if done with > > 20-threads, which works usually without error, it does not look like the > > pinning is turned on. > > > > Pinning is only turned on if mdrun can safely assume that the cores of the > node are not shared by multiple applications. This assumption can only be > made if all hardware threads of the entire node are used the run itself > (i.e. in your case 2x22 cores with HyperThreadince hence 2 threads each = > 88 threads). > > -ntmpi 1 -ntomp 1 -pin on; runs > > -ntmpi 1 -ntomp 2 -pin on; runs > > > > - ntmpi 24 -ntomp 1 -pinstride 1 -pin on; runs > > - ntmpi 24 -ntomp 1 -pinstride 2 -pin on; runs > > > > After patch supplied: > > - ntmpi 1 -ntomp 22 -pin on; sometime runs - sometimes doesn't* -> > > md_run.log at : > > https://it-service.zae-bayern.de/Team/index.php/s/ezXWnQ2pGNeFx6T > > > > md_norun.log at: > > https://it-service.zae-bayern.de/Team/index.php/s/wYPY7dWEJdwmqJi > > - ntmpi 1 -ntomp 22 -pin off; sometime runs - sometimes doesn't* (ran > > before) > > - ntmpi 1 -ntomp 23 -pin off; doesn't work* (ran before) > > > > - ntmpi 1 -ntomp 23 -pinstride 1 -pin on; doesn't work* > > > > - ntmpi 1 -ntomp 23 -pinstride 2 -pin on; doesn't work* (ran before) > > > > > The suspicious thing is that the patch I made only improves the verbosity > of the error reporting, it should have no impact on whether the error is > triggered or not. Considering the above behavior it seems that pinning (at > least the patters tried) has no
Re: [gmx-users] grompp error: Unknown bond_atomtype
On 3/26/19 8:22 AM, vico...@fizyka.umk.pl wrote: Hello everyone, I would call myself newbie gromacs user and need some help with task that was given to me. I'm supposed to take protein-ligand complex (bounded by covalence bond) and put it into membrane. I'm glad I've created the complex in amber force field. But now I stucked around membrane think. I have created DLPC-only membrane cluster in charmm-gui. I have found parameters for this type of lipid. I did add additional names for atom in atomtypes.atp, include ffbonded_lipid.itp and ffnonbonded_lipit.itp files to forcefrield.itp and put into amber forcefield directory t he lipids.rtp file. Gladly everything went smoothly with pdb2gmx with my membrane. I get topol.top file. Then I wanted to try minimize energy. I've prepared .mdp file and used gromp with: gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is defined in atomtypes.atp and the bond have its parameters inside the ffbond.itp file. It's really strange for me, beacuse I thought that if topol.top file was created there is no possibility to get some troubles with defined atoms, bonds, etc. Where did I make mistake? It looks like you're mixing force fields between AMBER and CHARMM. CTL3 is a CHARMM atom type. You cannot mix force fields; you must develop the topology under a single, consistent parameter set. -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 | (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.
Re: [gmx-users] extract chain information in xtc file
Hi Make use of gmx make_ndx option. Please refer the manual to use it. You can define your chain there and extract it separately On Tue 26 Mar, 2019, 6:49 PM , wrote: > Hello, > I barely discover Gromacs and I have to use it to study trajectory > results, so I wanted to know if it was possible from an xtc file to > generate several xtc files, one for each chain of the molecule that we want > to study, (in order to retrieve information and perform calculations) and > if it is possible, how? I found several information for concatenation or > even to cut a simulation of time N in several simulations of time n, but I > do not find anything concerning a possible cut according to the chains of > the molecule. > > Thanking you in advance for your answer. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] grompp error: Unknown bond_atomtype
Cytowanie RAHUL SURESH : On Tue 26 Mar, 2019, 6:18 PM , wrote: Cytowanie RAHUL SURESH : > On Tue 26 Mar, 2019, 6:00 PM , wrote: > >> Hello everyone, >> >> I would call myself newbie gromacs user and need some help with task >> that was given to me. I'm supposed to take protein-ligand complex >> (bounded by covalence bond) and put it into membrane. I'm glad I've >> created the complex in amber force field. But now I stucked around >> membrane think. >> >> I have created DLPC-only membrane cluster in charmm-gui. I have found >> parameters for this type of lipid. I did add additional names for atom >> in atomtypes.atp, include ffbonded_lipid.itp and >> ffnonbonded_lipit.itp files to forcefrield.itp and put into amber >> forcefield directory t he lipids.rtp file. Gladly everything went >> smoothly with pdb2gmx with my membrane. I get topol.top file. Then I >> wanted to try minimize energy. I've prepared .mdp file and used gromp >> with: >> >> gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr >> >> Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is >> defined in atomtypes.atp and the bond have its parameters inside the >> ffbond.itp file. It's really strange for me, beacuse I thought that if >> topol.top file was created there is no possibility to get some >> troubles with defined atoms, bonds, etc. >> > This CTL3 is that of ligand? No, I'm doing right now ONLY membrane. There are only lipids in the .gro file with solvataion and the CTL3 is atom of lipid. I just wanted to check if I'm able to create membrane-only system first. If everything will work I'll try to embed protein+ligand in this membrane. If I believe you are using amber ff for the lipids generated using charm GUI, then I should say the nomenclature of the lipid membrane will be in charmm format. Either you must use charmm ff or you have to use lipids for amber ff .. I just download PDB file with membrane cluster structure from charmm-gui. No topology, no parameters at all. Only coordinates. Then I found parameters in amber force field for this DLPC and proceeded both pdb structure and parameters .itp with pdb2gmx. Everything worked. But now got troubles with energy minimization/simulations. >> > >> > > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] extract chain information in xtc file
Hello, I barely discover Gromacs and I have to use it to study trajectory results, so I wanted to know if it was possible from an xtc file to generate several xtc files, one for each chain of the molecule that we want to study, (in order to retrieve information and perform calculations) and if it is possible, how? I found several information for concatenation or even to cut a simulation of time N in several simulations of time n, but I do not find anything concerning a possible cut according to the chains of the molecule. Thanking you in advance for your answer. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] GPU error
On Tue 26 Mar, 2019, 6:09 PM Justin Lemkul, wrote: > > > On 3/26/19 2:05 AM, RAHUL SURESH wrote: > > Hi Dr Mark > > > > System is pretty tiny only with 15000 atoms. 1 GpU is automatically > > selected. > > You will certainly not benefit from trying to use multiple GPUs for such > a small system. > > > I get a note stating potentially sub-optimal launch configuration, gmx > > started with less pp Mpi process for node than GPUs available. > > > > So the use of GPU is automated depending on the size of the system? > > mdrun will try to utilize everything it finds, and automatically tune > for the best performance, but in your case you definitely only want to > use 1 GPU. > > > Also, I can find a line in the log file, "Binary not matching Hardware- > you > > might be losing performance. > > > > Please help us understand this more. > > The last message suggests you have not compiled GROMACS in the best way > to maximize performance. At compilation, cmake will recommend what type > of hardware optimization to use. Follow its suggestion, or simply do not > override it with your own specification. > > -Justin > Thank you Dr 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 | (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. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] grompp error: Unknown bond_atomtype
On Tue 26 Mar, 2019, 6:18 PM , wrote: > Cytowanie RAHUL SURESH : > > > On Tue 26 Mar, 2019, 6:00 PM , wrote: > > > >> Hello everyone, > >> > >> I would call myself newbie gromacs user and need some help with task > >> that was given to me. I'm supposed to take protein-ligand complex > >> (bounded by covalence bond) and put it into membrane. I'm glad I've > >> created the complex in amber force field. But now I stucked around > >> membrane think. > >> > >> I have created DLPC-only membrane cluster in charmm-gui. I have found > >> parameters for this type of lipid. I did add additional names for atom > >> in atomtypes.atp, include ffbonded_lipid.itp and > >> ffnonbonded_lipit.itp files to forcefrield.itp and put into amber > >> forcefield directory t he lipids.rtp file. Gladly everything went > >> smoothly with pdb2gmx with my membrane. I get topol.top file. Then I > >> wanted to try minimize energy. I've prepared .mdp file and used gromp > >> with: > >> > >> gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr > >> > >> Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is > >> defined in atomtypes.atp and the bond have its parameters inside the > >> ffbond.itp file. It's really strange for me, beacuse I thought that if > >> topol.top file was created there is no possibility to get some > >> troubles with defined atoms, bonds, etc. > >> > > This CTL3 is that of ligand? > > No, I'm doing right now ONLY membrane. There are only lipids in the > .gro file with solvataion and the CTL3 is atom of lipid. I just wanted > to check if I'm able to create membrane-only system first. If > everything will work I'll try to embed protein+ligand in this > membrane. > > If I believe you are using amber ff for the lipids generated using charm > GUI, then I should say the nomenclature of the lipid membrane will be in > charmm format. Either you must use charmm ff or you have to use lipids for > amber ff .. > >> > > > > Where did I make mistake? > >> > >> Have did you manage to add ligand topology? > >> > > > > > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)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] grompp error: Unknown bond_atomtype
Cytowanie RAHUL SURESH : On Tue 26 Mar, 2019, 6:00 PM , wrote: Hello everyone, I would call myself newbie gromacs user and need some help with task that was given to me. I'm supposed to take protein-ligand complex (bounded by covalence bond) and put it into membrane. I'm glad I've created the complex in amber force field. But now I stucked around membrane think. I have created DLPC-only membrane cluster in charmm-gui. I have found parameters for this type of lipid. I did add additional names for atom in atomtypes.atp, include ffbonded_lipid.itp and ffnonbonded_lipit.itp files to forcefrield.itp and put into amber forcefield directory t he lipids.rtp file. Gladly everything went smoothly with pdb2gmx with my membrane. I get topol.top file. Then I wanted to try minimize energy. I've prepared .mdp file and used gromp with: gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is defined in atomtypes.atp and the bond have its parameters inside the ffbond.itp file. It's really strange for me, beacuse I thought that if topol.top file was created there is no possibility to get some troubles with defined atoms, bonds, etc. This CTL3 is that of ligand? No, I'm doing right now ONLY membrane. There are only lipids in the .gro file with solvataion and the CTL3 is atom of lipid. I just wanted to check if I'm able to create membrane-only system first. If everything will work I'll try to embed protein+ligand in this membrane. Where did I make mistake? Have did you manage to add ligand topology? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] WG: WG: Issue with CUDA and gromacs
Hi Szilárd, thanks again for your answer. Regarding the tests: without the new patch: -ntmpi 1 -ntomp 11 -pin on -pinstride 1:all ran -ntmpi 1 -ntomp 11 -pin on -pinstride 2:all ran -ntmpi 1 -ntomp 11 -pin on -pinstride 4:all ran -ntmpi 1 -ntomp 11 -pin on -pinstride 8:all ran and -ntmpi 1 -ntomp 22 -pin on -pinstride 1:none ran* -ntmpi 1 -ntomp 22 -pin on -pinstride 2:none ran* -ntmpi 1 -ntomp 22 -pin on -pinstride 4:one out of 5 ran With the new patch (devicebuffer.cuh had to be the original, right? The already patched didn't work as the lines didn't fit, as far as I understood.): -ntmpi 1 -ntomp 11 -pin on -pinstride 1:all ran -ntmpi 1 -ntomp 11 -pin on -pinstride 2:all ran -ntmpi 1 -ntomp 11 -pin on -pinstride 4:all ran -ntmpi 1 -ntomp 11 -pin on -pinstride 8:all ran and -ntmpi 1 -ntomp 22 -pin on -pinstride 1:none ran* -ntmpi 1 -ntomp 22 -pin on -pinstride 2:none ran* -ntmpi 1 -ntomp 22 -pin on -pinstride 4:none ran* * Fatal error: Asynchronous H2D copy failed: invalid argument Regarding the regressiontest: The LastTest.log is available here: https://it-service.zae-bayern.de/Team/index.php/s/3sdki7Cf2x2CEQi this was not given in the log: The following tests FAILED: 42 - regressiontests/complex (Timeout) 46 - regressiontests/essentialdynamics (Failed) Errors while running CTest CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target 'CMakeFiles/run-ctest-nophys' failed make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 CMakeFiles/Makefile2:1397: recipe for target 'CMakeFiles/run-ctest-nophys.dir/all'failed make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 CMakeFiles/Makefile2:1177: recipe for target 'CMakeFiles/check.dir/rule' failed make[1]: *** [CMakeFiles/check.dir/rule] Error 2 Makefile:626: recipe for target 'check' failed make: *** [check] Error 2 Many thanks again. Best wishes, Steffi -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Szilárd Páll Gesendet: Montag, 25. März 2019 20:13 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs Hi, -- Szilárd On Mon, Mar 18, 2019 at 2:34 PM Tafelmeier, Stefanie < stefanie.tafelme...@zae-bayern.de> wrote: > Hi, > > Many thanks again. > > Regarding the tests: > - ntmpi 1 -ntomp 22 -pin on > >OK, so this suggests that your previously successful 22-thread runs did > not > turn on pinning, I assume? > It seems so, yet it does not run successfully each time. But if done with > 20-threads, which works usually without error, it does not look like the > pinning is turned on. > Pinning is only turned on if mdrun can safely assume that the cores of the node are not shared by multiple applications. This assumption can only be made if all hardware threads of the entire node are used the run itself (i.e. in your case 2x22 cores with HyperThreadince hence 2 threads each = 88 threads). -ntmpi 1 -ntomp 1 -pin on; runs > -ntmpi 1 -ntomp 2 -pin on; runs > > - ntmpi 24 -ntomp 1 -pinstride 1 -pin on; runs > - ntmpi 24 -ntomp 1 -pinstride 2 -pin on; runs > > After patch supplied: > - ntmpi 1 -ntomp 22 -pin on; sometime runs - sometimes doesn't* -> > md_run.log at : > https://it-service.zae-bayern.de/Team/index.php/s/ezXWnQ2pGNeFx6T > > md_norun.log at: > https://it-service.zae-bayern.de/Team/index.php/s/wYPY7dWEJdwmqJi > - ntmpi 1 -ntomp 22 -pin off; sometime runs - sometimes doesn't* (ran > before) > - ntmpi 1 -ntomp 23 -pin off; doesn't work* (ran before) > > - ntmpi 1 -ntomp 23 -pinstride 1 -pin on; doesn't work* > > - ntmpi 1 -ntomp 23 -pinstride 2 -pin on; doesn't work* (ran before) > The suspicious thing is that the patch I made only improves the verbosity of the error reporting, it should have no impact on whether the error is triggered or not. Considering the above behavior it seems that pinning (at least the patters tried) has no influence on whether the runs work. Can you please try: -ntmpi 1 -ntomp 11 -pin on -pinstride 1 -ntmpi 1 -ntomp 11 -pin on -pinstride 2 -ntmpi 1 -ntomp 11 -pin on -pinstride 4 -ntmpi 1 -ntomp 11 -pin on -pinstride 8 and -ntmpi 1 -ntomp 22 -pin on -pinstride 1 -ntmpi 1 -ntomp 22 -pin on -pinstride 2 -ntmpi 1 -ntomp 22 -pin on -pinstride 4 And please run these 5 times each (-nsteps 0 is fine to make things quick). Also, please use this patch https://termbin.com/r8kk The same way as you did the one before, it adds another check that might shed some light on what's going on. - ntmpi 24 -ntomp 1 -pinstride 1 -pin on; runs > - ntmpi 24 -ntomp 1 -pinstride 2 -pin on; runs > > * Fatal error: > Asynchronous H2D copy failed: invalid argument > > When compiling, the make check shows that the regressiontest-complex and >
Re: [gmx-users] GPU error
On 3/26/19 2:05 AM, RAHUL SURESH wrote: Hi Dr Mark System is pretty tiny only with 15000 atoms. 1 GpU is automatically selected. You will certainly not benefit from trying to use multiple GPUs for such a small system. I get a note stating potentially sub-optimal launch configuration, gmx started with less pp Mpi process for node than GPUs available. So the use of GPU is automated depending on the size of the system? mdrun will try to utilize everything it finds, and automatically tune for the best performance, but in your case you definitely only want to use 1 GPU. Also, I can find a line in the log file, "Binary not matching Hardware- you might be losing performance. Please help us understand this more. The last message suggests you have not compiled GROMACS in the best way to maximize performance. At compilation, cmake will recommend what type of hardware optimization to use. Follow its suggestion, or simply do not override it with your own specification. -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 | (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.
Re: [gmx-users] grompp error: Unknown bond_atomtype
On Tue 26 Mar, 2019, 6:00 PM , wrote: > Hello everyone, > > I would call myself newbie gromacs user and need some help with task > that was given to me. I'm supposed to take protein-ligand complex > (bounded by covalence bond) and put it into membrane. I'm glad I've > created the complex in amber force field. But now I stucked around > membrane think. > > I have created DLPC-only membrane cluster in charmm-gui. I have found > parameters for this type of lipid. I did add additional names for atom > in atomtypes.atp, include ffbonded_lipid.itp and > ffnonbonded_lipit.itp files to forcefrield.itp and put into amber > forcefield directory t he lipids.rtp file. Gladly everything went > smoothly with pdb2gmx with my membrane. I get topol.top file. Then I > wanted to try minimize energy. I've prepared .mdp file and used gromp > with: > > gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr > > Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is > defined in atomtypes.atp and the bond have its parameters inside the > ffbond.itp file. It's really strange for me, beacuse I thought that if > topol.top file was created there is no possibility to get some > troubles with defined atoms, bonds, etc. > > This CTL3 is that of ligand? > Where did I make mistake? > > Have did you manage to add ligand topology? > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] Help regarding clustering of conformations
hello, i have the output files of 100ns production simulations. I have treated for PBC. I want to find clusters of the trajectories. This can be done using gmx cluster. But i want to do energy minimization of each snapshot in the trajectory and then make clusters. Is there any command or option or solution for this? Thank you -- Sidhanta Swayam Prakash Das -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] grompp error: Unknown bond_atomtype
Hello everyone, I would call myself newbie gromacs user and need some help with task that was given to me. I'm supposed to take protein-ligand complex (bounded by covalence bond) and put it into membrane. I'm glad I've created the complex in amber force field. But now I stucked around membrane think. I have created DLPC-only membrane cluster in charmm-gui. I have found parameters for this type of lipid. I did add additional names for atom in atomtypes.atp, include ffbonded_lipid.itp and ffnonbonded_lipit.itp files to forcefrield.itp and put into amber forcefield directory t he lipids.rtp file. Gladly everything went smoothly with pdb2gmx with my membrane. I get topol.top file. Then I wanted to try minimize energy. I've prepared .mdp file and used gromp with: gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is defined in atomtypes.atp and the bond have its parameters inside the ffbond.itp file. It's really strange for me, beacuse I thought that if topol.top file was created there is no possibility to get some troubles with defined atoms, bonds, etc. Where did I make mistake? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Help regarding clustering of conformations
hello, i have the output files of 100ns production simulations. I have treated for PBC. I want to find clusters of the trajectories. This can be done using gmx cluster. But i want to do energy minimization of each snapshot in the trajectory and then make clusters. Is there any command or option or solution for this? Thank you On Tue, Mar 26, 2019 at 5:42 PM Sidhanta Swayam Prakash Das < sidhanta@gmail.com> wrote: > hello, > i have the output files of 100ns production simulations. I have treated > for PBC. I want to find clusters of the trajectories. This can be done > using gmx cluster. > But i want to do energy minimization of each snapshot in the trajectory > and then make clusters. > Is there any command or option or solution for this? > > > > Thank you > -- > Sidhanta Swayam Prakash Das > -- Sidhanta Swayam Prakash Das -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] GPU error
Hi Dr Mark System is pretty tiny only with 15000 atoms. 1 GpU is automatically selected. I get a note stating potentially sub-optimal launch configuration, gmx started with less pp Mpi process for node than GPUs available. So the use of GPU is automated depending on the size of the system? Also, I can find a line in the log file, "Binary not matching Hardware- you might be losing performance. Please help us understand this more. Thank you On Mon 25 Mar, 2019, 6:41 PM Mark Abraham, wrote: > Hi, > > What did you learn from the log file when it chose to use only one GPU? If > your system is tiny then two won't help... > > Mark > > On Mon., 25 Mar. 2019, 11:28 RAHUL SURESH, > wrote: > > > Hi > > > > I have a system with 2 8 core gold processor and 2 1080Ti card. During > > mdrun, the job utilize only one GPU card. > > > > Command: gmx_mpi mdrun -v -deffnm md > > > > Trying various command line I could use both the card but end up with > very > > poor performance. > > > > command: mpirun -np 2 gmx_mpi mdrun -v -deffnm md -gpu_id 01 > > > > How to improve the performance of this system? > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)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.
