[gmx-users] domain decomposition
Dear all, I am simulating a system consisting urea molecules. After successfully generating tpr file while I am trying to run mdrun, the following error is appearing. Fatal error: There is no domain decomposition for 72 ranks that is compatible with the given box and a minimum cell size of 0.5924 nm Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings. All bonds are constrained are by LINCS algorithm in my system and dimension of my box is 3.40146 nm. I have checked gromacs site as well as mailing list but couldn't understand what to do. Please help me with the issue. Thanks and regards. Dhrubajyoti Maji -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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 generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure?
This is an issue with CGenFF, nothing to do with GROMACS. So you need to ask this question through the CGenFF help channel(s), wherever that may be. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Wed, 21 Aug 2019 at 08:25, Maryam Sadat Sadeghi < m_sade...@cmps2.iust.ac.ir> wrote: > Hi All, > > I have created a crystal structure of 2 polymer chains (PEG) and I need to > calculate the cohesive energy for my system using CHARMM36 FF. In this case > my fix_mol2 file includes 2 ligands, to convert to str file I get the > following error: > > readmol2 warning: non-unique atoms were renamed. Now processing molecule > LIG ... attype warning: carbon radical, carbocation or carbanion not > supported; skipped molecule. > > How can I fix this problem? Changing the ligand IDs and names does not > help. I even tried to make 2 separate mol2 files for each chain in the > crystal structure, but still get the same error while converting to str > file... > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure?
Hi All, I have created a crystal structure of 2 polymer chains (PEG) and I need to calculate the cohesive energy for my system using CHARMM36 FF. In this case my fix_mol2 file includes 2 ligands, to convert to str file I get the following error: readmol2 warning: non-unique atoms were renamed. Now processing molecule LIG ... attype warning: carbon radical, carbocation or carbanion not supported; skipped molecule. How can I fix this problem? Changing the ligand IDs and names does not help. I even tried to make 2 separate mol2 files for each chain in the crystal structure, but still get the same error while converting to str file... -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure?
Hi All, I have created a crystal structure of 2 polymer chains (PEG) and I need to calculate the cohesive energy for my system using CHARMM36 FF. In this case my fix_mol2 file includes 2 ligands, to convert to str file I get the following error: readmol2 warning: non-unique atoms were renamed. Now processing molecule LIG ... attype warning: carbon radical, carbocation or carbanion not supported; skipped molecule. How can I fix this problem? Changing the ligand IDs and names does not help. I even tried to make 2 separate mol2 files for each chain in the crystal structure, but still get the same error while converting to str file... -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Error when running pbs files using GROMACS on hpc cluster
On 8/20/19 5:56 PM, Anh Vo wrote: Hi everyone, I have submitted pbs files to run GROMACS on a high performance computing cluster, but I received error files showing these messages: "... librdmacm: Warning: couldn\'t read ABI version. librdmacm: Warning: assuming: 4 librdmacm: Fatal: unable to open /dev/infiniband/rdma_cm librdmacm: Fatal: unable to open /dev/infiniband/rdma_cm ..." and "-- mpirun noticed that process rank 28 with PID 0 on node shadow- 0119.hpc.msstate.edu exited on signal 11 (Segmentation fault). -- 40 total processes killed (some possibly by mpirun during cleanup)" This error happened when I used mpirun to run my jobs on several nodes (10 nodes in this case). When I didn't use mpirun and run with only 1 node, there is no error produced. The command I used are: *"gmx grompp -f step7_production_01.mdp -c step6.6_equilibration.gro -n index.ndx -p topol.top -o step7_1_01.tpr -maxwarn -1* *mpirun -np 200 gmx_mpi mdrun -v -deffnm step7_1_01"* Is that mpirun command correct? I'm not sure if those errors is relevant to using mpirun. I don't understand what the errors mean, or how should I fix them? Please help me with this problem. Thank you very much for sharing your time. None of those are GROMACS errors; they are coming from your system indicating there are problems with the MPI library. Consult your sysadmins. -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] Gromacs FEP tutorial
On 8/20/19 1:36 PM, Alex Mathew wrote: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html The protocol in the tutorial is simply the elimination of LJ parameters to compute the vdW contribution to free energy of solvation. It is not (by design) a complete cycle that computes a full free energy of solvation. -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] Error when running pbs files using GROMACS on hpc cluster
Hi everyone, I have submitted pbs files to run GROMACS on a high performance computing cluster, but I received error files showing these messages: "... librdmacm: Warning: couldn\'t read ABI version. librdmacm: Warning: assuming: 4 librdmacm: Fatal: unable to open /dev/infiniband/rdma_cm librdmacm: Fatal: unable to open /dev/infiniband/rdma_cm ..." and "-- mpirun noticed that process rank 28 with PID 0 on node shadow- 0119.hpc.msstate.edu exited on signal 11 (Segmentation fault). -- 40 total processes killed (some possibly by mpirun during cleanup)" This error happened when I used mpirun to run my jobs on several nodes (10 nodes in this case). When I didn't use mpirun and run with only 1 node, there is no error produced. The command I used are: *"gmx grompp -f step7_production_01.mdp -c step6.6_equilibration.gro -n index.ndx -p topol.top -o step7_1_01.tpr -maxwarn -1* *mpirun -np 200 gmx_mpi mdrun -v -deffnm step7_1_01"* Is that mpirun command correct? I'm not sure if those errors is relevant to using mpirun. I don't understand what the errors mean, or how should I fix them? Please help me with this problem. Thank you very much for sharing your time. Best regards, Anh Vo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs FEP tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Charmm36M neutral C-terminal Proline
On Tue, Aug 20, 2019 at 9:44 AM Akshay wrote: > Hello All, > > I seem to be having a very particular issue with the Charmm36M force-field > available at http://mackerell.umaryland.edu/charmm_ff.shtml. The issue > occurs when using pdb2gmx's -ter flag and selecting a neutral COOH terminal > when the C-terminal residue is a Proline. > > Then, when subsequent grompping, I get the two errors below where both > lines pertain to the Proline backbone CA-C bond. > > ERROR 1 [file topol.top, line 493]: > No default U-B types > ERROR 2 [file topol.top, line 649]: > No default Proper Dih. types > > Anyone else facing this issue or should I raise the issue with the 36M > developers? > Given how rare such a combination would be, no one has invested time in parametrizing this particular species. It’s simply not part of the force field. -Justin > Thanks, > Akshay > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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. 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] gpu usage
Dear Users, I am getting reasonable performance from two rtx -2080ti's - AMD 32 core and on another node two gtx-1080 ti's -AMD 16 core i.e 20-30 ns/day with 30 atoms. But in all my runs the % usage of the gpu's is typcially 40% to 60 % . Given that it is specialized software, I notice that Schrodinger will run a single gpu at 98%.. So the cards are apparently not defective The cpu runs at 2.9 Ghz. and the power supply a 1500 watts A typical run command might be" gmx mdrun -deffnm sys.npt -nb gpu -pme gpu -ntmpi 8 -ntomp 8 -npme 1 I have gone over http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html (https://link.getmailspring.com/link/1566319015.local-8bb7ace6-bf71-v1.5.3-420ce...@getmailspring.com/0?redirect=http%3A%2F%2Fmanual.gromacs.org%2Fdocumentation%2Fcurrent%2Fuser-guide%2Fmdrun-performance.html=Z214LXVzZXJzQGdyb21hY3Mub3Jn) ,and tried to incorporate what I could. The installation was basically that given in the manual for build 2019.1: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DCMAKE_CXX_COMPILER=/usr/bin/g++-6 -DCMAKE_C_COMPILER=/usr/bin/gcc-6 Both 2019.1 and 2019.3 run well but with the same "reduced" % workload. I am curious to learn why the gpu's are not pushed a littler harder. Or is this a typical result ? Or are there improvments to make in my setup. Paul -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] WARNING
If your trajectory has position information, then yes, it can be used to compute potential energies. > Thank you for your reply sir. In this case can I use .The file to compute > potential energies. > > On Tue 20 Aug, 2019, 4:40 PM Mark Abraham, > wrote: > >> Hi, >> >> You're doing a rerun from a trajectory file that probably doesn't have >> velocities in it. mdrun can compute potential energies from the position >> coordinates, but these other quantities can't be computed from just the >> position coordinates. mdrun can't know what you're expecting to be >> correct, >> so it's being helpful. (More recent versions of rerun simply don't >> attempt >> compute these things.) >> >> Mark >> >> On Tue, 20 Aug 2019 at 12:28, Bratin Kumar Das < >> 177cy500.bra...@nitk.edu.in> >> wrote: >> >> > Dear all, >> > During the calculation of interaction energy i found one >> > warning >> > WARNING: Some frames do not contain velocities. >> > Ekin, temperature and pressure are incorrect, >> > the virial will be incorrect when constraints are present.But >> in >> > the quilibration step the temp and pressure were attained properly. >> Why >> > this warning is coming? >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)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] typedefs.h in gromacs installation
Hi, You can use only GROMACS versions that gromos++ supports. Hopefully they've documented which ones those are :-) Mark On Tue, 20 Aug 2019 at 15:47, Johannes Hermann wrote: > Hi Justin, > > Thanks! So this is a gromos++ problem? The gromos++ developers should > update the linking during installation, right? > > All the best > > Johannes > > On 20.08.19 15:11, Justin Lemkul wrote: > > > > > > On 8/20/19 8:56 AM, Johannes Hermann wrote: > >> Dear all, > >> > >> I am currently installing gromos++ analysis software. When I link my > >> Gromacs 2018.6 or 2016.6 installation, I get the error: > >> > >> ../../contrib/gromacs2gromos.cc:101:30: fatal error: > >> gromacs/typedefs.h: No such file or directory > >> > >> However, if I link my gromacs 5.1.4 installation everything works fine. > >> > >> Why is there no typedefs.h file in gromacs 2018? > >> > > It was removed a few years ago and its contents moved to other, more > > relevant, files. > > > > -Justin > > > -- > __ > *Technische Universität München* > *Johannes Hermann, M.Sc.* > Lehrstuhl für Bioverfahrenstechnik > Boltzmannstr. 15 > D-85748 Garching > Tel: +49 8928915730 > Fax: +49 8928915714 > > Email: j.herm...@lrz.tum.de > http://www.biovt.mw.tum.de/ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] typedefs.h in gromacs installation
Hi Justin, Thanks! So this is a gromos++ problem? The gromos++ developers should update the linking during installation, right? All the best Johannes On 20.08.19 15:11, Justin Lemkul wrote: On 8/20/19 8:56 AM, Johannes Hermann wrote: Dear all, I am currently installing gromos++ analysis software. When I link my Gromacs 2018.6 or 2016.6 installation, I get the error: ../../contrib/gromacs2gromos.cc:101:30: fatal error: gromacs/typedefs.h: No such file or directory However, if I link my gromacs 5.1.4 installation everything works fine. Why is there no typedefs.h file in gromacs 2018? It was removed a few years ago and its contents moved to other, more relevant, files. -Justin -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Charmm36M neutral C-terminal Proline
Hello All, I seem to be having a very particular issue with the Charmm36M force-field available at http://mackerell.umaryland.edu/charmm_ff.shtml. The issue occurs when using pdb2gmx's -ter flag and selecting a neutral COOH terminal when the C-terminal residue is a Proline. Then, when subsequent grompping, I get the two errors below where both lines pertain to the Proline backbone CA-C bond. ERROR 1 [file topol.top, line 493]: No default U-B types ERROR 2 [file topol.top, line 649]: No default Proper Dih. types Anyone else facing this issue or should I raise the issue with the 36M developers? Thanks, Akshay -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] WARNING
Thank you for your reply sir. In this case can I use .The file to compute potential energies. On Tue 20 Aug, 2019, 4:40 PM Mark Abraham, wrote: > Hi, > > You're doing a rerun from a trajectory file that probably doesn't have > velocities in it. mdrun can compute potential energies from the position > coordinates, but these other quantities can't be computed from just the > position coordinates. mdrun can't know what you're expecting to be correct, > so it's being helpful. (More recent versions of rerun simply don't attempt > compute these things.) > > Mark > > On Tue, 20 Aug 2019 at 12:28, Bratin Kumar Das < > 177cy500.bra...@nitk.edu.in> > wrote: > > > Dear all, > > During the calculation of interaction energy i found one > > warning > > WARNING: Some frames do not contain velocities. > > Ekin, temperature and pressure are incorrect, > > the virial will be incorrect when constraints are present.But in > > the quilibration step the temp and pressure were attained properly. Why > > this warning is coming? > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)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] simulation on 2 gpus
Dear Szilard, thanks for the very clear answer. Following your suggestion I tried to run without DD; for the same system I run two simulations on two gpus: gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0 -gputasks 00 -pin on -pinoffset 0 -pinstride 1 gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0 -gputasks 11 -pin on -pinoffset 28 -pinstride 1 but again the system crashed; with this I mean that after few minutes the machine goes off (power off) without any error message, even without using all the threads. I then tried running the two simulations on the same gpu without DD: gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0 -gputasks 00 -pin on -pinoffset 0 -pinstride 1 gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0 -gputasks 00 -pin on -pinoffset 28 -pinstride 1 and I obtained better performance (about 70 ns/day) with a massive use of the gpu (around 90%), comparing to the two runs on two gpus I reported in the previous post (gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 4 -ntmpi 7 -npme 1 -gputasks 000 -pin on -pinoffset 0 -pinstride 1 gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 4 -ntmpi 7 -npme 1 -gputasks 111 -pin on -pinoffset 28 -pinstride 1). As for pinning, cpu topology according to log file is: hardware topology: Basic Sockets, cores, and logical processors: Socket 0: [ 0 32] [ 1 33] [ 2 34] [ 3 35] [ 4 36] [ 5 37] [ 6 38] [ 7 39] [ 16 48] [ 17 49] [ 18 50] [ 19 51] [ 20 52] [ 21 53] [ 22 54] [ 23 55] [ 8 40] [ 9 41] [ 10 42] [ 11 43] [ 12 44] [ 13 45] [ 14 46] [ 15 47] [ 24 56] [ 25 57] [ 26 58] [ 27 59] [ 28 60] [ 29 61] [ 30 62] [ 31 63] If I understand well (absolutely not sure) it should not be that convenient to pin to consecutive threads, and indeed I found a subtle degradation of performance for a single simulation, switching from: gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0 -gputasks 00 -pin on to gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0 -gputasks 00 -pin on -pinoffset 0 -pinstride 1. Thanks again Stefano Il giorno ven 16 ago 2019 alle ore 17:48 Szilárd Páll < pall.szil...@gmail.com> ha scritto: > On Mon, Aug 5, 2019 at 5:00 PM Stefano Guglielmo > wrote: > > > > Dear Paul, > > thanks for suggestions. Following them I managed to run 91 ns/day for the > > system I referred to in my previous post with the configuration: > > gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 4 -ntmpi 7 -npme 1 > -gputasks > > 111 -pin on (still 28 threads seems to be the best choice) > > > > and 56 ns/day for two independent runs: > > gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 4 -ntmpi 7 -npme 1 > -gputasks > > 000 -pin on -pinoffset 0 -pinstride 1 > > gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 4 -ntmpi 7 -npme 1 > -gputasks > > 111 -pin on -pinoffset 28 -pinstride 1 > > which is a fairly good result. > > Use no DD in single-GPU runs, i.e. for the latter, just simply > gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0 > -gputasks 00 -pin on -pinoffset 0 -pinstride 1 > > You can also have mdrun's multidir functionality manage an ensemble of > jobs (related or not) so you don't have to manually start, calculate > pinning, etc. > > > > I am still wondering if somehow I should pin the threads in some > different > > way in order to reflect the cpu topology and if this can influence > > performance (if I remember well NAMD allows the user to indicate > explicitly > > the cpu core/threads to use in a computation). > > Your pinning does reflect the CPU topology -- the 4x7=28 threads are > pinned to consecutive hardware threads (because of -pinstride 1, i.e. > don't skip the second hardware thread of the core). The mapping of > software to hardware threads happens based on a the topology-based > hardware thread indexing, see the hardware detection report in the log > file. > > > When I tried to run two simulations with the following configuration: > > gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 4 -ntmpi 8 -npme 1 > -gputasks > > -pin on -pinoffset 0 -pinstride 1 > > gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 4 -ntmpi 8 -npme 1 > -gputasks > > -pin on -pinoffset 0 -pinstride 32 > > the system crashed down. Probably this is normal and I am missing > something > > quite obvious. > > Not really. What do you mean by "crashed down", the machine should not > crash, nor should the simulation. Even though your machine has 32 > cores / 64 threads, using all of these may not always be beneficial as > using more threads where there is too little work to scale will have > an overhead. Have you tried using all cores but only 1 thread / core > (i.e. 32 threads in total with pinstride 2)? > > Cheers, > -- > Szilárd > > > > > Thanks again for the valuable advices > > Stefano > > > > > > > > Il giorno dom 4 ago 2019 alle ore 01:40 paul buscemi ha > >
Re: [gmx-users] AVX_512 and GROMACS
On Mon, Aug 19, 2019 at 12:00 PM tarzan p wrote: > > Hi all.I have a dual socket Xeon GOLD 6148 which has the capabilities for > > Instruction Set Extensions Intel® SSE4.2, Intel® AVX, Intel® AVX2, Intel® > AVX-512 > but hen why si gromacs giving the error for AVX_512 but takes AVX2_256??? > Adding the out put > > > /Downloads/gromacs-2019/build-gromacs$ cmake .. -DGMX_SIMD=AVX_512-- Enabling > RDTSCP support > -- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED > -- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed > -- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED > -- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED - Failed > -- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED > -- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED - Failed > -- Performing Test C_mavx512f_FLAG_ACCEPTED > -- Performing Test C_mavx512f_FLAG_ACCEPTED - Failed > -- Performing Test C_arch_AVX_FLAG_ACCEPTED > -- Performing Test C_arch_AVX_FLAG_ACCEPTED - Failed > -- Performing Test C_hgnu_FLAG_ACCEPTED > -- Performing Test C_hgnu_FLAG_ACCEPTED - Failed > -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS > -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed > -- Could not find any flag to build test source (this could be due to either > the compiler or binutils) > -- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED > -- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed > -- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED > -- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED - Failed > -- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED > -- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED - Failed > -- Performing Test CXX_mavx512f_FLAG_ACCEPTED > -- Performing Test CXX_mavx512f_FLAG_ACCEPTED - Failed > -- Performing Test CXX_arch_AVX_FLAG_ACCEPTED > -- Performing Test CXX_arch_AVX_FLAG_ACCEPTED - Failed > -- Performing Test CXX_hgnu_FLAG_ACCEPTED > -- Performing Test CXX_hgnu_FLAG_ACCEPTED - Failed > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed > -- Could not find any flag to build test source (this could be due to either > the compiler or binutils) > CMake Error at cmake/gmxManageSimd.cmake:51 (message): > Cannot find AVX 512F compiler flag. Use a newer compiler, or choose a > lower level of SIMD (slower). The reason is right here. Get newer compiler, I assume you have a dated distribution default compiler. -- Szilárd > Call Stack (most recent call first): > cmake/gmxManageSimd.cmake:186 > (gmx_give_fatal_error_when_simd_support_not_found) > CMakeLists.txt:719 (gmx_manage_simd) > > > -- Configuring incomplete, errors occurred! > See also > "/home/gdd/Downloads/gromacs-2019/build-gromacs/CMakeFiles/CMakeOutput.log". > See also > "/home/gdd/Downloads/gromacs-2019/build-gromacs/CMakeFiles/CMakeError.log". > > > ~/Downloads/gromacs-2019/build-gromacs$ cmake .. -DGMX_SIMD=AVX2_256-- > Performing Test C_mavx2_mfma_FLAG_ACCEPTED > -- Performing Test C_mavx2_mfma_FLAG_ACCEPTED - Success > -- Performing Test C_mavx2_mfma_COMPILE_WORKS > -- Performing Test C_mavx2_mfma_COMPILE_WORKS - Success > -- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED > -- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED - Success > -- Performing Test CXX_mavx2_mfma_COMPILE_WORKS > -- Performing Test CXX_mavx2_mfma_COMPILE_WORKS - Success > -- Enabling 256-bit AVX2 SIMD instructions using CXX flags: -mavx2 -mfma > -- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED > -- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success > -- The GROMACS-managed build of FFTW 3 will configure with the following > optimizations: --enable-sse2;--enable-avx;--enable-avx2 > -- Configuring done > -- Generating done > -- Build files have been written to: > /home/gdd/Downloads/gromacs-2019/build-gromacs > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] typedefs.h in gromacs installation
On 8/20/19 8:56 AM, Johannes Hermann wrote: Dear all, I am currently installing gromos++ analysis software. When I link my Gromacs 2018.6 or 2016.6 installation, I get the error: ../../contrib/gromacs2gromos.cc:101:30: fatal error: gromacs/typedefs.h: No such file or directory However, if I link my gromacs 5.1.4 installation everything works fine. Why is there no typedefs.h file in gromacs 2018? It was removed a few years ago and its contents moved to other, more relevant, files. -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] Error Report
Thank you very much sir. I will check On 8/18/19, Justin Lemkul wrote: > > > On 8/18/19 2:06 PM, Dr Adekunle Rowaiye wrote: >> Hello all, >> I need help. I got this while doing simulation. What do I do? >> >> File input/output error: >> protein_pr.gro > This means that either (1) if this is an input file, it simply is not in > the working directory or (2) if this is an output file, you do not have > write permission in the directory. > > In the future, please use a more descriptive subject line and include > the complete command you are issuing. > > -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. > -- Dr Adekunle Rowaiye (DVM, MSc, FAGAN, FCVSN) Asst. Director, Dept. of Medical Biotechnology, National Biotechnology Development Agency Abuja, Nigeria. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] typedefs.h in gromacs installation
Dear all, I am currently installing gromos++ analysis software. When I link my Gromacs 2018.6 or 2016.6 installation, I get the error: ../../contrib/gromacs2gromos.cc:101:30: fatal error: gromacs/typedefs.h: No such file or directory However, if I link my gromacs 5.1.4 installation everything works fine. Why is there no typedefs.h file in gromacs 2018? Thank you very much for your help! All the best Johannes -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Tetrahedral order parameter
On 8/20/19 7:51 AM, Omkar Singh wrote: Hello gromacs users, I am working on protein-water system. I am trying to calculate top(tetrahedral order parameter) by "gmx hydorder" command. After finding xpm how to proceed for xvg format. gmx hydorder does not produce such output. You may want to look into other optional output files like -or for raw data output, but I have no idea what is in that file or if it is what you need. -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] "comm-mode = Angular" gives error
On 8/20/19 5:21 AM, Jorden Cabal wrote: Hi Justin, Thank you for your response. In my case the cost of increasing simulation box is very large. I have already tried it by keeping distance between the periodic images of the macromolecule up to 50 Angstrom. Could you suggest me any other option to do this. In Gromacs, rotation around pivot can be enforced, is it possible to use this method somehow to counter the rotation? Even if its possible, how and to which extent do you think it will add biasness to the independent behavior of the macromolecule. Any suggestions, comments in this regard will help me. You can apply biasing potentials to avoid rotation, but then you're seriously perturbing the dynamics in a way that might completely bias your results (I don't have nearly enough context to say for sure, so I'll be a bit circumspect). If you have a large molecule that rotates, you need a large box that reflects that intrinsic symmetry. It's the same reason you can't build a long, rectangular box around a DNA duplex. If it rotations orthogonal to the longest axis, it sees it's image and the forces are invalid. There are no real "tricks" here. If you have a big molecule, you need a suitably large box. -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] question on ffG43a1p force field
On 8/20/19 2:11 AM, Lei Qian wrote: Thank you Dr. Lemkul, Could I ask one more question? Thank you! When I did the step for adding ions and minimization and equilibration steps, one warning always showed up. So I had to add -maxwarn 2 after the command gmx grompp. This warning is as follows: WARNING 1 [file topol.top, line 48]: The GROMOS force fields have been parametrized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the density, might differ from the intended values. Check if molecules in your system are affected by such issues before proceeding. Further information may be available at https://redmine.gromacs.org/issues/2884. It seems this warning is related to the GROMOS force field (for phosphorylation) you sent to me last week. Could I disregard this warning? There are significant concerns about the reproducibility of GROMOS force fields. The authors of a recent study ( https://pubs.acs.org/doi/10.1021/acs.jctc.8b00425) allege that GROMACS has bugs that affect results, but the GROMACS developers maintain that the GROMOS force fields were developed with incorrect algorithms in the GROMOS software (hence the warning, and see the related Redmine issue linked in the message). The issue is not specifically related to 43a1p (which is anyway an extremely old force field), but all of the GROMOS parameter sets. Proceed with caution. There are other force field options available that have been confirmed to work as expected across different software. -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] Analysing multiple cavities in ion Channel through CompEl simulations
Hi Carlos, > Am 20.08.2019 um 13:12 schrieb Carlos Navarro : > > Dear gmx-users, > I'm currently investigating ion permeability in a channel that displays > multiple cavities through ComEl simulations. Unfortunately one can just > define a single cylinder per membrane. Yes, this counting of ion permeations on the fly is just a convenience function for the most common use case of a single pore per channel. However, everything can be extracted from the output trajectory, given that the time gaps between the trajectory frames are not too long. > Considering the size of my system > (>440k atoms) I don't think is a viable idea to run n independent > simulations for the n cavities want to study, so I guess my only choice is > to run a single simulation creating a big cylinder that comprises all the If you need to script something that keeps track of the ion movements, you don’t even need that big cylinder, as it will only tell you which ions go through the upper and which go through the lower channel. But maybe that information facilitates things a bit. > cavities, and then by scripting check from which cavity the different ions > are passing. What do you think about this approach? I'm open to suggestions. If you don’t want to do too much scripting, you could easily output the position of each permeating ion directly after the permeation has finished. This should allow you to tell through which of several pores each ion has permeated. If you don’t mind to code a little bit, have a look at detect_flux_per_channel() in swapcoords.cpp. Look for line „Atom nr. %d finished passing %s“. You could output the ion’s position as well (atomposition[x/y/z]) to know where it has left the channel. You might need an xy position restraint on the centers of mass of the channels for easier interpretation (but it should work without a restraint as well, just with some more effort on the scripting side). Best, Carsten > Best regards. > Carlos > > -- > > Carlos Navarro Retamal > > Bioinformatic Engineering. PhD > > Postdoctoral Researcher in Center for Bioinformatics and Molecular > Simulations > > Universidad de Talca > > Av. Lircay S/N, Talca, Chile > > T: (+56) 712201 798 > > E: carlos.navarr...@gmail.com or cnava...@utalca.cl > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Tetrahedral order parameter
Hello gromacs users, I am working on protein-water system. I am trying to calculate top(tetrahedral order parameter) by "gmx hydorder" command. After finding xpm how to proceed for xvg format. 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.
Re: [gmx-users] Mailing list for Postdoctoral opportunities in Simulations
you can go to ccl.net I am also looking for the postdoctoral position in biological molecule simulations Warm Regards Akhil Kumar Research Associate IISc Bangalore INDIA. #09839263326 On Tue, Aug 20, 2019 at 11:55 AM Peter Mawanga < peter.mawanga.la...@gmail.com> wrote: > Hello everyone > > Can someone please send me mailing list addresses where I could get updates > on Postdoctoral positions available in the field of simulations. > > -- > Cheers > Peter > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] Analysing multiple cavities in ion Channel through CompEl simulations
Dear gmx-users, I'm currently investigating ion permeability in a channel that displays multiple cavities through ComEl simulations. Unfortunately one can just define a single cylinder per membrane. Considering the size of my system (>440k atoms) I don't think is a viable idea to run n independent simulations for the n cavities want to study, so I guess my only choice is to run a single simulation creating a big cylinder that comprises all the cavities, and then by scripting check from which cavity the different ions are passing. What do you think about this approach? I'm open to suggestions. Best regards. Carlos -- Carlos Navarro Retamal Bioinformatic Engineering. PhD Postdoctoral Researcher in Center for Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] WARNING
Hi, You're doing a rerun from a trajectory file that probably doesn't have velocities in it. mdrun can compute potential energies from the position coordinates, but these other quantities can't be computed from just the position coordinates. mdrun can't know what you're expecting to be correct, so it's being helpful. (More recent versions of rerun simply don't attempt compute these things.) Mark On Tue, 20 Aug 2019 at 12:28, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Dear all, > During the calculation of interaction energy i found one > warning > WARNING: Some frames do not contain velocities. > Ekin, temperature and pressure are incorrect, > the virial will be incorrect when constraints are present.But in > the quilibration step the temp and pressure were attained properly. Why > this warning is coming? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] WARNING
Dear all, During the calculation of interaction energy i found one warning WARNING: Some frames do not contain velocities. Ekin, temperature and pressure are incorrect, the virial will be incorrect when constraints are present.But in the quilibration step the temp and pressure were attained properly. Why this warning is coming? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] "comm-mode = Angular" gives error
Hi Justin, Thank you for your response. In my case the cost of increasing simulation box is very large. I have already tried it by keeping distance between the periodic images of the macromolecule up to 50 Angstrom. Could you suggest me any other option to do this. In Gromacs, rotation around pivot can be enforced, is it possible to use this method somehow to counter the rotation? Even if its possible, how and to which extent do you think it will add biasness to the independent behavior of the macromolecule. Any suggestions, comments in this regard will help me. Thank you On Mon, Aug 19, 2019 at 8:00 PM Justin Lemkul wrote: > > > On 8/19/19 12:39 AM, Jorden Cabal wrote: > > Dear Users, > > I am trying to perform simulation of a very large and complex system and > > which requires me to make the simulation box rectangular cube instead > (box > > dimension 24.5 nm * 12.5 nm * 12.3 nm) of perfect cuboid in order to > > minimize the number of atoms present in the system. > > > > I am facing the problem of interaction between periodic images due to > > rotational movement of the macro molecule. I have tried lowering the > > *nstcomm* (frequency of removal of center of mass velocity) to 10 and it > > seems it might work but the speed become very slow because it also > requires > > *nstcalcenergy* to 10. > > > > When I use *comm-mode="Angular"* with *comm-grps="system" *it says "*too > > many warnings*" and the warning is > > *"Removing the rotation around the center of mass in a periodic system, > > this can lead to artifacts. Only use this on a single (cluster of) > > molecules. This cluster should not cross periodic boundaries*" > > > > *"Although this problem can be ignored using -maxwarn option in the > grompp > > command. I want to know that if that is the correct thing to do?" * > > > > *Instead, *I have also tried to work this out by changing the* comm-grps= > > "Protein" *but then it throws two warnings first being the same as > > mentioned above and the second warning says "*Some atoms are not part of > > any center of mass motion removal group. This may lead to artifacts. In > > most cases one should use one group for the whole system*" > > > > Again this can be ignored using -maxwarn option but is that right to do? > > Please suggest me regarding this. > > This is not the purpose of comm-mode/comm-grps, which account for net > COM motion as a function of other errors in the simulation (Google the > "flying ice cube effect"). You can't prevent your molecules from > rotating in any physically realistic way. The simulation box needs to be > larger to avoid these interactions, and comm-mode/comm-grps is not the > way to get around it. > > -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.
[gmx-users] Mailing list for Postdoctoral opportunities in Simulations
Hello everyone Can someone please send me mailing list addresses where I could get updates on Postdoctoral positions available in the field of simulations. -- Cheers Peter -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] question on ffG43a1p force field
Thank you Dr. Lemkul, Could I ask one more question? Thank you! When I did the step for adding ions and minimization and equilibration steps, one warning always showed up. So I had to add -maxwarn 2 after the command gmx grompp. This warning is as follows: WARNING 1 [file topol.top, line 48]: The GROMOS force fields have been parametrized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the density, might differ from the intended values. Check if molecules in your system are affected by such issues before proceeding. Further information may be available at https://redmine.gromacs.org/issues/2884. It seems this warning is related to the GROMOS force field (for phosphorylation) you sent to me last week. Could I disregard this warning? Thanks! Lei On Sun, Aug 18, 2019 at 10:54 AM Justin Lemkul wrote: > > > On 8/18/19 3:24 AM, Lei Qian wrote: > > Could I ask one more question about your *gromos43a1p.ff* force filed ? > > Thanks! > > I ran $ gmx pdb2gmx -f myfile.pdb -o sort_processed.gro -water spce > > > > It shows a fatal error: > > "Fatal error: > > The residues in the chain xxx--xxx do not have a consistent type. The > first > > residue has type 'Protein', while residue *SEP is of type 'Other'*. > > Either there is a mistake in your chain, or it includes nonstandard > residue > > names that have not yet been added to the *residuetypes.dat file* in the > > GROMACS library directory." > > > > Then I found the *residuetypes.dat *in gromacs-2019.2/share/top, and add > > "SEP protein" to the list. > > However, the fatal error still shows up after this change. > > Could I ask how to solve this problem? > > You need to change the installed residuetypes.dat file, not the one in > the source. > > -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.
