Thanks for helping out. Have tried this it works fine I hope. On Wed, Mar 28, 2018 at 12:45 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
> Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: gmx mindist error (Jo?o Henriques) > 2. Re: Number of Xeon cores per GTX 1080Ti (Mark Abraham) > 3. mdrun on single node with GPU (Myunggi Yi) > 4. RMSD values consideration (SHYANTANI MAITI) > 5. Re: RMSD values consideration (Ahmed Mashaly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 27 Mar 2018 23:55:54 +0200 > From: Jo?o Henriques <joao.m.a.henriq...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] gmx mindist error > Message-ID: > <CAHv45qM2J-DE6xi43aqfkxnm38PzabRVk2NHBVBQ > 7ogko3y...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Yes, I understand what you and Justin refer to. Until your first email I > completely forgot to consider that certain simulations require variations > to the normal 3D periodicity, and thus my ramble about the box vectors. It > makes perfect sense now. > > Also, thank you suggesting the alternative using the PDB, really > appreciated. It can certainly make things easier in this particular case. > > Best regards, > J > > On Tue, Mar 27, 2018 at 9:48 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > Looking at the code, if your PDB file had suitable CRYST1 fields then you > > would not have needed a .tpr. I improved the docs a bit at > > https://gerrit.gromacs.org/#/c/7729/ > > > > Mark > > > > On Tue, Mar 27, 2018 at 8:58 PM Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > Hi, > > > > > > I have no idea how ACEMD works, but one can certainly imagine an MD > > > package that hard codes the assumption of a cubic box with normal 3D > > > periodicity. But there's nothing intrinsic to the file format that > > implies > > > any periodicity to a box. That's either a convention, or given by other > > > information from the user. > > > > > > Mark > > > > > > On Tue, Mar 27, 2018, 18:26 Jo?o Henriques < > joao.m.a.henriq...@gmail.com > > > > > > wrote: > > > > > >> I see, I didn't consider that. I was strictly thinking about the > > geometry > > >> of the box. > > >> > > >> Anyway, with some tricks I managed to build a tpr and am now able to > > >> calculate the mindist to the periodic image. > > >> > > >> Thanks! > > >> J > > >> > > >> On 18:19, Tue, Mar 27, 2018 Mark Abraham <mark.j.abra...@gmail.com> > > >> wrote: > > >> > > >> > Hi, > > >> > > > >> > The box sizes say nothing about whether the boundary is fully or > > >> partially > > >> > periodic, or screw, or not. > > >> > > > >> > Mark > > >> > > > >> > On Tue, Mar 27, 2018, 16:13 Jo?o Henriques < > > >> joao.m.a.henriq...@gmail.com> > > >> > wrote: > > >> > > > >> > > Thanks Justin, I was really trying to avoid making a tpr file, > > >> because my > > >> > > ACEMD uses the Amber format. I sort of hoped gmx mindist could > > figure > > >> it > > >> > > out from the box components present in the xtc file. In principle, > > >> > couldn't > > >> > > it be done by using that info alone? Just curious. > > >> > > > > >> > > J > > >> > > > > >> > > On Tue, Mar 27, 2018 at 4:04 PM, Justin Lemkul <jalem...@vt.edu> > > >> wrote: > > >> > > > > >> > > > > > >> > > > > > >> > > > On 3/27/18 9:59 AM, Jo?o Henriques wrote: > > >> > > > > > >> > > >> Dear users and developers, > > >> > > >> > > >> > > >> I am trying to use gmx mindist to calculate the minimum > distance > > >> > between > > >> > > >> periodic images but I get the following error: > > >> > > >> > > >> > > >> Fatal error: > > >> > > >> pbc = no is not supported by g_mindist > > >> > > >> > > >> > > >> This is the command I am running: > > >> > > >> > > >> > > >> gmx_mpi mindist -f output.xtc -s structure.pdb -od -pi -pbc > > >> > > >> > > >> > > >> Now, I have to admit that the .xtc file I'm using is generated > by > > >> > ACEMD > > >> > > >> and > > >> > > >> not mdrun, but I used gmx dump to check it and everything looks > > >> sane. > > >> > > The > > >> > > >> cuboid box sizes are clearly specified and I don't understand > > what > > >> the > > >> > > >> problem is... > > >> > > >> > > >> > > >> box (3x3): > > >> > > >> box[ 0]={ 8.16756e+00, 0.00000e+00, 0.00000e+00} > > >> > > >> box[ 1]={ 0.00000e+00, 8.25175e+00, 0.00000e+00} > > >> > > >> box[ 2]={ 0.00000e+00, 0.00000e+00, 9.73586e+00} > > >> > > >> > > >> > > >> Is gmx mindist reading the box vector lengths from the > structure > > >> file > > >> > > >> instead? > > >> > > >> > > >> > > > > > >> > > > When you don't provide a .tpr file, the program does not know > what > > >> type > > >> > > of > > >> > > > periodicity the simulation used, so it cannot do the requested > > >> > > calculation > > >> > > > because the shifts cannot be calculated. > > >> > > > > > >> > > > -Justin > > >> > > > > > >> > > > -- > > >> > > > ================================================== > > >> > > > > > >> > > > Justin A. Lemkul, Ph.D. > > >> > > > Assistant Professor > > >> > > > Virginia Tech Department of Biochemistry > > >> > > > > > >> > > > 303 Engel Hall > > >> > > > 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. > > >> > -- > > >> > Gromacs Users mailing list > > >> > > > >> > * Please search the archive at > > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > >> > posting! > > >> > > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > > >> > * For (un)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. > > > > > ------------------------------ > > Message: 2 > Date: Wed, 28 Mar 2018 02:31:43 +0000 > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Number of Xeon cores per GTX 1080Ti > Message-ID: > <CAMNuMAQuh25YUbhN4DJykWnP3Bc7KKGbthNHMEjMZwYL8RSuuQ@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub <j...@gwdg.de> wrote: > > > Dear Gromacs community, dear Mark, > > > > Mark showed in the webinar today that having more than 8 Xeon E5-26XXv4 > > cores does not help when using a GTX 1080Ti and PME on the GPU. > > > > ... for that particular simulation system. > > > > Unfortunately, there were no data points between 4 and 8 CPU cores, > > hence it was not clear at which #cores the performance actually levels > > off. With a GTX 1080 (not Ti) I once found that having more than 5 Xeon > > cores does not help, if not having UB potentials, but I don't have a > > 1080Ti at hand to test for that. > > > > Those data points may not have been run. Szilard might have the data - this > was GLIC 2fs comparing 1080 with 1080Ti from the recent plots he shared. > > > > So my questions are: > > > > - At which number of E5-26XXv4 cores does the performance for common > > systems level off with a 1080Ti for your test system (GLIC)? > > > > - Does the answer depend strongly on the mdp settings (in particular on > > the LJ cutoff)? > > > > Longer LJ cutoff (e.g. from different forcefields) will certainly require > more non-bonded work, so then fewer CPU cores would be needed to do the > remaining non-offloaded work. However any sweet spot for a particular .tpr > would be highly dependent on other effects, such as the ratio of solvent > (which typically has less LJ and simpler update) to solute, or the density > of dihedral or U-B interactions. And doing pulling or FEP is very different > again. The sweet spot for the next project will be elsewhere, sadly. > > This would help us a lot when choosing the appropriate CPU for a 1080Ti. > > > > Many thanks for any suggestions, > > Jochen > > > > -- > > --------------------------------------------------- > > Dr. Jochen Hub > > Computational Molecular Biophysics Group > > Institute for Microbiology and Genetics > > Georg-August-University of G?ttingen > > Justus-von-Liebig-Weg 11, 37077 G?ttingen, Germany > > <https://maps.google.com/?q=Justus-von-Liebig-Weg+11,+ > 37077+G%C3%B6ttingen,+Germany&entry=gmail&source=g> > > . > > Phone: +49-551-39-14189 <+49%20551%203914189> > > http://cmb.bio.uni-goettingen.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. > > > ------------------------------ > > Message: 3 > Date: Tue, 27 Mar 2018 23:26:15 -0400 > From: Myunggi Yi <myun...@pukyong.ac.kr> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Subject: [gmx-users] mdrun on single node with GPU > Message-ID: > <CAHXfRVMM1+TW33VzjQG5VmgndCfs7scx-aU- > x2zgwqkccpu...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear users, > > I am running simulation with gromacs 2018.1 version > on a computer with quad core and 1 gpu. > > I used to use the following command to run simulations. > > gmx mdrun -deffnm md > > > However, this time I've got the following message. > > ------------------------------------------------------- > Program: gmx mdrun, version 2018.1 > Source file: src/gromacs/taskassignment/resourcedivision.cpp (line 224) > > Fatal error: > When using GPUs, setting the number of OpenMP threads without specifying > the > number of ranks can lead to conflicting demands. Please specify the number > of > thread-MPI ranks as well (option -ntmpi). > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > > Can anyone help? > > > Thank you for any help in advance. > > > Myunggi Yi > > > ------------------------------ > > Message: 4 > Date: Wed, 28 Mar 2018 12:12:50 +0530 > From: SHYANTANI MAITI <shyantani.ma...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] RMSD values consideration > Message-ID: > <CAL54tGQy+T4F0dfQZAJiLT6BQ1JoYRa3t-HHR1W+2txVbfX+=g@mail.gmail. > com> > Content-Type: text/plain; charset="UTF-8" > > Dear all, > After using this command for computation of rmsd of backbone of protein > protein complex consisting of three proteins : > /home/locuz/apps/gromacs/5.1/bin/gmx_mpi rms -f md_0_1.trr -s md_0_1.tpr > The rmsd is drastically increasing from 1 to 6 nm and after that it again > decreases to 1nm. can I use this result for my analysis? Is the rmsd > correctly obtained? > -- > Best regards, > *Shyantani Maiti* > > > ------------------------------ > > Message: 5 > Date: Wed, 28 Mar 2018 07:05:42 +0000 (UTC) > From: Ahmed Mashaly <mashaly_1...@yahoo.com> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] RMSD values consideration > Message-ID: <1396487201.108939.1522220742...@mail.yahoo.com> > Content-Type: text/plain; charset=UTF-8 > > Try using trjconv to remove pbc before analysis > Regards,Ahmed > > On Wed, 28 Mar, 2018 at 8:43 am, SHYANTANI MAITI<shyantani.maiti@gmail. > com> wrote: Dear all, > After using this command for computation of rmsd of backbone of protein > protein complex consisting of three proteins : > /home/locuz/apps/gromacs/5.1/bin/gmx_mpi rms -f md_0_1.trr -s md_0_1.tpr > The rmsd is drastically increasing from 1 to 6 nm and after that it again > decreases to 1nm. can I use this result for my analysis? Is the rmsd > correctly obtained? > -- > Best regards, > *Shyantani Maiti* > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 167, Issue 139 > ******************************************************* > -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.