Re: [gmx-users] question on ffG43a1p force field
Thank you very much Dr. Lemkul, I downloaded your file and it works! Actually I downloaded the previous file from Gromacs web: http://www.gromacs.org/Downloads/User_contributions/Force_fields Thanks again for your help! On Fri, Aug 16, 2019 at 6:22 AM Justin Lemkul wrote: > > > On 8/16/19 2:15 AM, Lei Qian wrote: > > Sorry for this basic question. > > I read previous emails and tried to make pdb2gmx find ffG43a1p.ff. > > I added #include "ffG43a1p.itp" in FF.dat in ffG43a1p.ff folder. Also > tried > > to create a file called forcefield.doc and wrote "ffG43a1p" into it. > > I put these files in working directory > > and /usr/local/gromacs/share/gromacs/top/ directory. However, neither of > > them worked. > > Could I ask how to solve this problem? > > It sounds like you are trying to modify a very old and outdated version > of the files (potentially with an outdated version of GROMACS - FF.dat > is no longer used). The files you want for any post-4.0 version of > GROMACS are in: > > http://www.gromacs.org/@api/deki/files/235/=gromos43a1p-4.5.1.tgz > > -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] simulation on 2 gpus
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 > scritto: > > > Stefano, > > > > A recent run with 14 atoms, including 1 isopropanol molecules on > > top of an end restrained PDMS surface of 74000 atoms in a 20 20 30 nm > > box ran at 67 ns/d nvt with the mdrun conditions I posted. It took 120 ns > > for 100 molecules of an adsorbate to go from solution to the surface. I > > don't think this will set the world ablaze with any benchmarks but it is > > acceptable to get some work done. > > > > Linux Mint Mate 18, AMD Threadripper 32 core 2990wx 4.2Ghz, 32GB DDR4, 2x > > RTX 2080TI gmx2019 in the simplest gmx configuration for gpus, CUDA > > version 10, Nvidia 410.7p loaded from the repository > > > > Paul > > > > > On Aug 3, 2019, at 12:58 PM, paul buscemi wrote: > > > > > > Stefano, > > > > > > Here is a typical run > > > > > > fpr minimization mdrun -deffnm grofile. -nn gpu > > > > > > and for other runs for a 32 core > > > > > > gmx -deffnm grofile.nvt -nb gpu -pme gpu -ntomp 8 -ntmpi 8 -npme 1 > > -gputasks -pin on > > > > > > Depending on the molecular system/model -ntomp -4 -ntmpi 16 may be > > faster - of course adjusting -gputasks > > > > > > Rarely do I find that not using ntomp and ntpmi is faster, but it is > > never bad > > > > > > Let me know how it goes. > > > > > > Paul > > > > > >> On Aug 3, 2019, at 4:41 AM, Stefano Guglielmo < > > stefano.guglie...@unito.it> wrote: > > >> > > >> Hi Paul, > > >> thanks for the reply. Would you mind posting the command you used or > > >> telling how did you balance the work between cpu and gpu? > > >> > > >> What about pinning? Does anyone know how to deal with a cpu topology > > like > > >> the one reported in my previous post and if it is relevant for > > performance? > > >> Thanks > > >> Stefano > > >> > > >> Il giorno sabato 3 agosto 2019, Paul Buscemi ha > > scritto: > > >> > > >>> I run the same system and setup but no nvlink. Maestro runs both gpus > > at > > >>> 100 percent. Gromacs typically 50 --60 percent can do 600ns/d on 2 > > >>> atoms > > >>> > > >>> PB > > >>> > > On Jul 25, 2019, at 9:30 PM, Kevin Boyd wrote: > > > > Hi, > > > > I've done a lot of research/experimentation on this, so I can maybe > > get > > >>> you > > started - if anyone has any questions about the essay to follow, feel > > >>> free > > to email me personally, and I'll link it to the email thread if it >
Re: [gmx-users] continue run
Thanks both of you for your useful suggestions. I'll check accordingly. Thanks again for help. Dhrubajyoti On Fri, 16 Aug 2019 at 15:50, Justin Lemkul wrote: > > > On 8/16/19 6:09 AM, Dhrubajyoti Maji wrote: > > Hi all, > > I have a simulated trajectory of 50 ns but my desired property is not > > well converged. Therefore, I want to extend the run for another 50 ns. As > > far as I know if I use the last output files as input files for next > run, I > > can finally have two 50 ns run trajectory files. But if I want a 100 ns > > trajectory then what should I do? Any kind of help will be highly > > appreciated. > > By default, mdrun will append to the trajectory and give you one file. > If it can't (or you don't want it to, via -noappend), this is what > trjcat is for. > > -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] question on ffG43a1p force field
On 8/16/19 2:15 AM, Lei Qian wrote: Sorry for this basic question. I read previous emails and tried to make pdb2gmx find ffG43a1p.ff. I added #include "ffG43a1p.itp" in FF.dat in ffG43a1p.ff folder. Also tried to create a file called forcefield.doc and wrote "ffG43a1p" into it. I put these files in working directory and /usr/local/gromacs/share/gromacs/top/ directory. However, neither of them worked. Could I ask how to solve this problem? It sounds like you are trying to modify a very old and outdated version of the files (potentially with an outdated version of GROMACS - FF.dat is no longer used). The files you want for any post-4.0 version of GROMACS are in: http://www.gromacs.org/@api/deki/files/235/=gromos43a1p-4.5.1.tgz -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] continue run
On 8/16/19 6:09 AM, Dhrubajyoti Maji wrote: Hi all, I have a simulated trajectory of 50 ns but my desired property is not well converged. Therefore, I want to extend the run for another 50 ns. As far as I know if I use the last output files as input files for next run, I can finally have two 50 ns run trajectory files. But if I want a 100 ns trajectory then what should I do? Any kind of help will be highly appreciated. By default, mdrun will append to the trajectory and give you one file. If it can't (or you don't want it to, via -noappend), this is what trjcat is for. -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] continue run
Hi, you can generate a new .tpr file by extend flag ( time is in ps) then run your code again. Please replace the names carefully. Also, check this link : http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-convert-tpr.html gmx convert-tpr -s last.tpr -o new.tpr -extend 1 gmx mdrun -v -deffnm new -cpi last.cpt -noappend Best regards, Mohammadreza Niknam Hamidabad On Fri, Aug 16, 2019 at 12:09 PM Dhrubajyoti Maji wrote: > Hi all, >I have a simulated trajectory of 50 ns but my desired property is not > well converged. Therefore, I want to extend the run for another 50 ns. As > far as I know if I use the last output files as input files for next run, I > can finally have two 50 ns run trajectory files. But if I want a 100 ns > trajectory then what should I do? Any kind of help will be highly > appreciated. > 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. > -- 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] continue run
Hi all, I have a simulated trajectory of 50 ns but my desired property is not well converged. Therefore, I want to extend the run for another 50 ns. As far as I know if I use the last output files as input files for next run, I can finally have two 50 ns run trajectory files. But if I want a 100 ns trajectory then what should I do? Any kind of help will be highly appreciated. 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 create a group for a set of atoms with make_ndx
got it. Thank you all for your help. On Fri, Aug 16, 2019 at 12:40 PM Bratin Kumar Das < 177cy500.bra...@nitk.edu.in> wrote: > Hi.. > The command is given below > gmx make_ndx -f *.gro -o *.ndx > You need to see inside the gro file what are the residue index > corresponding to the particular residue > Next...When atom selection will appear you select the residues like > r66|r65|...So on upto the last residue...And you can name the group as you > wish > > On Thu 15 Aug, 2019, 9:52 PM Dhaniram Mahato, > wrote: > > > Index file is always in a serial no. You can check the residue serial no. > > by opening the pdb in text format. > > > > "gmx make_ndx " is the command to use to see all indices and then choose > > your residues accordingly. > > -- > > 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] question on ffG43a1p force field
Sorry for this basic question. I read previous emails and tried to make pdb2gmx find ffG43a1p.ff. I added #include "ffG43a1p.itp" in FF.dat in ffG43a1p.ff folder. Also tried to create a file called forcefield.doc and wrote "ffG43a1p" into it. I put these files in working directory and /usr/local/gromacs/share/gromacs/top/ directory. However, neither of them worked. Could I ask how to solve this problem? Thanks lei -- 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.
