Re: [gmx-users] mac OS Catalina segmentation fault
Hi Paul, Thank you for your e-mail. I forgot to note that without the plumed patch, the situation remains still problematic. The vanilla versions produce the same errors (segmentation faults), even without any specific input files. Just running the command e.g. gmx(_mpi) grompp, or gmx(_mpi) trjconv without any input files, a segmentation fault is produced, as it is in the case also with specific input files. Some tools, like editconf (v. 2019.4), just complain about missing input files, if none is given, but without a segmentation fault, as it should be. I attach the full CMake Config and log files. I will try and open an issue on redmine.gromacs.org thank you again, Vangelis. On Tue, Nov 5, 2019 at 11:30 PM Paul bauer wrote: > Hello, > > could you try running first with an unmodified version of GROMACS, so we > can check if the PLUMED modifications are responsible for the crashes > (unlikely for the tools, but we need to make sure)? > If the vanilla versions are still crashing, can you supply us with some > log files and input files/run scripts for the failures and open a new > issue on redmine.gromacs.org? > > Also, can you share the full CMakeConfig file? > > Cheers > > Paul > > On 05/11/2019 21:10, Daskalakis Vangelis wrote: > > Dear all, > > I am running Mac OS Catalina 10.15.1 (Xcode 11.2 11B52). I have > > successfully compiled several versions of Gromacs (5.1.5, 2018.8, or > > 2019.4) patched with plumed (v.2.4.6 for 5.1.5, or v.2.5.3 for 2018/2019 > > versions). The compilations are completed without any errors, employing > the > > configuration: > > # cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=on > > -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/gromacs -DCXX="$MPICXX" > > > > For example Gromacs v. 5.1.5 (but the same is happening on the other > > versions), I get segmentation faults, when I just run some tools, like: > > > > [MacBook-Pro:33466] *** Process received signal *** > > [MacBook-Pro:33466] Signal: Segmentation fault: 11 (11) > > [MacBook-Pro:33466] Signal code: (0) > > [MacBook-Pro:33466] Failing at address: 0x0 > > [MacBook-Pro:33466] [ 0] 0 libsystem_platform.dylib > > 0x7fff69e47b1d _sigtramp + 29 > > [MacBook-Pro:33466] [ 1] 0 libdyld.dylib > > 0x7fff69c3730e dyld_stub_binder + 282 > > [MacBook-Pro:33466] [ 2] 0 libgromacs_mpi.1.5.0.dylib > > 0x00010dd60f2e _ZN3gmx24CommandLineModuleManager3runEiPPc + 798 > > [MacBook-Pro:33466] [ 3] 0 gmx_mpi > > 0x00010dcc39d1 main + 129 > > [MacBook-Pro:33466] [ 4] 0 libdyld.dylib > > 0x7fff69c462e5 start + 1 > > [MacBook-Pro:33466] [ 5] 0 ??? > > 0x0002 0x0 + 2 > > [MacBook-Pro:33466] *** End of error message *** > > zsh: segmentation fault gmx_mpi trjconv > > > > switching MPI support on/ off on the configuration/ compilation stage > does > > not change the situation. Some tools are running smoothly, as editconf. > > However others, have segmentation faults. Grompp is running on v.5.1.5, > but > > gives a segmantation fault on v. 2019.4. > > > > I would appreciate some help, > > thank you, > > Vangelis. > > > -- > Paul Bauer, PhD > GROMACS Release Manager > KTH Stockholm, SciLifeLab > 0046737308594 > > -- > 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] gmx gangle in a for loop
Dear all,
Could one kindly let me know how $i should come in gmx gangle used in a for
loop to avoid syntax errors?
I tested different flavors like "$i", "${i}", ..., and still the problem is
here.
#!/bin/bash/
for i in {1..1000}
do
gmx gangle -g1 vector -group1 'group $i and name C10 plus group $i
and name C20' -g2 vector -group2 'cog of group 0 plus cog of group $i' -n
ind.ndx -f ind.xtc -s ind.tpr -oav aver$i.xvg -oh hist$i.xvg
done
Thank you
Alex
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Re: [gmx-users] defining parameters in a separate itp file
On 11/5/19 7:53 PM, Dave M wrote: Hi Justin, Will appreciate any suggestions about the error am getting with distance_restraints. Aside from using the pull code rather than this approach, I have no other suggestions. -Justin Thanks. regards, Dave On Thu, Oct 31, 2019 at 1:39 AM Dave M wrote: Hi Justin, Thanks, not sure [distance_restraints] also does not work for me. Though pull code works (like shared by other user Mustafa in recent discussions). My top files contain this: [ intermolecular_interactions ] [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 1 155 10 1 0.0 0.3 0.4 1.0 I get this error: NMR distance restraints with multiple copies of the same molecule are currently only supported with ensemble averaging. If you just want to restrain distances between atom pairs using a flat-bottomed potential, use a restraint potential (bonds type 10) instead. I do not have multiple copies of the same molecule (except water molecules!) and the atom numbers here belong to two different molecules. I also tried using type' = 2 but still error remains the same. Would have been great if distance_restraints work as it seems to be bit cleaner way than modifying a pull code. I want to keep number of small molecules near to a rod like bigger molecule; just like beads on a string. So distance_restraints or something similar will be great. Dave On Tue, Oct 29, 2019 at 5:45 AM Justin Lemkul wrote: On 10/28/19 6:21 PM, Dave M wrote: Hi Justin, Thanks for your reply but am getting error suggesting a intermolecular chemical bond is not allowed: Program: gmx grompp, version 2016.4 Source file: src/gromacs/gmxpreprocess/convparm.cpp (line 649) Fatal error: The intermolecular_interaction can not contain chemically bonding interactions [ molecules ] ; namenumber molA 1 molB 1 W 2420 [intermolecular_interactions] [ bonds ] 1 158 1 0.4 2000 This is coarse-grained model and as a simple test I used global atom numbers between two water single particles (intermolecular) but I get the same error. In that case, use a [distance_restraints] directive under [intermolecular_interactions] (though this will limit your domain decomposition setup) or use the pull code to maintain a restraint rather than messing with the topology. -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. -- == 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] defining parameters in a separate itp file
Hi Justin, Will appreciate any suggestions about the error am getting with distance_restraints. Thanks. regards, Dave On Thu, Oct 31, 2019 at 1:39 AM Dave M wrote: > Hi Justin, > > Thanks, not sure [distance_restraints] also does not work for me. Though > pull code works (like shared by other user Mustafa in recent discussions). > > My top files contain this: > [ intermolecular_interactions ] > > > [ distance_restraints ] > > ; ai aj type index type’ low up1 up2 fac > > 1 155 10 1 0.0 0.3 0.4 1.0 > > > I get this error: > > NMR distance restraints with multiple copies of the same molecule are > > currently only supported with ensemble averaging. If you just want to > restrain > > distances between atom pairs using a flat-bottomed potential, use a > restraint > > potential (bonds type 10) instead. > > I do not have multiple copies of the same molecule (except water > molecules!) and the atom numbers here belong to two different molecules. I > also tried using type' = 2 but still error remains the same. Would have > been great if distance_restraints work as it seems to be bit cleaner way > than modifying a pull code. I want to keep number of small molecules near > to a rod like bigger molecule; just like beads on a string. So > distance_restraints or something similar will be great. > > Dave > > On Tue, Oct 29, 2019 at 5:45 AM Justin Lemkul wrote: > >> >> >> On 10/28/19 6:21 PM, Dave M wrote: >> > Hi Justin, >> > >> > Thanks for your reply but am getting error suggesting a intermolecular >> > chemical bond is not allowed: >> > >> > Program: gmx grompp, version 2016.4 >> > >> > Source file: src/gromacs/gmxpreprocess/convparm.cpp (line 649) >> > >> > Fatal error: >> > >> > The intermolecular_interaction can not contain chemically bonding >> > interactions >> > >> > [ molecules ] >> > >> > ; namenumber >> > >> > molA 1 >> > >> > molB 1 >> > >> > W 2420 >> > >> > >> > [intermolecular_interactions] >> > >> > [ bonds ] >> > >> > 1 158 1 0.4 2000 >> > >> > This is coarse-grained model and as a simple test I used global atom >> > numbers between two water single particles (intermolecular) but I get >> the >> > same error. >> >> In that case, use a [distance_restraints] directive under >> [intermolecular_interactions] (though this will limit your domain >> decomposition setup) or use the pull code to maintain a restraint rather >> than messing with the topology. >> >> -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] gromos force field
Hi, I'm coming late, but I may add a few words. The GROMOS force fields have been parameterized with the GROMOS software using a twin-range cutoff (0.8/1.4), but this option is no longer available in recent versions of GROMACS. However, in a recent study (https://doi.org/10.1021/acs.jctc.8b00758), it was showed that using a single range cutoff (rlist = rcoulomb = rvdw = 1.4 and nstlist = 1) + reaction field (coulombtype = Generalized-Reaction-Field) together with the group scheme for neighbor searching (cutoff-scheme=group, even if this is deprecated since version 5.1, it is still usable) reproduces results generated with the GROMOS software and FF. One other study on lipids points to the same conclusion regarding the use of single range cutoff (https://doi.org/10.1021/acs.jctc.7b00178) as an alternative to twin-range cutoff. That was also tested in this redmine issue: https://redmine.gromacs.org/issues/1400. This solution increases significantly the computational cost compared to former twin-range cutoff, but it is probably the one which gives the closest results to the original GROMOS FF. Alternatively, it was found in a recent paper (https://pubs.acs.org/doi/10.1021/acs.jctc.8b00425) that it is possible to use the Verlet scheme for neighbour searching with rvdw = 1.2 and PME for electrostatics (with rcoulomb = 1.2 since it has to equal rvdw) as an acceptable option to reproduce some liquid properties calculated with the GROMOS software. Regarding the remark about the GROMOS software, I'm not aware of any "problems". Best, Patrick Le 23/09/2019 à 12:49, Justin Lemkul a écrit : On 9/21/19 12:44 PM, p buscemi wrote: Dear Users, I often use Gromos force field because ATB provides top files for reasonably large molecules - 1000 atoms. With Gromacs 2019.3 the error now appears: 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. while message is clear enough, just how large an error in density is anticipated ? A 10 % error in polymer solution may be tolerable. A 2 % error in a crystal or binding site may be a concern. Gromacs indicated that Gromos may be dropped for v 2020. Is there no other option - llike fixing the time-stepping-scheme. Or must I not use the twin-cutoff typically presented in the mpd files ? There is a conversion from Gromos top to Amber, but would not the error be translated as well ? The problem is that the GROMOS force fields were derived using software that has problems, therefore rendering all of the behaviors of this force field in other software questionable. There should be a paper forthcoming from the core developers that describes the situation sometime soon. -Justin -- 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] mac OS Catalina segmentation fault
Hello, could you try running first with an unmodified version of GROMACS, so we can check if the PLUMED modifications are responsible for the crashes (unlikely for the tools, but we need to make sure)? If the vanilla versions are still crashing, can you supply us with some log files and input files/run scripts for the failures and open a new issue on redmine.gromacs.org? Also, can you share the full CMakeConfig file? Cheers Paul On 05/11/2019 21:10, Daskalakis Vangelis wrote: Dear all, I am running Mac OS Catalina 10.15.1 (Xcode 11.2 11B52). I have successfully compiled several versions of Gromacs (5.1.5, 2018.8, or 2019.4) patched with plumed (v.2.4.6 for 5.1.5, or v.2.5.3 for 2018/2019 versions). The compilations are completed without any errors, employing the configuration: # cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=on -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/gromacs -DCXX="$MPICXX" For example Gromacs v. 5.1.5 (but the same is happening on the other versions), I get segmentation faults, when I just run some tools, like: [MacBook-Pro:33466] *** Process received signal *** [MacBook-Pro:33466] Signal: Segmentation fault: 11 (11) [MacBook-Pro:33466] Signal code: (0) [MacBook-Pro:33466] Failing at address: 0x0 [MacBook-Pro:33466] [ 0] 0 libsystem_platform.dylib 0x7fff69e47b1d _sigtramp + 29 [MacBook-Pro:33466] [ 1] 0 libdyld.dylib 0x7fff69c3730e dyld_stub_binder + 282 [MacBook-Pro:33466] [ 2] 0 libgromacs_mpi.1.5.0.dylib 0x00010dd60f2e _ZN3gmx24CommandLineModuleManager3runEiPPc + 798 [MacBook-Pro:33466] [ 3] 0 gmx_mpi 0x00010dcc39d1 main + 129 [MacBook-Pro:33466] [ 4] 0 libdyld.dylib 0x7fff69c462e5 start + 1 [MacBook-Pro:33466] [ 5] 0 ??? 0x0002 0x0 + 2 [MacBook-Pro:33466] *** End of error message *** zsh: segmentation fault gmx_mpi trjconv switching MPI support on/ off on the configuration/ compilation stage does not change the situation. Some tools are running smoothly, as editconf. However others, have segmentation faults. Grompp is running on v.5.1.5, but gives a segmantation fault on v. 2019.4. I would appreciate some help, thank you, Vangelis. -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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] mac OS Catalina segmentation fault
Dear all, I am running Mac OS Catalina 10.15.1 (Xcode 11.2 11B52). I have successfully compiled several versions of Gromacs (5.1.5, 2018.8, or 2019.4) patched with plumed (v.2.4.6 for 5.1.5, or v.2.5.3 for 2018/2019 versions). The compilations are completed without any errors, employing the configuration: # cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=on -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/gromacs -DCXX="$MPICXX" For example Gromacs v. 5.1.5 (but the same is happening on the other versions), I get segmentation faults, when I just run some tools, like: [MacBook-Pro:33466] *** Process received signal *** [MacBook-Pro:33466] Signal: Segmentation fault: 11 (11) [MacBook-Pro:33466] Signal code: (0) [MacBook-Pro:33466] Failing at address: 0x0 [MacBook-Pro:33466] [ 0] 0 libsystem_platform.dylib 0x7fff69e47b1d _sigtramp + 29 [MacBook-Pro:33466] [ 1] 0 libdyld.dylib 0x7fff69c3730e dyld_stub_binder + 282 [MacBook-Pro:33466] [ 2] 0 libgromacs_mpi.1.5.0.dylib 0x00010dd60f2e _ZN3gmx24CommandLineModuleManager3runEiPPc + 798 [MacBook-Pro:33466] [ 3] 0 gmx_mpi 0x00010dcc39d1 main + 129 [MacBook-Pro:33466] [ 4] 0 libdyld.dylib 0x7fff69c462e5 start + 1 [MacBook-Pro:33466] [ 5] 0 ??? 0x0002 0x0 + 2 [MacBook-Pro:33466] *** End of error message *** zsh: segmentation fault gmx_mpi trjconv switching MPI support on/ off on the configuration/ compilation stage does not change the situation. Some tools are running smoothly, as editconf. However others, have segmentation faults. Grompp is running on v.5.1.5, but gives a segmantation fault on v. 2019.4. I would appreciate some help, thank you, Vangelis. -- 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 in DNA.itp file
On 11/5/19 11:55 AM, Najamuddin Memon wrote: You may use Amber99sb force field for DNA-protein simulation and also put residue type.dat file in your folder. It will work The nucleic acid parameter sets packaged with these GROMACS ports are wildly outdated. I suggest finding better parameters from other sources. People have ported AMBER parameters, though they should be checked thoroughly. -Justin On Tue, Nov 5, 2019, 6:59 PM Paul bauer wrote: Hello, the error states that you are missing parameters for your system. Did you check that the forcefield contains all the special parameters you need for the conjugate molecule? Also, I would recommend to not use a prehistoric version of GROMACS for new studies, if there are no specific reasons preventing you from using a more recent one that is still supported (such as 2018 or 2019). Cheers Paul On 05/11/2019 14:47, Ayesha Kanwal wrote: Hi all, i am preparing system of DNA-protein complex, downloaded it from RCSB website, by using GROMACS-version 4.5.5; force field AMBER03WS with water Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type. but the problem is that when i use command for energy minimization the following error has occurred. Error shows that problem is in .itp file Dih. types. For protein .itp files,there was no problem. Only DNA .itp files have issue. Its my first time i am preparing this kind of system please let me know how can i resolve this problem and why these errors were generated ? I have searched out previous mail but could not find relevant answer so i am posting it now here. i have attached .mdp file with this e-mail. checking input for internal consistency... Generated 2412 of the 2415 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2415 of the 2415 1-4 parameter combinations ERROR 1 [file dna-his_DNA_chain_I.itp, line 44148]: No default Improper Dih. types ERROR 2 [file dna-his_DNA_chain_J.itp, line 44148]: No default Improper Dih. types -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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.
Re: [gmx-users] Error in DNA.itp file
Residue type.dat file having definition of nucleotides On Tue, Nov 5, 2019, 9:55 PM Najamuddin Memon wrote: > You may use Amber99sb force field for DNA-protein simulation and also put > residue type.dat file in your folder. It will work > > > On Tue, Nov 5, 2019, 6:59 PM Paul bauer wrote: > >> Hello, >> >> the error states that you are missing parameters for your system. Did >> you check that the forcefield contains all the special parameters you >> need for the conjugate molecule? >> Also, I would recommend to not use a prehistoric version of GROMACS for >> new studies, if there are no specific reasons preventing you from using >> a more recent one that is still supported (such as 2018 or 2019). >> >> Cheers >> >> Paul >> >> On 05/11/2019 14:47, Ayesha Kanwal wrote: >> > Hi all, >> > i am preparing system of DNA-protein complex, downloaded it from RCSB >> website, by using GROMACS-version 4.5.5; force field AMBER03WS with water >> Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type. >> > but the problem is that when i use command for energy minimization the >> following error has occurred. Error shows that problem is in .itp file Dih. >> types. For protein .itp files,there was no problem. Only DNA .itp files >> have issue. Its my first time i am preparing this kind of system please let >> me know how can i resolve this problem and why these errors were generated >> ? I have searched out previous mail but could not find relevant answer so i >> am posting it now here. i have attached .mdp file with this e-mail. >> > >> > checking input for internal consistency... >> > Generated 2412 of the 2415 non-bonded parameter combinations >> > Generating 1-4 interactions: fudge = 0.5 >> > Generated 2415 of the 2415 1-4 parameter combinations >> > >> > ERROR 1 [file dna-his_DNA_chain_I.itp, line 44148]: >> >No default Improper Dih. types >> > >> > >> > ERROR 2 [file dna-his_DNA_chain_J.itp, line 44148]: >> >No default Improper Dih. types >> > >> > >> >> -- >> Paul Bauer, PhD >> GROMACS Release Manager >> KTH Stockholm, SciLifeLab >> 0046737308594 >> >> -- >> 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] Error in DNA.itp file
You may use Amber99sb force field for DNA-protein simulation and also put residue type.dat file in your folder. It will work On Tue, Nov 5, 2019, 6:59 PM Paul bauer wrote: > Hello, > > the error states that you are missing parameters for your system. Did > you check that the forcefield contains all the special parameters you > need for the conjugate molecule? > Also, I would recommend to not use a prehistoric version of GROMACS for > new studies, if there are no specific reasons preventing you from using > a more recent one that is still supported (such as 2018 or 2019). > > Cheers > > Paul > > On 05/11/2019 14:47, Ayesha Kanwal wrote: > > Hi all, > > i am preparing system of DNA-protein complex, downloaded it from RCSB > website, by using GROMACS-version 4.5.5; force field AMBER03WS with water > Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type. > > but the problem is that when i use command for energy minimization the > following error has occurred. Error shows that problem is in .itp file Dih. > types. For protein .itp files,there was no problem. Only DNA .itp files > have issue. Its my first time i am preparing this kind of system please let > me know how can i resolve this problem and why these errors were generated > ? I have searched out previous mail but could not find relevant answer so i > am posting it now here. i have attached .mdp file with this e-mail. > > > > checking input for internal consistency... > > Generated 2412 of the 2415 non-bonded parameter combinations > > Generating 1-4 interactions: fudge = 0.5 > > Generated 2415 of the 2415 1-4 parameter combinations > > > > ERROR 1 [file dna-his_DNA_chain_I.itp, line 44148]: > >No default Improper Dih. types > > > > > > ERROR 2 [file dna-his_DNA_chain_J.itp, line 44148]: > >No default Improper Dih. types > > > > > > -- > Paul Bauer, PhD > GROMACS Release Manager > KTH Stockholm, SciLifeLab > 0046737308594 > > -- > 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] Slurm for GROMACS
Hi, SLURM and OpenMPI do different things. SLURM is a resource manager, from which you might request multiple compute nodes. OpenMPI is a parallelism library that allows a program to run on those nodes. GROMACS is the program, and it doesn't care which MPI library is in use, or which resource manager sits above that. So SLURM + OpenMPI + GROMACS is fine. Mark On Tue, 5 Nov 2019 at 14:51, Shradheya R.R. Gupta wrote: > Researchers, > Is slrum required to run GROMACS on multiple computers or OpenMPI is fine? > > Thank you > Shradheya > DBT-BIF University of Rajasthan > -- > 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] Error in DNA.itp file
Hello, the error states that you are missing parameters for your system. Did you check that the forcefield contains all the special parameters you need for the conjugate molecule? Also, I would recommend to not use a prehistoric version of GROMACS for new studies, if there are no specific reasons preventing you from using a more recent one that is still supported (such as 2018 or 2019). Cheers Paul On 05/11/2019 14:47, Ayesha Kanwal wrote: Hi all, i am preparing system of DNA-protein complex, downloaded it from RCSB website, by using GROMACS-version 4.5.5; force field AMBER03WS with water Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type. but the problem is that when i use command for energy minimization the following error has occurred. Error shows that problem is in .itp file Dih. types. For protein .itp files,there was no problem. Only DNA .itp files have issue. Its my first time i am preparing this kind of system please let me know how can i resolve this problem and why these errors were generated ? I have searched out previous mail but could not find relevant answer so i am posting it now here. i have attached .mdp file with this e-mail. checking input for internal consistency... Generated 2412 of the 2415 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2415 of the 2415 1-4 parameter combinations ERROR 1 [file dna-his_DNA_chain_I.itp, line 44148]: No default Improper Dih. types ERROR 2 [file dna-his_DNA_chain_J.itp, line 44148]: No default Improper Dih. types -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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] Slurm for GROMACS
Researchers, Is slrum required to run GROMACS on multiple computers or OpenMPI is fine? Thank you Shradheya DBT-BIF University of Rajasthan -- 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 in DNA.itp file
Hi all, i am preparing system of DNA-protein complex, downloaded it from RCSB website, by using GROMACS-version 4.5.5; force field AMBER03WS with water Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type. but the problem is that when i use command for energy minimization the following error has occurred. Error shows that problem is in .itp file Dih. types. For protein .itp files,there was no problem. Only DNA .itp files have issue. Its my first time i am preparing this kind of system please let me know how can i resolve this problem and why these errors were generated ? I have searched out previous mail but could not find relevant answer so i am posting it now here. i have attached .mdp file with this e-mail. checking input for internal consistency... Generated 2412 of the 2415 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2415 of the 2415 1-4 parameter combinations ERROR 1 [file dna-his_DNA_chain_I.itp, line 44148]: No default Improper Dih. types ERROR 2 [file dna-his_DNA_chain_J.itp, line 44148]: No default Improper Dih. types -- 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] Ruuning MD simulation on laptop
So the answer is yes, you can, but I'm not sure you should. Assuming you have a mid to high end gaming laptop - say something like a i7-8750H with a Nvidia MaxQ 1070 (i.e. a Gigabyte Aero 15x or equivalent; I'm just going with what I have), you will get decent performance (I can get circa 80 ns / day with 2018.6 and a 60k atom system & I'm sure 2019/2020 will improve this). However, this will absolutely thrash the system, and your GPU and CPU temperatures will be near the limits very quickly (mine hit 85-90 C within a couple minutes). Prolonged usage at those temperatures will damage your laptop and your CPU will be forced to throttle (which is going to lower performance); hence why I only ever use my laptop for things like setting up simulations, analysis and testing methodologies on toy systems. For the sake of your own personal hardware, get a desktop. It'll cost a lot less, stay cooler (so will be around for longer) and will have faster components. As this paper shows; you really don't need to spend a lot at all: https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.26011 Hope that helps, Matthew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Billy Williams-Noonan Sent: 05 November 2019 06:32 To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Ruuning MD simulation on laptop Commonly used gaming cards can accelerate MD simulations quote quickly, but you'd be wanting to invest about a grand on one. There would also be a problem with load imbalance then, where the CPUs are struggling to keep up with the GPUs. So you'd want to have a decent number of decent quality logical cores running alongside the GPU as well. You'd probably want to spend at least AU$2000 on the lap top. Cheers, Billy On Tue., 5 Nov. 2019, 5:22 pm Swapnil Bhujbal, wrote: > Dear users, > > I'm a Ph.D. student. Usually, I do protein-ligand MD simulation for > 50-100ns in my lab. So can I use any gaming laptop with a good graphics > card in it for running the simulation? Would you recommend to install > Gromacs on a GPU in a laptop? > Your suggestions are highly appreciated. > Thank you in advance. > > Sincerely, > Mr. Swapnil Bhujbal > PhD Scholar, > School of Medicine, > Chosun University, > South Korea. > -- > 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] (no subject)
Hi all, i am preparing system of DNA-protein complex, downloaded it from RCSB website, by using GROMACS force field AMBER03WS with water Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type. but the problem is that when i use command for energy minimization the following error has occurred. Error shows that problem is in .itp file Dih. types. Its my first time i am preparing this kind of system please let me know how can i resolve this problem and why this error generated ? I have searched out previous mail but could not find relevant answer so i am posting it now here. i have attached .mdp file with this e-mail. checking input for internal consistency... Generated 2412 of the 2415 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2415 of the 2415 1-4 parameter combinations ERROR 1 [file dna-his_DNA_chain_I.itp, line 44148]: No default Improper Dih. types ERROR 2 [file dna-his_DNA_chain_J.itp, line 44148]: No default Improper Dih. types -- 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] Regarding force field for silicon oxide
Den 2019-11-05 kl. 01:59, skrev Mijiddorj B: Dear Prof. David van der Spoel, Thank you very much for your reply and sending an amazing work. I am sorry for asking further questions. Can you give me an advice to use the parameters which were considered in the ref#44 in this work? Ref#44 uses the OPLS force field and expresses LJ parameters for the contents. The OPLS files for gromacs 4.6 contain this non-standard addition to nonbonded types This is what was used in my paper and ref 44. Note that there is no GROMACS force field, so just refer to this as parameters used in those papers. ; Added by DvdS 05/2005 copied from GROMACS force field. SI SI 14 28.08000 0.000 A3.38550e-01 2.44704e+00 Best regards, Mijiddorj -- Message: 4 Date: Fri, 1 Nov 2019 17:44:38 +0100 From: David van der Spoel To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Regarding force field for silicon oxide Message-ID: <68c1ff39-9979-14ac-a1f9-eb1788be0...@xray.bmc.uu.se> Content-Type: text/plain; charset=windows-1252; format=flowed Den 2019-11-01 kl. 17:07, skrev Mijiddorj B: I would like to simulate a system which contains a silicon oxide surface and a polymer. Is it possible to simulate in gromacs? I thought that GROMOS force field could be applied in this purpose. Is it right? I am not sure. If you have a potential function that supports it and software to build topologies it works, e.g.: David van der Spoel, Erik J. W. Wensink and Alex C. Hoffmann: Lifting a glass from a wet table: a microscopic picture Langmuir 22 pp. 5666-5672 (2006) http://pubs.acs.org/cgi-bin/download.pl?la053284f/X8nx However please do not ask me for the files :) Also, is it possible to use InterfaceFF and Charmm force fields for this system? I mean that the silicon oxide could be treated by InterfaceFF, and CharmmFF could be applied for polymer structure. Do you have any experience, please let me advice. Thanks for your help. Best regards, Mijiddorj -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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.
