Hi Mark, *So, for the record, the actual issue is that GROMACS does not implement *some kind of tapering of non-bonded interactions that would apply between *particle pairs at short range?
This is the extract from the supporting information of the paper I refer to that explains the issue (³http://irep.ntu.ac.uk/id/eprint/4652/7/4652__Perry_SI.pdf²): "Full inclusion of attractive nonbond interactions between 1,4 bonded atoms in most force fields (CHARMM, CVFF, PCFF, COMPASS) requires a 4% increase in r (the equilibrium bond length parameter of the forcefield) Partial inclusion of attractive nonbond interactions between 1,4 bonded atoms (50% of Lennard-Jones interactions and 5/6 of Coulomb interactions in AMBER) requires only a 2.5% increase, and 12-6 LJ parameters identical to these in CVFF and CHARMM can then be used." My particular issue was that I assumed gen-pairs=yes in the [ default ] section of the topology file meant that Gromacs automatically generated a list of atoms undergoing 1-4 interactions (as well as automatically generating the modified LJ and Coulomb parameters for those interactions). When I proceeded to manually specify the list of atoms undergoing 1-4 interactions within the [pairs] section of the topology, the silica system compressed during the simulation to produce the correct equilibrium bond length observed experimentally. Thanks, Amanda On 03/07/2017, 06:34, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of 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: Anybody using Silica InterfaceFF on Gromacs? (Mark Abraham) > 2. Re: Can not open file: run.trr (Mark Abraham) > 3. Re: Can not open file: run.trr (Mark Abraham) > 4. Re: Anybody using Silica InterfaceFF on Gromacs? (Alex) > 5. Multiple output log. xtc .edr files generated using mpirun > (Abhishek Acharya) > 6. Grid Spacing (Apramita Chand) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Mon, 03 Jul 2017 00:03:52 +0000 >From: Mark Abraham <mark.j.abra...@gmail.com> >To: gmx-us...@gromacs.org >Subject: Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs? >Message-ID: > <camnumas5yomy5nd7ewgixxc+bqop5eht1e5wejzoy-0bmjv...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Hi, > >On Fri, Jun 30, 2017 at 2:46 AM Alex <nedoma...@gmail.com> wrote: > >> > >> > >> >> >> >> He he, childish :) >> > >> > David, no offense intended. I just think that when applied to solids, >>the >> entire concept of what works so well for biomolecular systems becomes a >>bit >> of a joke. And vice versa, to be fair. Spoken from experience, really >>-- we >> here used Gromacs to simulate things that I keep telling people not to >> simulate with Gromacs, and it got published!. :) >> > >Sure - one should use a tool capable of doing the job, and use its >optional >capabilities accordingly. Choosing non-bonded exclusions based on bonds, >in >a way that does not implement the intended model physics, is indeed wrong, >but that doesn't make the use of modified 1-4 pair interactions "childish" >in general ;-) > > >> In any case, I second what was said above re: # of exclusions. >>Solid-state >> potentials use smooth drop-offs to exclude long-range interactions >>between >> close neighbor sharing elements, so looking into David's suggestion may >>in >> fact fix the issues immediately. >> > >So, for the record, the actual issue is that GROMACS does not implement >some kind of tapering of non-bonded interactions that would apply between >particle pairs at short range? > >Mark > > >> Alex >> -- >> 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: Mon, 03 Jul 2017 00:06:16 +0000 >From: Mark Abraham <mark.j.abra...@gmail.com> >To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se >Subject: Re: [gmx-users] Can not open file: run.trr >Message-ID: > <CAMNuMARRYPPQNhjvaG0452Bor4jDRZM08Ekj1-zF7QJKFpX=h...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Hi, > >Use tools like rsync to do your file copies and preserve suitable >permissions automatically. And try to avoid copying files > 2GB to >partitions formatted in Windows-friendly fashion to e.g. FAT32 file >sytems, >as external hard drives might be formatted. > >Mark > >On Sun, Jul 2, 2017 at 10:59 PM Samith Rathnayake <samithz...@gmail.com> >wrote: > >> Hi everyone, >> >> Recently I was run a 30ns gromacs simulation.And for the analysis part, >>i >> was copied down the entire file directory of the simulation into an >> external hard disk and shift it into another computer with same OS and >>same >> version of gromacs (ubuntu 14.04 and gromacs 4.6.5). After copied down >>to >> another computer, I was work with the file permission scenario by using >>the >> command: chmod 777 for every and each file .Then I was run the g_rms >> command for the RMSD analysis.But i was got the : >> >> >>......................................................................... >>............................................... >> Program g_rms, VERSION 4.6.5 >> Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/gmxfio.c, line: >> 524 >> >> Can not open file: >> run70.trr >> For more information and tips for troubleshooting, please check the >>GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> >> >>......................................................................... >>.............................................. >> The command worked with the same files when those files were in the >> previous (original location) computer.Even i arranged the file >>permission >> on the new computer (new space) the trr files cant open. >> How to overcome this situation? >> >> >> thank you in advance. >> -- >> 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: Mon, 03 Jul 2017 00:06:16 +0000 >From: Mark Abraham <mark.j.abra...@gmail.com> >To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se >Subject: Re: [gmx-users] Can not open file: run.trr >Message-ID: > <CAMNuMARRYPPQNhjvaG0452Bor4jDRZM08Ekj1-zF7QJKFpX=h...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Hi, > >Use tools like rsync to do your file copies and preserve suitable >permissions automatically. And try to avoid copying files > 2GB to >partitions formatted in Windows-friendly fashion to e.g. FAT32 file >sytems, >as external hard drives might be formatted. > >Mark > >On Sun, Jul 2, 2017 at 10:59 PM Samith Rathnayake <samithz...@gmail.com> >wrote: > >> Hi everyone, >> >> Recently I was run a 30ns gromacs simulation.And for the analysis part, >>i >> was copied down the entire file directory of the simulation into an >> external hard disk and shift it into another computer with same OS and >>same >> version of gromacs (ubuntu 14.04 and gromacs 4.6.5). After copied down >>to >> another computer, I was work with the file permission scenario by using >>the >> command: chmod 777 for every and each file .Then I was run the g_rms >> command for the RMSD analysis.But i was got the : >> >> >>......................................................................... >>............................................... >> Program g_rms, VERSION 4.6.5 >> Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/gmxfio.c, line: >> 524 >> >> Can not open file: >> run70.trr >> For more information and tips for troubleshooting, please check the >>GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> >> >>......................................................................... >>.............................................. >> The command worked with the same files when those files were in the >> previous (original location) computer.Even i arranged the file >>permission >> on the new computer (new space) the trr files cant open. >> How to overcome this situation? >> >> >> thank you in advance. >> -- >> 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: 4 >Date: Sun, 2 Jul 2017 18:27:05 -0600 >From: Alex <nedoma...@gmail.com> >To: gmx-us...@gromacs.org >Subject: Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs? >Message-ID: <15f6281f-d32c-4f72-4014-f592f24b1...@gmail.com> >Content-Type: text/plain; charset=utf-8; format=flowed > > >> Sure - one should use a tool capable of doing the job, and use its >>optional >> capabilities accordingly. Choosing non-bonded exclusions based on >>bonds, in >> a way that does not implement the intended model physics, is indeed >>wrong, >> but that doesn't make the use of modified 1-4 pair interactions >>"childish" >> in general ;-) >> >You are correct. My point only holds in a situation where people indeed >are doing that: using an inappropriate tool. And you see how many people >on this list ask questions about doing solid-state simulations with >Gromacs. I have a dual background and could give many examples where the >use of what works for proteins/lipids in water is, well, childish, for >lack of a better word in solid-state systems. I hope noone takes >offense. :) The "problem" is that, thanks to your hard work, Gromacs is >delightful to use, much more so than LAMMPS, and my hope is that one day >you guys will just implement things like REBO and ReaxFF and MEAM, and >Weber-Stillinger and what-not. If you do that, I will fly to your >location, give you a hug, and personally buy you a steak dinner. In >other words, my hope is that one day Gromacs will be an appropriate tool >for all of classical MD, solid or liquid state. >> So, for the record, the actual issue is that GROMACS does not implement >> some kind of tapering of non-bonded interactions that would apply >>between >> particle pairs at short range? >> >Within the question initially posed (about silica), Gromacs is fairly >capable of everything necessary, it is just a matter of carefully >reading the documentation on the original solid-state potential and then >setting up the adopted forcefield, including the nrexl, etc. The much >bigger issue (with solid-state things in general) is the springs for >bonds, angles, etc, and use permanent molecular topologies. Wrong phonon >spectra, wrong elastic properties away from 0K, wrong rippling spectra >of graphene and likely all atomically thin membranes, inability to do >covalent bond breaking/formation, etc, etc. That is, things Gromacs was >never intended for. But then again, see what I said above. > >Alex > > >------------------------------ > >Message: 5 >Date: Mon, 3 Jul 2017 10:58:47 +0530 >From: Abhishek Acharya <abhi117acha...@gmail.com> >To: Discussion list for GROMACS users <gmx-us...@gromacs.org> >Subject: [gmx-users] Multiple output log. xtc .edr files generated > using mpirun >Message-ID: > <cab1aw3w3ooni1bjmuw5hwcryzor9xfp1+1ecy-xbcnpdb7i...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Hello GROMACS users, > >I am trying to run a simulation on a university cluster; I am using >gromacs-5.1.2. The problem is while running mdrun, using the following >command: > >mpirun -np 32 gmx mdrun -s prod.tpr -deffnm prod_out -pin on ### I >expected gmx mdrun_mpi here but it was not available. > >I am getting multiple log files, xtc, edr files as the output and all the >log files say the following: > > >Running on 1 node with total 16 cores, 16 logical cores >Hardware detected: > CPU info: > Vendor: GenuineIntel > Brand: Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz > Family: 6 model: 45 stepping: 7 > CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr >nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 >sse4.2 ssse3 tdt x2apic > SIMD instructions most likely to fit this hardware: AVX_256 > SIMD instructions selected at GROMACS compile time: AVX_256 > >This in itself is pretty weird. I am guessing that the package is not >properly installed by the admin. My question is what is the exact problem >with the setup and what is the solution; i need to communicate this to the >admin. Although, I reported the issue previously, but it seems he doesn't >understand where the problem seems to be. > > >Thanks in advance. > >Sincerely, >Abhishek Acharya >Research Associate, >Department of Molecular Nutrition >CSIR-Central Food Technological Research Institute, >Mysuru-570020 > > >------------------------------ > >Message: 6 >Date: Mon, 3 Jul 2017 11:04:56 +0530 >From: Apramita Chand <apramita.ch...@gmail.com> >To: gromacs.org_gmx-users@maillist.sys.kth.se >Subject: [gmx-users] Grid Spacing >Message-ID: > <CA+gTzoZ5xCZudtXPsZkOoZxkvGdMy=dfw4znizkna25k6uf...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Dear All, >Which is more appropriate fourier grid spacing for gromos53a6 ff with >cutoffs being 0.9 and 1.4nm? >0.16 or 0.12?? >I've not seen too many papers with 0.16 being used for this forcefield and >that too with cutoffs like 1.0 for rcoulomb and rvdw. > >Is there any problem if I use fourier spacing of 0.16 with these >cutoffs(0.9,1.4)? > >Also,should the grid spacing be same for equilibration and production >runs?? > >Yours sincerely, >Apramita > > >------------------------------ > >-- >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 159, Issue 8 >***************************************************** -- 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.
