Re: [gmx-users] Linear CG beads, grompp doesn't work
I think your original problem is that you define only one charge group for the entire molecule/polymer. You need to define each bead in a separate charge group and things will be fine :)) you do not have charges anyways. As far as I know angles have never made martini unstable but the conventional dihedral potential are not suited for martini or any flexible molecule. XAvier. On Jan 2, 2013, at 4:55, Justin Lemkul wrote: > > > On 1/1/13 10:51 PM, Xu Dong Huang wrote: >> @Justin, >> >> Does the philosophy described in your tutorial apply to CG martini bead >> models where 1 bead describes the entire CO2 atom? (If I were to do that, >> assuming) > > Presumably. As long as you satisfy the criteria mentioned in the tutorial > (moment of inertia and total mass), you should be able to get it to work. > I've never dealt with polymers and have very little personal experience with > CG models, so I don't know if there are other methodological issues that one > might encounter. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Linear CG beads, grompp doesn't work
On 1/1/13 10:51 PM, Xu Dong Huang wrote: @Justin, Does the philosophy described in your tutorial apply to CG martini bead models where 1 bead describes the entire CO2 atom? (If I were to do that, assuming) Presumably. As long as you satisfy the criteria mentioned in the tutorial (moment of inertia and total mass), you should be able to get it to work. I've never dealt with polymers and have very little personal experience with CG models, so I don't know if there are other methodological issues that one might encounter. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Linear CG beads, grompp doesn't work
@Justin, Does the philosophy described in your tutorial apply to CG martini bead models where 1 bead describes the entire CO2 atom? (If I were to do that, assuming) Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 1, 2013, at 10:46 PM, Xu Dong Huang wrote: > Dear Justin, > > My .itp does not contain angles or dihedrals because we are simply interested > in the very simple generic case of a linear (what we assume by defining a > coordinate file of linear beads) polymer model. I will go through the > tutorial and try to see if it resolves my issue. > > > Xu Dong Huang > Chemical & Biochemical Engineering > Rutgers School of Engineering > xudo...@eden.rutgers.edu > > On Jan 1, 2013, at 10:38 PM, Justin Lemkul wrote: > >> >> >> On 1/1/13 10:33 PM, Xu Dong Huang wrote: >>> Dear advanced gromac users, >>> >>> I am trying to simulate a long linear chain of polymer using CG beads. >>> (about 200 beads), all with same type charge interactions. (examples >>> shown:) I read on previous gromacs mailing list that linear systems with >>> same charges make the system unstable? But is there anyway to go around >>> that? >>> >> >> It's the angles that make the system unstable. One can use virtual sites to >> get around the issue. There is a trivial example in a tutorial I wrote: >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html >> >> The bigger question is whether or not the angles in the molecule impose >> linearity, or whether the initial configuration is simply a line of >> particles that may deviate according to angle and dihedral potentials. You >> haven't shown the [angles] or [dihedrals] directives, so it's not clear what >> you're intending, exactly. >> >>> [atoms] >>> 1 P3 O1 mon 1 0.00 >>> 2 P3 O1 mon 2 0.00 >>> 3 P3 O1 mon 3 0.00 >>> 4 P3 O1 mon 4 0.00 >>> 5 P3 O1 mon 5 0.00 >>> 6 P3 O1 mon 6 0.00 >>> 7 P3 O1 mon 7 0.00 >>> 8 P3 O1 mon 8 0.00 >>> 9 P3 O1 mon 9 0.00 >>> ……. >>> [ bonds ] >>> 1 2 1 0.4317000 >>> 2 3 1 0.4317000 >>> 3 4 1 0.4317000 >>> 4 5 1 0.4317000 >>> …… >>> >>> However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr >>> -it returns the error of: >>> Fatal error: >>> The largest charge group contains 200 atoms. The maximum is 32. >>> For more information and tips for troubleshooting, please check the GROMACS >>> website at http://www.gromacs.org/Documentation/Errors >>> >>> Please let me know if there is a way to go around that. Thank you. >>> >> >> Do as the error message says and put fewer than 32 atoms in each charge >> group. The size of the charge group has implications for neighbor searching >> if using a group-based cutoff scheme. >> >> -Justin >> >> -- >> >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Linear CG beads, grompp doesn't work
On 1/1/13 10:46 PM, Xu Dong Huang wrote: Dear Justin, My .itp does not contain angles or dihedrals because we are simply interested in the very simple generic case of a linear (what we assume by defining a coordinate file of linear beads) polymer model. I will go through the tutorial and try to see if it resolves my issue. The molecule will not remain linear simply due to consecutive bonds. Hopefully the tutorial explains some of the necessary methodology for creating species that are indeed to be kept linear, though the example therein (CO2) is considerably less complex than what you seek to do. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Linear CG beads, grompp doesn't work
Dear Justin, My .itp does not contain angles or dihedrals because we are simply interested in the very simple generic case of a linear (what we assume by defining a coordinate file of linear beads) polymer model. I will go through the tutorial and try to see if it resolves my issue. Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 1, 2013, at 10:38 PM, Justin Lemkul wrote: > > > On 1/1/13 10:33 PM, Xu Dong Huang wrote: >> Dear advanced gromac users, >> >> I am trying to simulate a long linear chain of polymer using CG beads. >> (about 200 beads), all with same type charge interactions. (examples shown:) >> I read on previous gromacs mailing list that linear systems with same >> charges make the system unstable? But is there anyway to go around that? >> > > It's the angles that make the system unstable. One can use virtual sites to > get around the issue. There is a trivial example in a tutorial I wrote: > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html > > The bigger question is whether or not the angles in the molecule impose > linearity, or whether the initial configuration is simply a line of particles > that may deviate according to angle and dihedral potentials. You haven't > shown the [angles] or [dihedrals] directives, so it's not clear what you're > intending, exactly. > >> [atoms] >> 1P3 O1 mon 1 0.00 >> 2P3 O1 mon 2 0.00 >> 3P3 O1 mon 3 0.00 >> 4P3 O1 mon 4 0.00 >> 5P3 O1 mon 5 0.00 >> 6P3 O1 mon 6 0.00 >> 7P3 O1 mon 7 0.00 >> 8P3 O1 mon 8 0.00 >> 9P3 O1 mon 9 0.00 >> ……. >> [ bonds ] >> 12 1 0.4317000 >> 23 1 0.4317000 >> 34 1 0.4317000 >> 45 1 0.4317000 >> …… >> >> However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr >> -it returns the error of: >> Fatal error: >> The largest charge group contains 200 atoms. The maximum is 32. >> For more information and tips for troubleshooting, please check the GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> Please let me know if there is a way to go around that. Thank you. >> > > Do as the error message says and put fewer than 32 atoms in each charge > group. The size of the charge group has implications for neighbor searching > if using a group-based cutoff scheme. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Linear CG beads, grompp doesn't work
On 1/1/13 10:33 PM, Xu Dong Huang wrote: Dear advanced gromac users, I am trying to simulate a long linear chain of polymer using CG beads. (about 200 beads), all with same type charge interactions. (examples shown:) I read on previous gromacs mailing list that linear systems with same charges make the system unstable? But is there anyway to go around that? It's the angles that make the system unstable. One can use virtual sites to get around the issue. There is a trivial example in a tutorial I wrote: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html The bigger question is whether or not the angles in the molecule impose linearity, or whether the initial configuration is simply a line of particles that may deviate according to angle and dihedral potentials. You haven't shown the [angles] or [dihedrals] directives, so it's not clear what you're intending, exactly. [atoms] 1 P3 O1 mon 1 0.00 2 P3 O1 mon 2 0.00 3 P3 O1 mon 3 0.00 4 P3 O1 mon 4 0.00 5 P3 O1 mon 5 0.00 6 P3 O1 mon 6 0.00 7 P3 O1 mon 7 0.00 8 P3 O1 mon 8 0.00 9 P3 O1 mon 9 0.00 ……. [ bonds ] 1 2 1 0.4317000 2 3 1 0.4317000 3 4 1 0.4317000 4 5 1 0.4317000 …… However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr -it returns the error of: Fatal error: The largest charge group contains 200 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please let me know if there is a way to go around that. Thank you. Do as the error message says and put fewer than 32 atoms in each charge group. The size of the charge group has implications for neighbor searching if using a group-based cutoff scheme. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Linear CG beads, grompp doesn't work
Dear advanced gromac users, I am trying to simulate a long linear chain of polymer using CG beads. (about 200 beads), all with same type charge interactions. (examples shown:) I read on previous gromacs mailing list that linear systems with same charges make the system unstable? But is there anyway to go around that? [atoms] 1 P3 O1 mon 1 0.00 2 P3 O1 mon 2 0.00 3 P3 O1 mon 3 0.00 4 P3 O1 mon 4 0.00 5 P3 O1 mon 5 0.00 6 P3 O1 mon 6 0.00 7 P3 O1 mon 7 0.00 8 P3 O1 mon 8 0.00 9 P3 O1 mon 9 0.00 ……. [ bonds ] 1 2 1 0.4317000 2 3 1 0.4317000 3 4 1 0.4317000 4 5 1 0.4317000 …… However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr -it returns the error of: Fatal error: The largest charge group contains 200 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please let me know if there is a way to go around that. Thank you. Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
