Re: [gmx-users] Extract LJ-14 energy
On 1/2/20 6:11 AM, Suvardhan Jonnalagadda wrote: Hi, Thanks for the reply. In the log file I could not find any 'LJ14' term, but 'LJ (SR) term is present. My molecule has 17 atoms, and there are 1-4 interactions. 1.) Is the LJ(SR) term not the same as LJ14, in my case, since I have only one molecule? They are different. Depending on how your topology was constructed, LJ(SR) may encompass LJ14, but they are not equivalent. 2.) Also, how to see what 1-4 interactions gromacs has considered for the calculations? When I calculated for the molecule, manually, the 1-4 LJ contribution is mismatching. Use gmx dump on your .tpr file. 1-4 interactions are computed for topologies with nrexcl = 3 and defined [pairs]. If you did not do this, you have no 1-4 energy term, but it will be computed as part of LJ(SR) unless nrexcl > 3. -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] Extract LJ-14 energy
Hi, Thanks for the reply. In the log file I could not find any 'LJ14' term, but 'LJ (SR) term is present. My molecule has 17 atoms, and there are 1-4 interactions. 1.) Is the LJ(SR) term not the same as LJ14, in my case, since I have only one molecule? 2.) Also, how to see what 1-4 interactions gromacs has considered for the calculations? When I calculated for the molecule, manually, the 1-4 LJ contribution is mismatching. Sorry for late response. Thanks and regards, On Sat, 21 Dec, 2019, 7:04 AM Justin Lemkul, wrote: > > > On 12/20/19 6:07 AM, Suvardhan Jonnalagadda wrote: > > Hi, > > Thanks for the reply. > > I have included it and rerun my system. Still problem prevails. > > energrps are not required for LJ 1-4 energies, as these are > intramolecular and energygrps correspond strictly to intermolecular > interaction energies. > > There is no need for enemat, which in any case is not practical to use > enemat, just extract the energies with gmx energy. As Mark said, if your > topology specifies 1-4 interactions, the energy contribution will be > there. If it's not, there are no 1-4 interactions. > > -Justin > > > > > > > On Fri, 20 Dec, 2019, 7:22 AM Bratin Kumar Das, < > 177cy500.bra...@nitk.edu.in> > > wrote: > > > >> Hi > >> You have to mention energygrous in your .mdp file and rerun the > >> simulation. The details you'll get in gromacs protein- ligand complex > >> tutorial. > >> > >> On Thu 19 Dec, 2019, 11:11 PM Suvardhan Jonnalagadda, < > >> j.su.vard...@gmail.com> wrote: > >> > >>> Hi All, > >>> > >>> *"GROMACS: VERSION 4.5.5; Precision: single"* > >>> I have performed an md simulation for 1 time step, on a single molecule > >>> with 17 atoms. I want to calculate all the energies (angle, dihedrals, > >>> bonds, 1-4 interactions), and compare. However, I am not able to get > the > >>> LJ-14 interactions energy from the '*.edr'* file. When i searched in > the > >>> manual, I came across *'gmx enemat'* command. > >>> I gave the following command > >>> > >>> *'gmx enemat -f nvt_single.edr -groups groups.dat -lj14'* > >>> In the groups.dat I have entered the molecule name (as in the *.itp > >>> *file). > >>> > >>> So, the error and warnings I get after the above command are as > follows: > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> *" group 16WARNING! could not find group Coul-SR:C16-C16 (16,16)in > >> energy > >>> fileWARNING! could not find group LJ-SR:C16-C16 (16,16)in energy > >>> fileWARNING! could not find group LJ-14:C16-C16 (16,16)in energy > fileWill > >>> select half-matrix of energies with 0 elementsLast energy frame read 0 > >>> time0.000Will build energy half-matrix of 17 groups, 0 > >>> elements, over 1 framesSegmentation fault (core dumped) "* > >>> Is this a bug? or am I missing something? > >>> Also, what does 'LJ(SR)' term in the energies include? In my case, I > have > >>> only one molecule. So, what does this LJ short range include? > >>> > >>> Thank you, > >>> > >>> Best regards, > >>> Vardhan > >>> -- > >>> 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. > >> > > -- > == > > 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] Extract LJ-14 energy
On 12/20/19 6:07 AM, Suvardhan Jonnalagadda wrote: Hi, Thanks for the reply. I have included it and rerun my system. Still problem prevails. energrps are not required for LJ 1-4 energies, as these are intramolecular and energygrps correspond strictly to intermolecular interaction energies. There is no need for enemat, which in any case is not practical to use enemat, just extract the energies with gmx energy. As Mark said, if your topology specifies 1-4 interactions, the energy contribution will be there. If it's not, there are no 1-4 interactions. -Justin On Fri, 20 Dec, 2019, 7:22 AM Bratin Kumar Das, <177cy500.bra...@nitk.edu.in> wrote: Hi You have to mention energygrous in your .mdp file and rerun the simulation. The details you'll get in gromacs protein- ligand complex tutorial. On Thu 19 Dec, 2019, 11:11 PM Suvardhan Jonnalagadda, < j.su.vard...@gmail.com> wrote: Hi All, *"GROMACS: VERSION 4.5.5; Precision: single"* I have performed an md simulation for 1 time step, on a single molecule with 17 atoms. I want to calculate all the energies (angle, dihedrals, bonds, 1-4 interactions), and compare. However, I am not able to get the LJ-14 interactions energy from the '*.edr'* file. When i searched in the manual, I came across *'gmx enemat'* command. I gave the following command *'gmx enemat -f nvt_single.edr -groups groups.dat -lj14'* In the groups.dat I have entered the molecule name (as in the *.itp *file). So, the error and warnings I get after the above command are as follows: *" group 16WARNING! could not find group Coul-SR:C16-C16 (16,16)in energy fileWARNING! could not find group LJ-SR:C16-C16 (16,16)in energy fileWARNING! could not find group LJ-14:C16-C16 (16,16)in energy fileWill select half-matrix of energies with 0 elementsLast energy frame read 0 time0.000Will build energy half-matrix of 17 groups, 0 elements, over 1 framesSegmentation fault (core dumped) "* Is this a bug? or am I missing something? Also, what does 'LJ(SR)' term in the energies include? In my case, I have only one molecule. So, what does this LJ short range include? Thank you, Best regards, Vardhan -- 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. -- == 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] Extract LJ-14 energy
Hi, I am facing the same issue in version 5.1.4 as well. I have 1-4 interactions in my system (mentioned 'gen-pair' yes in 'forcefield.itp file) Is there a way to extract the 1-4 interaction energy? Thank you On Fri, Dec 20, 2019 at 2:43 PM Mark Abraham wrote: > Hi, > > On Thu., 19 Dec. 2019, 18:41 Suvardhan Jonnalagadda, < > j.su.vard...@gmail.com> > wrote: > > > Hi All, > > > > *"GROMACS: VERSION 4.5.5; Precision: single"* > > > > This software is nearly a decade old and is no longer supported. Please > update. > > I have performed an md simulation for 1 time step, on a single molecule > > with 17 atoms. I want to calculate all the energies (angle, dihedrals, > > bonds, 1-4 interactions), and compare. However, I am not able to get the > > LJ-14 interactions energy from the '*.edr'* file. > > > The simplest reason would be if the model has none. Or maybe that ancient > version does something buggy. > > When > > > i searched in the > > manual, I came across *'gmx enemat'* command. > > I gave the following command > > > > That won't help if the data was never in the file. > > Mark > > *'gmx enemat -f nvt_single.edr -groups groups.dat -lj14'* > > In the groups.dat I have entered the molecule name (as in the *.itp > > *file). > > > > So, the error and warnings I get after the above command are as follows: > > > > > > > > > > > > > > > > > > > > *" group 16WARNING! could not find group Coul-SR:C16-C16 (16,16)in > energy > > fileWARNING! could not find group LJ-SR:C16-C16 (16,16)in energy > > fileWARNING! could not find group LJ-14:C16-C16 (16,16)in energy fileWill > > select half-matrix of energies with 0 elementsLast energy frame read 0 > > time0.000Will build energy half-matrix of 17 groups, 0 > > elements, over 1 framesSegmentation fault (core dumped) "* > > Is this a bug? or am I missing something? > > Also, what does 'LJ(SR)' term in the energies include? In my case, I have > > only one molecule. So, what does this LJ short range include? > > > > Thank you, > > > > Best regards, > > Vardhan > > -- > > 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. > -- *suvardhan* -- 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] Extract LJ-14 energy
Hi, On Thu., 19 Dec. 2019, 18:41 Suvardhan Jonnalagadda, wrote: > Hi All, > > *"GROMACS: VERSION 4.5.5; Precision: single"* > This software is nearly a decade old and is no longer supported. Please update. I have performed an md simulation for 1 time step, on a single molecule > with 17 atoms. I want to calculate all the energies (angle, dihedrals, > bonds, 1-4 interactions), and compare. However, I am not able to get the > LJ-14 interactions energy from the '*.edr'* file. The simplest reason would be if the model has none. Or maybe that ancient version does something buggy. When > i searched in the > manual, I came across *'gmx enemat'* command. > I gave the following command > That won't help if the data was never in the file. Mark *'gmx enemat -f nvt_single.edr -groups groups.dat -lj14'* > In the groups.dat I have entered the molecule name (as in the *.itp > *file). > > So, the error and warnings I get after the above command are as follows: > > > > > > > > > > *" group 16WARNING! could not find group Coul-SR:C16-C16 (16,16)in energy > fileWARNING! could not find group LJ-SR:C16-C16 (16,16)in energy > fileWARNING! could not find group LJ-14:C16-C16 (16,16)in energy fileWill > select half-matrix of energies with 0 elementsLast energy frame read 0 > time0.000Will build energy half-matrix of 17 groups, 0 > elements, over 1 framesSegmentation fault (core dumped) "* > Is this a bug? or am I missing something? > Also, what does 'LJ(SR)' term in the energies include? In my case, I have > only one molecule. So, what does this LJ short range include? > > Thank you, > > Best regards, > Vardhan > -- > 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] Extract LJ-14 energy
Hi, Thanks for the reply. I have included it and rerun my system. Still problem prevails. On Fri, 20 Dec, 2019, 7:22 AM Bratin Kumar Das, <177cy500.bra...@nitk.edu.in> wrote: > Hi >You have to mention energygrous in your .mdp file and rerun the > simulation. The details you'll get in gromacs protein- ligand complex > tutorial. > > On Thu 19 Dec, 2019, 11:11 PM Suvardhan Jonnalagadda, < > j.su.vard...@gmail.com> wrote: > > > Hi All, > > > > *"GROMACS: VERSION 4.5.5; Precision: single"* > > I have performed an md simulation for 1 time step, on a single molecule > > with 17 atoms. I want to calculate all the energies (angle, dihedrals, > > bonds, 1-4 interactions), and compare. However, I am not able to get the > > LJ-14 interactions energy from the '*.edr'* file. When i searched in the > > manual, I came across *'gmx enemat'* command. > > I gave the following command > > > > *'gmx enemat -f nvt_single.edr -groups groups.dat -lj14'* > > In the groups.dat I have entered the molecule name (as in the *.itp > > *file). > > > > So, the error and warnings I get after the above command are as follows: > > > > > > > > > > > > > > > > > > > > *" group 16WARNING! could not find group Coul-SR:C16-C16 (16,16)in > energy > > fileWARNING! could not find group LJ-SR:C16-C16 (16,16)in energy > > fileWARNING! could not find group LJ-14:C16-C16 (16,16)in energy fileWill > > select half-matrix of energies with 0 elementsLast energy frame read 0 > > time0.000Will build energy half-matrix of 17 groups, 0 > > elements, over 1 framesSegmentation fault (core dumped) "* > > Is this a bug? or am I missing something? > > Also, what does 'LJ(SR)' term in the energies include? In my case, I have > > only one molecule. So, what does this LJ short range include? > > > > Thank you, > > > > Best regards, > > Vardhan > > -- > > 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.
Re: [gmx-users] Extract LJ-14 energy
Hi You have to mention energygrous in your .mdp file and rerun the simulation. The details you'll get in gromacs protein- ligand complex tutorial. On Thu 19 Dec, 2019, 11:11 PM Suvardhan Jonnalagadda, < j.su.vard...@gmail.com> wrote: > Hi All, > > *"GROMACS: VERSION 4.5.5; Precision: single"* > I have performed an md simulation for 1 time step, on a single molecule > with 17 atoms. I want to calculate all the energies (angle, dihedrals, > bonds, 1-4 interactions), and compare. However, I am not able to get the > LJ-14 interactions energy from the '*.edr'* file. When i searched in the > manual, I came across *'gmx enemat'* command. > I gave the following command > > *'gmx enemat -f nvt_single.edr -groups groups.dat -lj14'* > In the groups.dat I have entered the molecule name (as in the *.itp > *file). > > So, the error and warnings I get after the above command are as follows: > > > > > > > > > > *" group 16WARNING! could not find group Coul-SR:C16-C16 (16,16)in energy > fileWARNING! could not find group LJ-SR:C16-C16 (16,16)in energy > fileWARNING! could not find group LJ-14:C16-C16 (16,16)in energy fileWill > select half-matrix of energies with 0 elementsLast energy frame read 0 > time0.000Will build energy half-matrix of 17 groups, 0 > elements, over 1 framesSegmentation fault (core dumped) "* > Is this a bug? or am I missing something? > Also, what does 'LJ(SR)' term in the energies include? In my case, I have > only one molecule. So, what does this LJ short range include? > > Thank you, > > Best regards, > Vardhan > -- > 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.
