Re: [gmx-users] tabulated potential - problem
Sorry, I forgot to change the caption. Gesendet: Montag, 07. September 2015 um 18:14 Uhr Von: "Liz Bell" <lizb...@gmx.at> An: gmx-us...@gromacs.org Betreff: [gmx-users] tabulated potential - problem Dear all, Is there a possibility to plot the intramolecular energy terms? 3. of "Diagnosing an Unstable System" of the page http://www.gromacs.org/Documentation/Terminology/Blowing_Up sounds as if this is possible. Gmx energy only shows the interaction energys of the energy groups but not of the energy terms like angle or dihedrals Any idea? Tank you very much in advance. Best, Liz -- 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] tabulated potential - problem
Dear all, Is there a possibility to plot the intramolecular energy terms? 3. of "Diagnosing an Unstable System" of the page http://www.gromacs.org/Documentation/Terminology/Blowing_Up sounds as if this is possible. Gmx energy only shows the interaction energys of the energy groups but not of the energy terms like angle or dihedrals Any idea? Tank you very much in advance. Best, Liz -- 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] tabulated potential - problem
On 9/7/15 12:14 PM, Liz Bell wrote: Dear all, Is there a possibility to plot the intramolecular energy terms? 3. of "Diagnosing an Unstable System" of the page http://www.gromacs.org/Documentation/Terminology/Blowing_Up sounds as if this is possible. Gmx energy only shows the interaction energys of the energy groups but not of the energy terms like angle or dihedrals Any idea? Internal terms are always printed to the .edr file, irrespective of energygrps, because internal terms are not decomposed. If they aren't showing up in the list of options, that means there are no internals in the topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] tabulated potential - problem
Sorry I did not know how to deal with the fact that I posted my question with a wrong topic. Thank you for your answer. But I do not really understand what you mean. My topology contains those things like bond, angle and dihedral terms: [ bonds ] ;ai aj bondTyp n k 1 2 8 1 1 2 3 8 2 1 [ angles ] ; ai aj ak angleTyp n k 1 2 3 8 1 1 4 5 6 8 1 1 [ dihedrals ] ; ai aj ak al dihedralTyp n k 1 7 10 13 8 0 1 52 55 58 4 8 0 1 but the gmx energy options to chose are only the common ones like ... 6 Potential 7 Kinetic-En. 8 Total-Energy ... and furthermore this: LJ-SR:P_1-P_1 Coul-SR:P_1-P_1 which are the LJ/coulomb short range of my energy group P_1. But it is not possible to calculate the bonded energy between the specific bond ai and aj. Is it possible with any of the gromacs tools to visualise the potential engergy of specific bond types? The potential energy of my system grows further until the system crashes. Considering the simulation until it stops shows that there might be a problem with the bonded potential and therefore I wanted to compute this particular potential energy. Thank you, Liz Gesendet: Montag, 07. September 2015 um 18:37 Uhr Von: "Justin Lemkul" <jalem...@vt.edu> An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] tabulated potential - problem On 9/7/15 12:14 PM, Liz Bell wrote: > Dear all, > Is there a possibility to plot the intramolecular energy terms? > 3. of "Diagnosing an Unstable System" of the page > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > sounds as if this is possible. Gmx energy only shows the interaction energys of > the energy groups but not of the energy terms like > angle or dihedrals > Any idea? Internal terms are always printed to the .edr file, irrespective of energygrps, because internal terms are not decomposed. If they aren't showing up in the list of options, that means there are no internals in the topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] tabulated potential - problem
On 9/7/15 1:04 PM, Liz Bell wrote: Sorry I did not know how to deal with the fact that I posted my question with a wrong topic. Thank you for your answer. But I do not really understand what you mean. My topology contains those things like bond, angle and dihedral terms: [ bonds ] ;ai aj bondTyp nk 128 11 238 21 [ angles ] ; ai aj akangleTyp nk 123 8 11 456 8 11 [ dihedrals ] ; aiaj ak al dihedralTyp nk 17 10 13 801 52 55 584 801 but the gmx energy options to chose are only the common ones like ... 6 Potential7 Kinetic-En. 8 Total-Energy ... It would be helpful if you posted the entire list of choices, rather than some subset. Perhaps bonded terms are off in the case of tabulated potentials, but I've never seen such a thing happen. and furthermore this: LJ-SR:P_1-P_1 Coul-SR:P_1-P_1 which are the LJ/coulomb short range of my energy group P_1. But it is not possible to calculate the bonded energy between the specific bond ai and aj. Is it possible with any of the gromacs tools to visualise the potential engergy of specific bond types? No, but you can calculate it by measuring the distance between the atoms of interest and applying whatever functional form you're using. -Justin The potential energy of my system grows further until the system crashes. Considering the simulation until it stops shows that there might be a problem with the bonded potential and therefore I wanted to compute this particular potential energy. Thank you, Liz *Gesendet:* Montag, 07. September 2015 um 18:37 Uhr *Von:* "Justin Lemkul" <jalem...@vt.edu> *An:* gmx-us...@gromacs.org *Betreff:* Re: [gmx-users] tabulated potential - problem On 9/7/15 12:14 PM, Liz Bell wrote: > Dear all, > Is there a possibility to plot the intramolecular energy terms? > 3. of "Diagnosing an Unstable System" of the page > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > sounds as if this is possible. Gmx energy only shows the interaction energys of > the energy groups but not of the energy terms like > angle or dihedrals > Any idea? Internal terms are always printed to the .edr file, irrespective of energygrps, because internal terms are not decomposed. If they aren't showing up in the list of options, that means there are no internals in the topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] tabulated potential - problem
Thank you very much Justin. I am going to do follow your recommendation and calculate the distance. Gesendet: Montag, 07. September 2015 um 19:20 Uhr Von: "Justin Lemkul" <jalem...@vt.edu> An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] tabulated potential - problem On 9/7/15 1:04 PM, Liz Bell wrote: > Sorry I did not know how to deal with the fact that I posted my question with a > wrong topic. > Thank you for your answer. But I do not really understand what you mean. My > topology contains those things like > bond, angle and dihedral terms: > [ bonds ] > ;ai aj bondTyp n k > 1 2 8 1 1 > 2 3 8 2 1 > [ angles ] > ; ai aj ak angleTyp n k > 1 2 3 8 1 1 > 4 5 6 8 1 1 > [ dihedrals ] > ; ai aj ak al dihedralTyp n k > 1 7 10 13 8 0 1 > 52 55 58 4 8 0 1 > but the gmx energy options to chose are only the common ones like ... 6 > Potential 7 Kinetic-En. 8 Total-Energy ... It would be helpful if you posted the entire list of choices, rather than some subset. Perhaps bonded terms are off in the case of tabulated potentials, but I've never seen such a thing happen. > and furthermore this: > LJ-SR:P_1-P_1 > Coul-SR:P_1-P_1 > which are the LJ/coulomb short range of my energy group P_1. > But it is not possible to calculate the bonded energy between the specific bond > ai and aj. Is it possible with any of the gromacs tools to > visualise the potential engergy of specific bond types? No, but you can calculate it by measuring the distance between the atoms of interest and applying whatever functional form you're using. -Justin > The potential energy of my system grows further until the system crashes. > Considering the simulation until it stops shows that there might be > a problem with the bonded potential and therefore I wanted to compute this > particular potential energy. > Thank you, > Liz > *Gesendet:* Montag, 07. September 2015 um 18:37 Uhr > *Von:* "Justin Lemkul" <jalem...@vt.edu> > *An:* gmx-us...@gromacs.org > *Betreff:* Re: [gmx-users] tabulated potential - problem > > > On 9/7/15 12:14 PM, Liz Bell wrote: > > Dear all, > > Is there a possibility to plot the intramolecular energy terms? > > 3. of "Diagnosing an Unstable System" of the page > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > > sounds as if this is possible. Gmx energy only shows the interaction energys of > > the energy groups but not of the energy terms like > > angle or dihedrals > > Any idea? > > Internal terms are always printed to the .edr file, irrespective of energygrps, > because internal terms are not decomposed. If they aren't showing up in the > list of options, that means there are no internals in the topology. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] tabulated potential - problem
Dear all, I have a question about the handling of the tabulated interactions. I am using tabulated potentials for my simulations. With grompp there is no problem, i.e. no error messages. Running mdrun produces: Fatal error: A tabulated bond interaction table number 1 is out of the table range: r 13.532542, between table indices 135325 and 135326, table length 6 I really do not understand this error. Considering my system it seems to be senseless. The value for r in the first column of my table is ranged from 0 to 6nm with a step size of 0.001nm. My box size is 6nm. So how is it possible that a bonded interaction is greater than the box itselfs? I am actually thinking, that it should be enough that the table is ranged from 0 to 2 or 3nm as the interaction is a bonded one. Or does this error message only occur, because of the fact that my system is crashing - so as a result from an other error in my files? Tank you very much in advance. Best, Liz -- 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] tabulated potential - problem
Hi, This is almost certainly a problem with simulation instability, so please follow the approaches here http://www.gromacs.org/Documentation/Terminology/Blowing_Up to discover more about what is wrong. Mark On Tue, Aug 18, 2015 at 3:09 PM Liz Bell lizb...@gmx.at wrote: Dear all, I have a question about the handling of the tabulated interactions. I am using tabulated potentials for my simulations. With grompp there is no problem, i.e. no error messages. Running mdrun produces: Fatal error: A tabulated bond interaction table number 1 is out of the table range: r 13.532542, between table indices 135325 and 135326, table length 6 I really do not understand this error. Considering my system it seems to be senseless. The value for r in the first column of my table is ranged from 0 to 6nm with a step size of 0.001nm. My box size is 6nm. So how is it possible that a bonded interaction is greater than the box itselfs? I am actually thinking, that it should be enough that the table is ranged from 0 to 2 or 3nm as the interaction is a bonded one. Or does this error message only occur, because of the fact that my system is crashing - so as a result from an other error in my files? Tank you very much in advance. Best, Liz -- 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.
