[gmx-users] Interaction energy between specific residue in a set of residues
Dear all, I am looking how I can extract the interaction energy between specific residue in a set of residues. example: I have DT and DA residues, I would like to plot only the energy of the DT. I can extract the DT with the index file, But I am missing information on how to plot the energy base on my index file where I can select only DT. I was only looking the way to extract the c5-c6 distance of adjacent DT without include DA. I will be very grateful to receive any suggestions I wish you all a wonderful day... Collins -- 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] Interaction energy between specific residue in a set of residues
On 7/31/13 4:20 PM, Collins Nganou wrote: Dear all, I am looking how I can extract the interaction energy between specific residue in a set of residues. Nonbonded energy terms are decomposed using energygrps in the .mdp file along with suitable index groups. example: I have DT and DA residues, I would like to plot only the energy of the DT. I can extract the DT with the index file, But I am missing information on how to plot the energy base on my index file where I can select only DT. You can create index groups for any base or bases you want individually. You haven't shown us what you've done, so it's hard to critique beyond that. I was only looking the way to extract the c5-c6 distance of adjacent DT without include DA. Distances are calculated with g_dist and suitable index groups. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] interaction energy using g_enemat
Dear All, I want to calculate interaction energy per residue. Below is the command i used: g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm my groups.dat file contains these lines: 3 strand1_SER_34 strand1_THR_36 strand1_TYR_37 When i execute the above g_enemat command i get the below error message: WARNING! could not find group LJ-SR:strand1_SER_34 -strand1_THR_36 (34,36)in energy file WARNING! could not find group Coul-SR:strand1_SER_34 -strand1_TYR_37 (34,37)in energy file My strand.edr file looks like this: LJ-SR:strand1_SER_34-strand1_THR_36 Coul-SR:strand1_SER_34-strand1_TYR_37 Please can I get some suggestions on how to get around this problem. Kind Regards, Chetan Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt Das Forschungszentrum oeffnet seine Tueren am Sonntag, 29. September, von 10:00 bis 17:00 Uhr: http://www.tagderneugier.de -- 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] interaction energy using g_enemat
On 7/24/13 7:47 AM, Poojari, Chetan wrote: Dear All, I want to calculate interaction energy per residue. Below is the command i used: g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm my groups.dat file contains these lines: 3 strand1_SER_34 strand1_THR_36 strand1_TYR_37 When i execute the above g_enemat command i get the below error message: WARNING! could not find group LJ-SR:strand1_SER_34 -strand1_THR_36 (34,36)in energy file WARNING! could not find group Coul-SR:strand1_SER_34 -strand1_TYR_37 (34,37)in energy file My strand.edr file looks like this: LJ-SR:strand1_SER_34-strand1_THR_36 Coul-SR:strand1_SER_34-strand1_TYR_37 Please can I get some suggestions on how to get around this problem. I think g_enemat is buggy. People post the same issue or slight variants of it all the time. My version 4.6 installation fares even worse, as group names aren't even recognized (set to 'null' for everything). You can get interaction energies over time using g_energy, but I don't think g_enemat currently functions properly. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] interaction energy
HI I'm simulating gold-protein interaction by gromacs. after MD simulation I want to calculate interaction energy of each aminoacids with AU surface. Enon-bond = E(vdw) + E(elec) gold atoms charge in simulation were considered 0, then E non-bonded=E(vdw) Is this true? The interaction energy is equal to the van der Waals energy? Fatemeh Ramezani -- 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] interaction energy
On 4/18/13 2:00 AM, fatemeh ramezani wrote: HI I'm simulating gold-protein interaction by gromacs. after MD simulation I want to calculate interaction energy of each aminoacids with AU surface. Enon-bond = E(vdw) + E(elec) gold atoms charge in simulation were considered 0, then E non-bonded=E(vdw) Is this true? The interaction energy is equal to the van der Waals energy? If charges are zero, then yes. -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] Interaction energy between two molecules.
Dear Gromacs User, I am simulating two constrained fullerenes to analyze the interaction energy between these two in vacuum. To do that I specified energygrps in .mdp file as CB1 and CB2 which corrospond to the residue name of first and second fullerene respectively. The charge of the atoms of fullerenes are zero. Therefore, only the LJ-SR of CB1-CB2 should be the total interaction energy between these two. My understanding is, this total interaction energy is the combination of both attractive and repulsive term of Lennard-Jones potential. Is there anyway to find only the attraction energy (-C6/r^6) which is contributing to this total interaction energy between these two fullerenes? Or, in other words I would like to know the attractive energy (-C6/r^6) between these two fullerenes. I would really appreciate if anyone can help me. Thanks in advance. Regards, Mortuza -- 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] Interaction energy between two molecules.
On 12/2/12 10:38 PM, Mortuza Munna wrote: Dear Gromacs User, I am simulating two constrained fullerenes to analyze the interaction energy between these two in vacuum. To do that I specified energygrps in .mdp file as CB1 and CB2 which corrospond to the residue name of first and second fullerene respectively. The charge of the atoms of fullerenes are zero. Therefore, only the LJ-SR of CB1-CB2 should be the total interaction energy between these two. My understanding is, this total interaction energy is the combination of both attractive and repulsive term of Lennard-Jones potential. Is there anyway to find only the attraction energy (-C6/r^6) which is contributing to this total interaction energy between these two fullerenes? Or, in other words I would like to know the attractive energy (-C6/r^6) between these two fullerenes. I would really appreciate if anyone can help me. The approach that comes to mind is to create a custom topology in which the relevant C6 or C12 parameters are alternatively set to zero. You can then create new .tpr files that have either only attractive or only repulsive terms. Then use the mdrun -rerun feature with this new .tpr file and the existing trajectory file to have the energies recalculated. -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] Interaction energy..
Hi justin, As per your advice, g_enemat -f ener.edr -groups groups.dat -nocoul -nolj Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 0 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames Segmentation fault (core dumped) What is the reason ??? thank you in advance. With best wishes and regards Rama david. On Sat, Oct 6, 2012 at 6:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/6/12 6:26 AM, rama david wrote: Hi justin, I tried as per your suggestion. command line g_enemat -f ener.edr -groups groups.dat -temp 310 -nolj -free the out put is like , Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 3 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames Segmentation fault (core dumped) why program not work ?? Is it bug??? or Am I doing any stupid mistake??? It might be a bug, but I'm not sure yet. Please run the command without the -free option (and thus without -temp) to further reduce complexity. Then manually add the -coul flag. It should be set by default, but at this point the screen output seems to indicate that no energy terms are being detected. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Interaction energy..
On 10/8/12 5:40 AM, rama david wrote: Hi justin, As per your advice, g_enemat -f ener.edr -groups groups.dat -nocoul -nolj Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 0 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames Segmentation fault (core dumped) What is the reason ??? I told you to add the -coul flag, not -nocoul. With the above command, you're explicitly telling g_enemat to not do anything useful. -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] Interaction energy..
Hi justin, I correct command as follow and g_enemat -f ener.edr -groups groups.dat -coul -lj out-put is like Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 9 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 9 elements, over 50001 frames Segmentation fault (core dumped) On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/8/12 5:40 AM, rama david wrote: Hi justin, As per your advice, g_enemat -f ener.edr -groups groups.dat -nocoul -nolj Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 0 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames Segmentation fault (core dumped) What is the reason ??? I told you to add the -coul flag, not -nocoul. With the above command, you're explicitly telling g_enemat to not do anything useful. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Interaction energy..
On 10/8/12 6:00 AM, rama david wrote: Hi justin, I correct command as follow and g_enemat -f ener.edr -groups groups.dat -coul -lj out-put is like Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 9 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 9 elements, over 50001 frames Segmentation fault (core dumped) Let me be a bit more specific again. I previously suggested there was a problem with the -lj flag activating more than one option in the code, so that is a potential problem. I suggested adding -nolj -coul to test this theory. Please use those options (not -coul -lj) and see what happens. -Justin On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/8/12 5:40 AM, rama david wrote: Hi justin, As per your advice, g_enemat -f ener.edr -groups groups.dat -nocoul -nolj Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 0 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames Segmentation fault (core dumped) What is the reason ??? I told you to add the -coul flag, not -nocoul. With the above command, you're explicitly telling g_enemat to not do anything useful. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Interaction energy..
Hi justin, g_enemat -f ener.edr -groups groups.dat -coul -nolj Out-put is like Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 3 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames Segmentation fault (core dumped) Thank you in advance Rama david. Let me be a bit more specific again. I previously suggested there was a problem with the -lj flag activating more than one option in the code, so that is a potential problem. I suggested adding -nolj -coul to test this theory. Please use those options (not -coul -lj) and see what happens. -Justin On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/8/12 5:40 AM, rama david wrote: Hi justin, As per your advice, g_enemat -f ener.edr -groups groups.dat -nocoul -nolj Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 0 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames Segmentation fault (core dumped) What is the reason ??? I told you to add the -coul flag, not -nocoul. With the above command, you're explicitly telling g_enemat to not do anything useful. -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/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Interaction energy..
On 10/8/12 7:09 AM, rama david wrote: Hi justin, g_enemat -f ener.edr -groups groups.dat -coul -nolj Out-put is like Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 3 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames Segmentation fault (core dumped) At this point, I honestly have no idea why it's not working. If you want me to try to debug the issue a bit, you can send me the .edr file (off-list) if it can be sent via email. If it is too large of a file, use eneconv to cut down some frames. -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] Interaction energy..
Hi justin, the out put of g_energy are like - 1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Kinetic-En. 13 Total-Energy14 Temperature 15 Pres.-DC16 Pressure 17 Constr.-rmsd18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X48 Mu-Y 49 Mu-Z50 Coul-SR:energy-energy 51 LJ-SR:energy-energy 52 LJ-LR:energy-energy 53 Coul-14:energy-energy 54 LJ-14:energy-energy 55 Coul-SR:energy-extra34 56 LJ-SR:energy-extra34 57 LJ-LR:energy-extra3458 Coul-14:energy-extra34 59 LJ-14:energy-extra3460 Coul-SR:energy-rest 61 LJ-SR:energy-rest 62 LJ-LR:energy-rest 63 Coul-14:energy-rest 64 LJ-14:energy-rest 65 Coul-SR:extra34-extra34 66 LJ-SR:extra34-extra34 67 LJ-LR:extra34-extra34 68 Coul-14:extra34-extra34 69 LJ-14:extra34-extra34 70 Coul-SR:extra34-rest 71 LJ-SR:extra34-rest 72 LJ-LR:extra34-rest 73 Coul-14:extra34-rest74 LJ-14:extra34-rest 75 Coul-SR:rest-rest 76 LJ-SR:rest-rest 77 LJ-LR:rest-rest 78 Coul-14:rest-rest 79 LJ-14:rest-rest 80 T-Protein 81 T-non-Protein 82 Lamb-Protein 83 Lamb-non-Protein When I used g_enemat with the groups.dat file like these 2 extra34 energy I got the output roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy file WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file WARNING! could not find group (null):extra34-energy (0,1)in energy file group 1WARNING! could not find group (null):energy-energy (1,1)in energy file Will select half-matrix of energies with 4 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames Segmentation fault (core dumped) Now When I changed the groups.dat like 2 energy extra34 ( change in the order of the index groups ) I got the following output, Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 6 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames Segmentation fault (core dumped) So What is wrong ?? Is I am doing any wrong ?? 2. I am using the temp 310 so the reference temp by default is 300 Should I have to change it to 310 (-tempreal 300 reference temperature for free energy calculation ) Any suggestion on these topic, is helpful to me. Thank you in advance, With best wishes and regards, Rama david. -- 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] Interaction energy..
On 10/6/12 2:28 AM, rama david wrote: Hi justin, the out put of g_energy are like - 1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Kinetic-En. 13 Total-Energy14 Temperature 15 Pres.-DC16 Pressure 17 Constr.-rmsd18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X48 Mu-Y 49 Mu-Z50 Coul-SR:energy-energy 51 LJ-SR:energy-energy 52 LJ-LR:energy-energy 53 Coul-14:energy-energy 54 LJ-14:energy-energy 55 Coul-SR:energy-extra34 56 LJ-SR:energy-extra34 57 LJ-LR:energy-extra3458 Coul-14:energy-extra34 59 LJ-14:energy-extra3460 Coul-SR:energy-rest 61 LJ-SR:energy-rest 62 LJ-LR:energy-rest 63 Coul-14:energy-rest 64 LJ-14:energy-rest 65 Coul-SR:extra34-extra34 66 LJ-SR:extra34-extra34 67 LJ-LR:extra34-extra34 68 Coul-14:extra34-extra34 69 LJ-14:extra34-extra34 70 Coul-SR:extra34-rest 71 LJ-SR:extra34-rest 72 LJ-LR:extra34-rest 73 Coul-14:extra34-rest74 LJ-14:extra34-rest 75 Coul-SR:rest-rest 76 LJ-SR:rest-rest 77 LJ-LR:rest-rest 78 Coul-14:rest-rest 79 LJ-14:rest-rest 80 T-Protein 81 T-non-Protein 82 Lamb-Protein 83 Lamb-non-Protein When I used g_enemat with the groups.dat file like these 2 extra34 energy I got the output roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy file WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file WARNING! could not find group (null):extra34-energy (0,1)in energy file group 1WARNING! could not find group (null):energy-energy (1,1)in energy file Will select half-matrix of energies with 4 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames Segmentation fault (core dumped) Now When I changed the groups.dat like 2 energy extra34 ( change in the order of the index groups ) I got the following output, Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 6 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames Segmentation fault (core dumped) Based on the energy names, this is the appropriate setup, but unfortunately I have no idea why it does not work. I have noticed that there is a problem with g_enemat - the -lj flag specifies both LJ-SR and LJ-LR terms to be written - which may be complicating matters. Please try your command with -nolj to test. So What is wrong ?? Is I am doing any wrong ?? 2. I am using the temp 310 so the reference temp by default is 300 Should I have to change it to 310 (-tempreal 300 reference temperature for free energy calculation ) As stated in the description, the -temp option is for free energy calculations. Are you requesting a free energy calculation? You haven't provided your command line. -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] Interaction energy..
Hi justin, I tried as per your suggestion. command line g_enemat -f ener.edr -groups groups.dat -temp 310 -nolj -free the out put is like , Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 3 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames Segmentation fault (core dumped) why program not work ?? Is it bug??? or Am I doing any stupid mistake??? Thank you in advance .. With best wishes and regards, Rama david On Sat, Oct 6, 2012 at 3:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/6/12 2:28 AM, rama david wrote: Hi justin, the out put of g_energy are like --**--**- 1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Kinetic-En. 13 Total-Energy14 Temperature 15 Pres.-DC16 Pressure 17 Constr.-rmsd18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X48 Mu-Y 49 Mu-Z50 Coul-SR:energy-energy 51 LJ-SR:energy-energy 52 LJ-LR:energy-energy 53 Coul-14:energy-energy 54 LJ-14:energy-energy 55 Coul-SR:energy-extra34 56 LJ-SR:energy-extra34 57 LJ-LR:energy-extra3458 Coul-14:energy-extra34 59 LJ-14:energy-extra3460 Coul-SR:energy-rest 61 LJ-SR:energy-rest 62 LJ-LR:energy-rest 63 Coul-14:energy-rest 64 LJ-14:energy-rest 65 Coul-SR:extra34-extra34 66 LJ-SR:extra34-extra34 67 LJ-LR:extra34-extra34 68 Coul-14:extra34-extra34 69 LJ-14:extra34-extra34 70 Coul-SR:extra34-rest 71 LJ-SR:extra34-rest 72 LJ-LR:extra34-rest 73 Coul-14:extra34-rest74 LJ-14:extra34-rest 75 Coul-SR:rest-rest 76 LJ-SR:rest-rest 77 LJ-LR:rest-rest 78 Coul-14:rest-rest 79 LJ-14:rest-rest 80 T-Protein 81 T-non-Protein 82 Lamb-Protein 83 Lamb-non-Protein When I used g_enemat with the groups.dat file like these 2 extra34 energy I got the output roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy file WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file WARNING! could not find group (null):extra34-energy (0,1)in energy file group 1WARNING! could not find group (null):energy-energy (1,1)in energy file Will select half-matrix of energies with 4 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames Segmentation fault (core dumped) Now When I changed the groups.dat like 2 energy extra34 ( change in the order of the index groups ) I got the following output, Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 6 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames Segmentation fault (core dumped) Based on the energy names, this is the appropriate setup, but unfortunately I have no idea why it does not work. I have noticed that there is a problem with g_enemat - the -lj flag specifies both LJ-SR and LJ-LR terms to be written - which may be complicating matters. Please try your command with -nolj to test. So What is wrong ?? Is I am doing any wrong ?? 2. I am using the temp 310 so the reference temp by default is 300 Should I have to change it to 310 (-tempreal 300
Re: [gmx-users] Interaction energy..
On 10/6/12 6:26 AM, rama david wrote: Hi justin, I tried as per your suggestion. command line g_enemat -f ener.edr -groups groups.dat -temp 310 -nolj -free the out put is like , Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 3 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames Segmentation fault (core dumped) why program not work ?? Is it bug??? or Am I doing any stupid mistake??? It might be a bug, but I'm not sure yet. Please run the command without the -free option (and thus without -temp) to further reduce complexity. Then manually add the -coul flag. It should be set by default, but at this point the screen output seems to indicate that no energy terms are being detected. -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] Interaction energy calculation..
On 10/5/12 5:49 AM, rama david wrote: Hi Friends, I want to study the interaction energy between the selected residues of protein and ligand. ( Non-bonded energy should include : vanderwall and electrostatics) How to do it??? This is what the energygrps keyword in the .mdp file is for. Beware the interpretation and utility of these quantities. -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] Interaction energy calculation..
Hi justin, I completed the simulation , Now I want to use the selected residues of protein and ligand. How to do it Would you explain me in detail?? With best wishes and regards, Rama david. On Fri, Oct 5, 2012 at 3:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/5/12 5:49 AM, rama david wrote: Hi Friends, I want to study the interaction energy between the selected residues of protein and ligand. ( Non-bonded energy should include : vanderwall and electrostatics) How to do it??? This is what the energygrps keyword in the .mdp file is for. Beware the interpretation and utility of these quantities. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Interaction energy calculation..
On 10/5/12 6:15 AM, rama david wrote: Hi justin, I completed the simulation , Now I want to use the selected residues of protein and ligand. How to do it Would you explain me in detail?? Create a new .tpr file from an .mdp file with suitable energygrps. Use mdrun -rerun to recalculate energies. -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] Interaction energy calculation..
Hi justin, thank you for reply. With best wishes and regards Rama david. On Fri, Oct 5, 2012 at 4:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/5/12 6:15 AM, rama david wrote: Hi justin, I completed the simulation , Now I want to use the selected residues of protein and ligand. How to do it Would you explain me in detail?? Create a new .tpr file from an .mdp file with suitable energygrps. Use mdrun -rerun to recalculate energies. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Interaction energy..
On 10/5/12 10:16 AM, rama david wrote: Hi gromacs friends, I completed the simulation of receptor and ligand, I visualized the trajectory in the vmd I found most of the time C terminal (ARG) interact with receptor ( 320 ASP) . I want to find out these interaction energy between these two residues in the simulation. How to find these interaction energy ( include the LJ and electrostatic interaction).. I explained how to do this already. You need properly set energygrps in the .mdp file and an index file that specifies those groups. The quantities you want will then be in the .edr file like all other energy terms. -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] Interaction energy..
Thank you for your Help. I did the following tc-groups tcoupl= V-rescale; modified Berendsen thermostat tc-grps= extra34 Non-Protein energy; two coupling groups - more accurate tau_t= 0.10.1 0.1; time constant, in ps ref_t= 310310 310 ; reference temperature, one for each group, in K ; Energy contain the residues that i needed extra34 contain all the remaining ligand and receptor atom non-protein contain sol and ion. I got the energy file after mdrun -rerun I used the g_energy term It give me the following output End your selection with an empty line or a zero. --- 1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Kinetic-En. 13 Total-Energy14 Temperature 15 Pres.-DC16 Pressure 17 Constr.-rmsd18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X48 Mu-Y 49 Mu-Z50 T-extra34 51 T-non-Protein 52 T-energy 53 Lamb-extra3454 Lamb-non-Protein 55 Lamb-energy So I confused. though it shows the energy group, which option should i have to choose ?? What is Lamb-energy??? Is I did any mistake??? or I have to use any else command ?? Thank you in advance With best wishes and regards. Rama david. On Fri, Oct 5, 2012 at 7:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/5/12 10:16 AM, rama david wrote: Hi gromacs friends, I completed the simulation of receptor and ligand, I visualized the trajectory in the vmd I found most of the time C terminal (ARG) interact with receptor ( 320 ASP) . I want to find out these interaction energy between these two residues in the simulation. How to find these interaction energy ( include the LJ and electrostatic interaction).. I explained how to do this already. You need properly set energygrps in the .mdp file and an index file that specifies those groups. The quantities you want will then be in the .edr file like all other energy terms. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Interaction energy..
On 10/5/12 11:46 AM, rama david wrote: Thank you for your Help. I did the following tc-groups tcoupl= V-rescale; modified Berendsen thermostat tc-grps= extra34 Non-Protein energy; two coupling groups - more accurate tau_t= 0.10.1 0.1; time constant, in ps ref_t= 310310 310 ; reference temperature, one for each group, in K ; Energy contain the residues that i needed extra34 contain all the remaining ligand and receptor atom non-protein contain sol and ion. I got the energy file after mdrun -rerun I used the g_energy term It give me the following output End your selection with an empty line or a zero. --- 1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Kinetic-En. 13 Total-Energy14 Temperature 15 Pres.-DC16 Pressure 17 Constr.-rmsd18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X48 Mu-Y 49 Mu-Z50 T-extra34 51 T-non-Protein 52 T-energy 53 Lamb-extra3454 Lamb-non-Protein 55 Lamb-energy So I confused. though it shows the energy group, which option should i have to choose ?? What is Lamb-energy??? It is related to temperature coupling. Is I did any mistake??? or I have to use any else command ?? I have told you to use energygrps (which is described in the manual) and you're specifying tc-grps. Temperature coupling and energy calculation groups are very different concepts. -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] Interaction energy..
Hi justin, Ok now I get I have to modify mdp parameter .. Thank you, With best wishes and regards, Rama david On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/5/12 11:46 AM, rama david wrote: Thank you for your Help. I did the following tc-groups tcoupl= V-rescale; modified Berendsen thermostat tc-grps= extra34 Non-Protein energy; two coupling groups - more accurate tau_t= 0.10.1 0.1; time constant, in ps ref_t= 310310 310 ; reference temperature, one for each group, in K ; Energy contain the residues that i needed extra34 contain all the remaining ligand and receptor atom non-protein contain sol and ion. I got the energy file after mdrun -rerun I used the g_energy term It give me the following output End your selection with an empty line or a zero. --**--**--- 1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Kinetic-En. 13 Total-Energy14 Temperature 15 Pres.-DC16 Pressure 17 Constr.-rmsd18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X48 Mu-Y 49 Mu-Z50 T-extra34 51 T-non-Protein 52 T-energy 53 Lamb-extra3454 Lamb-non-Protein 55 Lamb-energy So I confused. though it shows the energy group, which option should i have to choose ?? What is Lamb-energy??? It is related to temperature coupling. Is I did any mistake??? or I have to use any else command ?? I have told you to use energygrps (which is described in the manual) and you're specifying tc-grps. Temperature coupling and energy calculation groups are very different concepts. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Interaction energy..
Hi, I got the result by g_energy. Thank you for these . but when I used g_enemat with the edr file ( out put from mdrun -rerun ) g_enemat -f ener.edr -groups groups.dat i got following out put roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy file WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file WARNING! could not find group (null):extra34-energy (0,1)in energy file group 1WARNING! could not find group (null):energy-energy (1,1)in energy file Will select half-matrix of energies with 4 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames Segmentation fault (core dumped) i used the following groups.dat file 2 extra34 energy What is reason for the error ?? Is I did any mistake again?? Thank you in advance. With best wishes and regards, Rama david On Fri, Oct 5, 2012 at 10:32 PM, rama david ramadavidgr...@gmail.comwrote: Hi justin, Ok now I get I have to modify mdp parameter .. Thank you, With best wishes and regards, Rama david On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/5/12 11:46 AM, rama david wrote: Thank you for your Help. I did the following tc-groups tcoupl= V-rescale; modified Berendsen thermostat tc-grps= extra34 Non-Protein energy; two coupling groups - more accurate tau_t= 0.10.1 0.1; time constant, in ps ref_t= 310310 310 ; reference temperature, one for each group, in K ; Energy contain the residues that i needed extra34 contain all the remaining ligand and receptor atom non-protein contain sol and ion. I got the energy file after mdrun -rerun I used the g_energy term It give me the following output End your selection with an empty line or a zero. --**--**--- 1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Kinetic-En. 13 Total-Energy14 Temperature 15 Pres.-DC16 Pressure 17 Constr.-rmsd18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X48 Mu-Y 49 Mu-Z50 T-extra34 51 T-non-Protein 52 T-energy 53 Lamb-extra3454 Lamb-non-Protein 55 Lamb-energy So I confused. though it shows the energy group, which option should i have to choose ?? What is Lamb-energy??? It is related to temperature coupling. Is I did any mistake??? or I have to use any else command ?? I have told you to use energygrps (which is described in the manual) and you're specifying tc-grps. Temperature coupling and energy calculation groups are very different concepts. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Interaction energy..
On 10/5/12 1:26 PM, rama david wrote: Hi, I got the result by g_energy. Thank you for these . but when I used g_enemat with the edr file ( out put from mdrun -rerun ) g_enemat -f ener.edr -groups groups.dat i got following out put roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy file WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file WARNING! could not find group (null):extra34-energy (0,1)in energy file group 1WARNING! could not find group (null):energy-energy (1,1)in energy file Will select half-matrix of energies with 4 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames Segmentation fault (core dumped) i used the following groups.dat file 2 extra34 energy What is reason for the error ?? Is I did any mistake again?? It seems as though the requested energy groups do not exist, though if you have obtained quantities through g_energy, this doesn't make much sense. Can you please provide the list of energy terms in the .edr file (from the g_energy screen output)? -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] Interaction energy
On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? For such information, you have to specify these groups as energygrps in the .mdp file. You can rerun the trajectory using mdrun -rerun and a new .tpr file specifying these groups, but depending on the output frequency, the result may not be as accurate as you'd like. -Justin Thank you Justin. Now I have two groups sepcified in my mdp file: energygrps = Protein LIG How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues: 91GLY 92TYR . 161LIG 162LIG... Will it be correct like this energygrps = 91GLY 92 TYR ... 161LIG 162LIG... If yes, will this simulation take longer? Thank you Steven -- 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] Interaction energy
Steven Neumann wrote: On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? For such information, you have to specify these groups as energygrps in the .mdp file. You can rerun the trajectory using mdrun -rerun and a new .tpr file specifying these groups, but depending on the output frequency, the result may not be as accurate as you'd like. -Justin Thank you Justin. Now I have two groups sepcified in my mdp file: energygrps = Protein LIG How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues: 91GLY 92TYR . 161LIG 162LIG... Will it be correct like this energygrps = 91GLY 92 TYR ... 161LIG 162LIG... No. The names must correspond to valid groups in an index file. If yes, will this simulation take longer? Thank you Perhaps, but certainly your energy file will be considerably larger. -Justin Steven -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Interaction energy
On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? For such information, you have to specify these groups as energygrps in the .mdp file. You can rerun the trajectory using mdrun -rerun and a new .tpr file specifying these groups, but depending on the output frequency, the result may not be as accurate as you'd like. -Justin Thank you Justin. Now I have two groups sepcified in my mdp file: energygrps = Protein LIG How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues: 91GLY 92TYR . 161LIG 162LIG... Will it be correct like this energygrps = 91GLY 92 TYR ... 161LIG 162LIG... No. The names must correspond to valid groups in an index file. So do you mean that that I should add my index file with grompp -f md.mdp -c npt.gro -n *index.ndx* -t npt.cpt -p topol.top -o md.tpr with specified groups in md.mdp file like they are specified in index file? :) Then just to mdrun -rerun -deffnm md2 Please, let me know whether I am correct or not. Steven If yes, will this simulation take longer? Thank you Perhaps, but certainly your energy file will be considerably larger. -Justin Steven -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Interaction energy
Steven Neumann wrote: On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? For such information, you have to specify these groups as energygrps in the .mdp file. You can rerun the trajectory using mdrun -rerun and a new .tpr file specifying these groups, but depending on the output frequency, the result may not be as accurate as you'd like. -Justin Thank you Justin. Now I have two groups sepcified in my mdp file: energygrps = Protein LIG How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues: 91GLY 92TYR . 161LIG 162LIG... Will it be correct like this energygrps = 91GLY 92 TYR ... 161LIG 162LIG... No. The names must correspond to valid groups in an index file. So do you mean that that I should add my index file with grompp -f md.mdp -c npt.gro -n *index.ndx* -t npt.cpt -p topol.top -o md.tpr with specified groups in md.mdp file like they are specified in index file? :) Then just to mdrun -rerun -deffnm md2 Please, let me know whether I am correct or not. Yes. -Justin Steven If yes, will this simulation take longer? Thank you Perhaps, but certainly your energy file will be considerably larger. -Justin Steven -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Interaction energy
Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? Thank you, Steven -- 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] Interaction energy
Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? For such information, you have to specify these groups as energygrps in the .mdp file. You can rerun the trajectory using mdrun -rerun and a new .tpr file specifying these groups, but depending on the output frequency, the result may not be as accurate as you'd like. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] interaction energy
Dear Users ! Now i am able to do the protein solvent interaction ! thanks ! i have understood ! when i used the energygrps , when i used the g_energy -f em.edr this command it prints all terms and asks to make selection as below, 1 Bond 2 Angle3 Proper-Dih. 4 Ryckaert-Bell. 5 LJ-146 Coulomb-14 7 LJ-(SR) 8 LJ-(LR) 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Pressure 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X 33 Mu-Y34 Mu-Z 35 Coul-SR:Protein-Protein 36 LJ-SR:Protein-Protein 37 LJ-LR:Protein-Protein 38 Coul-14:Protein-Protein 39 LJ-14:Protein-Protein 40 Coul-SR:Protein-SOL 41 LJ-SR:Protein-SOL 42 LJ-LR:Protein-SOL 43 Coul-14:Protein-SOL 44 LJ-14:Protein-SOL 45 Coul-SR:SOL-SOL 46 LJ-SR:SOL-SOL 47 LJ-LR:SOL-SOL 48 Coul-14:SOL-SOL 49 LJ-14:SOL-SOL 50 T-rest --- how one can write this all to a file ! thanks in advance ! -- 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] interaction energy
balaji nagarajan wrote: Dear Users ! Now i am able to do the protein solvent interaction ! thanks ! i have understood ! when i used the energygrps , when i used the g_energy -f em.edr this command it prints all terms and asks to make selection as below, 1 Bond 2 Angle3 Proper-Dih. 4 Ryckaert-Bell. 5 LJ-146 Coulomb-14 7 LJ-(SR) 8 LJ-(LR) 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Pressure 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X 33 Mu-Y34 Mu-Z 35 Coul-SR:Protein-Protein 36 LJ-SR:Protein-Protein 37 LJ-LR:Protein-Protein 38 Coul-14:Protein-Protein 39 LJ-14:Protein-Protein 40 Coul-SR:Protein-SOL 41 LJ-SR:Protein-SOL 42 LJ-LR:Protein-SOL 43 Coul-14:Protein-SOL 44 LJ-14:Protein-SOL 45 Coul-SR:SOL-SOL 46 LJ-SR:SOL-SOL 47 LJ-LR:SOL-SOL 48 Coul-14:SOL-SOL 49 LJ-14:SOL-SOL 50 T-rest --- how one can write this all to a file ! As prompted by g_energy: Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. Writing all terms to the same output file will result in nothing but an incoherent mess. Choose terms wisely based on what you actually need to analyze. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] interaction energy
Dear Users ! i would like to do this to a set of files ! so how to print the required values in the text mode or is there any flag for this in g_energy , thanks in advance Date: Fri, 1 Jul 2011 13:40:28 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] interaction energy balaji nagarajan wrote: Dear Users ! Now i am able to do the protein solvent interaction ! thanks ! i have understood ! when i used the energygrps , when i used the g_energy -f em.edr this command it prints all terms and asks to make selection as below, 1 Bond 2 Angle3 Proper-Dih. 4 Ryckaert-Bell. 5 LJ-146 Coulomb-14 7 LJ-(SR) 8 LJ-(LR) 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Pressure 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X 33 Mu-Y34 Mu-Z 35 Coul-SR:Protein-Protein 36 LJ-SR:Protein-Protein 37 LJ-LR:Protein-Protein 38 Coul-14:Protein-Protein 39 LJ-14:Protein-Protein 40 Coul-SR:Protein-SOL 41 LJ-SR:Protein-SOL 42 LJ-LR:Protein-SOL 43 Coul-14:Protein-SOL 44 LJ-14:Protein-SOL 45 Coul-SR:SOL-SOL 46 LJ-SR:SOL-SOL 47 LJ-LR:SOL-SOL 48 Coul-14:SOL-SOL 49 LJ-14:SOL-SOL 50 T-rest --- how one can write this all to a file ! As prompted by g_energy: Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. Writing all terms to the same output file will result in nothing but an incoherent mess. Choose terms wisely based on what you actually need to analyze. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] interaction energy
balaji nagarajan wrote: Dear Users ! i would like to do this to a set of files ! so how to print the required values in the text mode or is there any flag for this in I quoted the help description for how to do this. Is there some problem? For instance, if you want to write the potential energy to an .xvg file, type: 11 0 and hit Enter. The values will be printed. -Justin g_energy , thanks in advance Date: Fri, 1 Jul 2011 13:40:28 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] interaction energy balaji nagarajan wrote: Dear Users ! Now i am able to do the protein solvent interaction ! thanks ! i have understood ! when i used the energygrps , when i used the g_energy -f em.edr this command it prints all terms and asks to make selection as below, 1 Bond 2 Angle 3 Proper-Dih. 4 Ryckaert-Bell. 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 LJ-(LR) 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Pressure 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X 33 Mu-Y 34 Mu-Z 35 Coul-SR:Protein-Protein 36 LJ-SR:Protein-Protein 37 LJ-LR:Protein-Protein 38 Coul-14:Protein-Protein 39 LJ-14:Protein-Protein 40 Coul-SR:Protein-SOL 41 LJ-SR:Protein-SOL 42 LJ-LR:Protein-SOL 43 Coul-14:Protein-SOL 44 LJ-14:Protein-SOL 45 Coul-SR:SOL-SOL 46 LJ-SR:SOL-SOL 47 LJ-LR:SOL-SOL 48 Coul-14:SOL-SOL 49 LJ-14:SOL-SOL 50 T-rest --- how one can write this all to a file ! As prompted by g_energy: Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. Writing all terms to the same output file will result in nothing but an incoherent mess. Choose terms wisely based on what you actually need to analyze. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list gmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] interaction energy
Dear users ! thanks for the reply I was able to do that , otherwise we can select the number of the option one by one and enter then after that if we leave a empty line and enter it gives all the needed energy terms ! my intension is not to do like this is it possible to give it along the g_energy like g_energy -f em.edr --- ( any options can be given along with this , i tried g_energy -f em.edr 11 0 ( it is not working ) how it can be done ? Date: Fri, 1 Jul 2011 13:53:59 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] interaction energy balaji nagarajan wrote: Dear Users ! i would like to do this to a set of files ! so how to print the required values in the text mode or is there any flag for this in I quoted the help description for how to do this. Is there some problem? For instance, if you want to write the potential energy to an .xvg file, type: 11 0 and hit Enter. The values will be printed. -Justin g_energy , thanks in advance Date: Fri, 1 Jul 2011 13:40:28 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] interaction energy balaji nagarajan wrote: Dear Users ! Now i am able to do the protein solvent interaction ! thanks ! i have understood ! when i used the energygrps , when i used the g_energy -f em.edr this command it prints all terms and asks to make selection as below, 1 Bond 2 Angle 3 Proper-Dih. 4 Ryckaert-Bell. 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 LJ-(LR) 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Pressure 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X 33 Mu-Y 34 Mu-Z 35 Coul-SR:Protein-Protein 36 LJ-SR:Protein-Protein 37 LJ-LR:Protein-Protein 38 Coul-14:Protein-Protein 39 LJ-14:Protein-Protein 40 Coul-SR:Protein-SOL 41 LJ-SR:Protein-SOL 42 LJ-LR:Protein-SOL 43 Coul-14:Protein-SOL 44 LJ-14:Protein-SOL 45 Coul-SR:SOL-SOL 46 LJ-SR:SOL-SOL 47 LJ-LR:SOL-SOL 48 Coul-14:SOL-SOL 49 LJ-14:SOL-SOL 50 T-rest --- how one can write this all to a file ! As prompted by g_energy: Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. Writing all terms to the same output file will result in nothing but an incoherent mess. Choose terms wisely based on what you actually need to analyze. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list gmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] interaction energy
balaji nagarajan wrote: Dear users ! thanks for the reply I was able to do that , otherwise we can select the number of the option one by one and enter then after that if we leave a empty line and enter it gives all the needed energy terms ! my intension is not to do like this is it possible to give it along the g_energy like g_energy -f em.edr --- ( any options can be given along with this , i tried g_energy -f em.edr 11 0 ( it is not working ) how it can be done ? http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive -Justin Date: Fri, 1 Jul 2011 13:53:59 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] interaction energy balaji nagarajan wrote: Dear Users ! i would like to do this to a set of files ! so how to print the required values in the text mode or is there any flag for this in I quoted the help description for how to do this. Is there some problem? For instance, if you want to write the potential energy to an .xvg file, type: 11 0 and hit Enter. The values will be printed. -Justin g_energy , thanks in advance Date: Fri, 1 Jul 2011 13:40:28 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] interaction energy balaji nagarajan wrote: Dear Users ! Now i am able to do the protein solvent interaction ! thanks ! i have understood ! when i used the energygrps , when i used the g_energy -f em.edr this command it prints all terms and asks to make selection as below, 1 Bond 2 Angle 3 Proper-Dih. 4 Ryckaert-Bell. 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 LJ-(LR) 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Pressure 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X 33 Mu-Y 34 Mu-Z 35 Coul-SR:Protein-Protein 36 LJ-SR:Protein-Protein 37 LJ-LR:Protein-Protein 38 Coul-14:Protein-Protein 39 LJ-14:Protein-Protein 40 Coul-SR:Protein-SOL 41 LJ-SR:Protein-SOL 42 LJ-LR:Protein-SOL 43 Coul-14:Protein-SOL 44 LJ-14:Protein-SOL 45 Coul-SR:SOL-SOL 46 LJ-SR:SOL-SOL 47 LJ-LR:SOL-SOL 48 Coul-14:SOL-SOL 49 LJ-14:SOL-SOL 50 T-rest --- how one can write this all to a file ! As prompted by g_energy: Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. Writing all terms to the same output file will result in nothing but an incoherent mess. Choose terms wisely based on what you actually need to analyze. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list gmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list gmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] Interaction energy
Dear all, I have simulated a small peptide (+2 charge at pH=7) in water. Then i calculate the interaction energy using energy_grps = Protein SOL. The value of different energy terms are as follows: Coul-SR:SOL_CL--Protein: -1290 (KJ/mol) LJ-SR:SOL_CL--Protein: -157 (KJ/mol) LJ-LR:SOL_CL--Protein: -13 (KJ/mol) Are these values are reasonable? Thanks in advance. Anindita -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] interaction energy
Hi I want to obtain interaction energy between protein and dna in simulation pr-dna complex. what command is suitable for that? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] interaction energy of bulk TIP3P
sandeep somani wrote: i see. i reran the trajectory with reaction field electrostatics and that gave a more negative energy value which was closer to what i was expecting. i guess the missing reciprocal space contributions explains this discrepancy. is there a way to get the full interaction energy with PME ? I've never heard of a groupwise decomposition of the reciprocal space sum. For a single component system, there might to be some cunning way of deducing it from the total energy. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] interaction energy of bulk TIP3P
i see. i reran the trajectory with reaction field electrostatics and that gave a more negative energy value which was closer to what i was expecting. i guess the missing reciprocal space contributions explains this discrepancy. is there a way to get the full interaction energy with PME ? thnx for the reply -sandeep On Nov 17, 2007 8:18 PM, Mark Abraham [EMAIL PROTECTED] wrote: Hi All I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and PME for 400 ps and extracted the interaction energy of a randomly picked water molecule with rest of the system. Simulation was done at 298K and 1bar and usual procedure for generating a water box and equilibration were used. Average interaction energy reported in the log file was Epot (kJ/mol)Coul-SR LJ-SR WAT-rest -8.13828e+011.21886e+01 giving a total of -8.13828e+01 + 1.21886e+01 = -69.194 kJ/mol Comparing with published numbers using other MD programs this should be in the range of -81 +/- 1 kJ/mol i.e. ~11 kJ/mol less. any clues on origin of this discrepancy ? relevant .top , .mdp files are below. The PME algorithm does an approximation to the full periodic Coulomb summation, but does so with a calculation in direct space, as above, and another in reciprocal space, where your energy groups are not meaningful. So you're only getting the direct-space component of the interaction energy. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] interaction energy of bulk TIP3P
Hi All
I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and PME
for 400 ps and extracted the interaction energy of a randomly picked water
molecule with rest of the system.
Simulation was done at 298K and 1bar and usual procedure for generating a
water box and equilibration were used.
Average interaction energy reported in the log file was
Epot (kJ/mol)Coul-SR LJ-SR
WAT-rest -8.13828e+011.21886e+01
giving a total of -8.13828e+01 + 1.21886e+01 = -69.194 kJ/mol
Comparing with published numbers using other MD programs this should be in
the range of -81 +/- 1 kJ/mol i.e. ~11 kJ/mol less.
any clues on origin of this discrepancy ? relevant .top , .mdp files are
below.
Thanks
Sandeep
;---
*;MD.MDP for bulk TIP3P *
;---
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 20 ; 400 ps
nstcomm = 1
nstxout = 50
nstlog = 50
nstenergy = 50
nstxtcout = 50
nstlist = 5
energygrps = WAT
ns_type = grid
;PME
coulombtype = PME
rlist = 0.9
rcoulomb= 0.9
rvdw= 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
optimize_fft= yes
; Temperature coupling
Tcoupl = berendsen
tc-grps = SOL WAT
tau_t = 0.1 0.1
ref_t = 298 298
; Pressure coupling is on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
;---
*; TOP FILE FOR TIP3P BULK *
; Include forcefield parameters
#include ffoplsaa.itp
; Include water topology
#include tip3p.itp
[ system ]
; Name
bulk water
[ molecules ]
; Compound#mols
SOL 2180
--
*bits of log file from production run:*
== ### ==
A V E R A G E S
== ### ==
Energies (kJ/mol)
LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En.
1.35174e+04 -8.91571e+04 -1.10392e+04 -8.66790e+041.61998e+04
Total EnergyTemperature Pressure (bar)
-7.04792e+042.97985e+022.27514e+00
Box-X Box-Y Box-Z Volume Density (SI)
4.06327e+004.06327e+004.06327e+006.70858e+019.72133e+02
pV
9.03527e+00
Total Virial (kJ/mol)
5.40366e+03 -6.97436e+002.78681e+00
-6.97436e+005.38940e+03 -2.37439e+00
2.78681e+00 -2.37439e+005.39318e+03
Pressure (bar)
-2.28378e+003.27978e+00 -1.13390e+00
3.27978e+004.65423e+001.52221e+00
-1.13390e+001.52221e+004.45496e+00
Total Dipole (Debye)
3.23351e+00 -1.12569e+011.42062e+01
Epot (kJ/mol)Coul-SR LJ-SR
WAT-WAT0.0e+000.0e+00
WAT-rest -8.13828e+011.21886e+01
rest-rest -8.90758e+041.35052e+04
T-SOL T-WAT
2.97985e+022.97422e+02
M E G A - F L O P S A C C O U N T I N G
RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
NF=No Forces
Computing:M-Number M-Flops % of Flops
---
Coul(T) + LJ [W3-W3] 21419.733112 8182338.04878466.4
Outer nonbonded loop 3168.78223231687.822320 0.3
Spread Q Bspline 83712.418560 167424.837120 1.4
Gather F Bspline 83712.418560 1004549.022720 8.2
3D-FFT 263902.919508 2111223.35606417.1
Solve PME 4287.521437 274401.372000 2.2
NS-Pairs 10955.692493 230069.542353 1.9
Reset In Box261.606540 2354.458860 0.0
Shift-X2616.01308015696.078480 0.1
CG-CoM 87.202180 2528.863220 0.0
Virial 1313.40656723641.318206 0.2
Update 1308.00654040548.202740 0.3
Stop-CM1308.0013080.00 0.1
P-Coupling 1308.006540 7848.039240 0.1
Calc-Ekin 1308.01308035316.353160 0.3
Constraint-V 1308.006540 7848.039240 0.1
Constraint-Vir 1308.01962031392.470880 0.3
Settle 436.006540 140830.112420 1.1
---
Total 12322777.937807 100.0
Re: [gmx-users] interaction energy of bulk TIP3P
Hi All I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and PME for 400 ps and extracted the interaction energy of a randomly picked water molecule with rest of the system. Simulation was done at 298K and 1bar and usual procedure for generating a water box and equilibration were used. Average interaction energy reported in the log file was Epot (kJ/mol)Coul-SR LJ-SR WAT-rest -8.13828e+011.21886e+01 giving a total of -8.13828e+01 + 1.21886e+01 = -69.194 kJ/mol Comparing with published numbers using other MD programs this should be in the range of -81 +/- 1 kJ/mol i.e. ~11 kJ/mol less. any clues on origin of this discrepancy ? relevant .top , .mdp files are below. The PME algorithm does an approximation to the full periodic Coulomb summation, but does so with a calculation in direct space, as above, and another in reciprocal space, where your energy groups are not meaningful. So you're only getting the direct-space component of the interaction energy. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] interaction energy between the ligand and protein
Rui Li wrote: Hello! Can I estimate the inhibit capability by interaction energy between the ligand and protein? Only about as well as you can estimate the results of a Formula One racing season from the marks the drivers got on their drivers license exams. And how can I get the interaction energy in Gromacs? Energy groups. See the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Interaction energy calculation in a radius
Hi all, I want to calculate interaction energy between my ligand and residues of proetins which come within 6A of any atoms of the raidus. I have defined those residues and ligand as different groups. But how to select water around 6A radius of the ligand during dynamicsfor the calculation. If I consider all the water atoms for my calculation, huge contribution by water molecules, i guess is giving lots of background and so I am getting +ve values! Any suggestion would be highly appreciated alok ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
