Re: [gmx-users] Energy calculation
Hi, "Every charge group must be a subset of an energy group or fully disjoint from it." Does it mean that I could not set up the HBD and HBA in the ligand at the same time, but the HBD in ligand and HBA in lipid bilayer could be calculate? or Each atoms in the ligand must belong to the disjointed subset? For the guess 2, I try to modify the .ndx file and add the nHB (non-HB-system). The atoms in nHB are excluded from HBA and HBD in the ligand. [ nHB ] 17366 17368 17369 17370 17371 17372 17373 17374 17376 17377 17378 17379 17380 17383 17386 17389 17390 17391 17392 17393 17394 17395 17396 17397 17398 17399 17401 17402 17403 17405 17406 17407 17408 17409 17410 17411 17413 17414 17415 17416 17417 17420 17423 17426 17427 17428 17429 17430 17431 17432 17433 17434 17435 17436 17438 17439 17440 17442 17443 17444 17445 17446 17447 17448 17450 17451 17452 17453 17454 17457 17460 17463 17464 17465 17466 17467 17468 17469 17470 17471 17472 17473 17475 17476 17477 17479 17480 17481 17482 17483 17484 17485 17487 17488 17489 17490 17491 17494 17497 17500 17501 17502 17503 17504 17505 17506 17507 17508 17509 17510 17512 17513 17514 17516 17517 17518 17519 17520 17521 17522 17524 17525 17526 17527 17528 17531 17534 17537 17538 17539 17540 17541 17542 17543 17544 17545 17546 17547 17549 17550 [ HBD ] 17385 17382 17422 17419 17459 17456 17496 17493 17533 17530 [ HBA ] 17367 17375 17381 17384 17387 17388 17400 17404 17412 17418 17421 17424 17425 17437 17441 17449 17455 17458 17461 17462 17474 17478 17486 17492 17495 17498 17499 17511 17515 17523 17529 17532 17535 17536 17548 But the error msg. is alike. Fatal error: atoms 17366 and 17367 in charge group 1 of molecule type 'LIG' are in different energy groups Do you have any methods for calculating the HB energy in the intramolecules? Thanks for your any comments. Best, Chia-yun Chang 2011/3/16 Mark Abraham > > > On 16/03/11, *"C.Y. Chang" * wrote: > > Hi, > > I try to calculate the Hbond in the ligand and remove the duplicate atoms > in the .ndx file dumped from g_hbond. > This is the contents in the .ndx file. > > [ HBD ] > 17385 17382 17422 17419 17459 17456 17496 17493 17533 17530 > [ HBA ] > 17367 17375 17381 17384 17387 17388 17400 17404 17412 17418 > 17421 17424 17425 17437 17441 > 17449 17455 17458 17461 17462 17474 17478 17486 17492 17495 > 17498 17499 17511 17515 17523 > 17529 17532 17535 17536 17548 > > And then, I perfrom the grompp. > It shows the error msg. > > Fatal error: > atoms 17366 and 17367 in charge group 1 of molecule type 'LIG' are in > different energy groups > > How should I deal with the problem? > > > Redefine charge or energy groups as appropriate for whatever you're trying > to do. Non-bonded interactions are calculated by looping over atom-atom > interactions grouped by charge group and then by energy group. Every charge > group must be a subset of an energy group or fully disjoint from it. > > > On the other side, I read the information in the web page ( > http://www.mail-archive.com/gmx-users@gromacs.org/msg34617.html) > I remove the lines in the [bonds] region in .top files. > But I still get these terms > > 1 Angle2 G96Angle 3 Proper-Dih. 4 > Ryckaert-Bell. > 5 Improper-Dih.6 LJ-147 Coulomb-14 8 LJ-(SR) > 9 Disper.-corr. 10 Coulomb-(SR)11 Coul.-recip.12 > Position-Rest. > 13 Potential 14 Kinetic-En. 15 Total-Energy16 > Temperature > 17 Pres.-DC18 Pressure19 Constr.-rmsd20 Box-X > 21 Box-Y 22 Box-Z 23 Volume 24 Density > 25 pV 26 Enthalpy27 Vir-XX 28 Vir-XY > 29 Vir-XZ 30 Vir-YX 31 Vir-YY 32 Vir-YZ > 33 Vir-ZX 34 Vir-ZY 35 Vir-ZZ 36 Pres-XX > 37 Pres-XY 38 Pres-XZ 39 Pres-YX 40 Pres-YY > 41 Pres-YZ 42 Pres-ZX 43 Pres-ZY 44 Pres-ZZ > 45 #Surf*SurfTen 46 Mu-X47 Mu-Y48 Mu-Z > 49 Coul-SR:LIG-LIG 50 LJ-SR:LIG-LIG > 51 Coul-14:LIG-LIG 52 LJ-14:LIG-LIG > 53 Coul-SR:LIG-DPPC_SOL54 LJ-SR:LIG-DPPC_SOL > 55 Coul-14:LIG-DPPC_SOL56 LJ-14:LIG-DPPC_SOL > 57 Coul-SR:DPPC_SOL-DPPC_SOL 58 LJ-SR:DPPC_SOL-DPPC_SOL > 59 Coul-14:DPPC_SOL-DPPC_SOL 60 LJ-14:DPPC_SOL-DPPC_SOL > 61 T-DPPC 62 T-SOL 63 T-LIG 64 Lamb-DPPC > 65 Lamb-SOL66 Lamb-LIG > > And I try to remove lines in [bonds], [pairs], [angles] and [ dihedrals ], > but it is the same. > Where is the wrong process? And how could I get the angle and dihedral > ene
Re: [gmx-users] Energy calculation
On 16/03/11, "C.Y. Chang" wrote: > Hi, > > I try to calculate the Hbond in the ligand and remove the duplicate atoms in > the .ndx file dumped from g_hbond. > This is the contents in the .ndx file. > > [ HBD ] > 17385 17382 17422 17419 17459 17456 17496 17493 17533 17530 > > [ HBA ] > 17367 17375 17381 17384 17387 17388 17400 17404 17412 17418 17421 > 17424 17425 17437 17441 > 17449 17455 17458 17461 17462 17474 17478 17486 17492 17495 17498 > 17499 17511 17515 17523 > > 17529 17532 17535 17536 17548 > > And then, I perfrom the grompp. > It shows the error msg. > > Fatal error: > atoms 17366 and 17367 in charge group 1 of molecule type 'LIG' are in > different energy groups > > > How should I deal with the problem? > Redefine charge or energy groups as appropriate for whatever you're trying to do. Non-bonded interactions are calculated by looping over atom-atom interactions grouped by charge group and then by energy group. Every charge group must be a subset of an energy group or fully disjoint from it. > On the other side, I read the information in the web page > (http://www.mail-archive.com/gmx-users@gromacs.org/msg34617.html) > > I remove the lines in the [bonds] region in .top files. > But I still get these terms > > 1 Angle 2 G96Angle 3 Proper-Dih. 4 > Ryckaert-Bell. > 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR) > > 9 Disper.-corr. 10 Coulomb-(SR) 11 Coul.-recip. 12 > Position-Rest. > 13 Potential 14 Kinetic-En. 15 Total-Energy 16 Temperature > 17 Pres.-DC 18 Pressure 19 Constr.-rmsd 20 Box-X > > 21 Box-Y 22 Box-Z 23 Volume 24 Density > 25 pV 26 Enthalpy 27 Vir-XX 28 Vir-XY > 29 Vir-XZ 30 Vir-YX 31 Vir-YY 32 Vir-YZ > > 33 Vir-ZX 34 Vir-ZY 35 Vir-ZZ 36 Pres-XX > 37 Pres-XY 38 Pres-XZ 39 Pres-YX 40 Pres-YY > 41 Pres-YZ 42 Pres-ZX 43 Pres-ZY 44 Pres-ZZ > > 45 #Surf*SurfTen 46 Mu-X 47 Mu-Y 48 Mu-Z > 49 Coul-SR:LIG-LIG 50 LJ-SR:LIG-LIG > 51 Coul-14:LIG-LIG 52 LJ-14:LIG-LIG > 53 Coul-SR:LIG-DPPC_SOL 54 LJ-SR:LIG-DPPC_SOL > > 55 Coul-14:LIG-DPPC_SOL 56 LJ-14:LIG-DPPC_SOL > 57 Coul-SR:DPPC_SOL-DPPC_SOL 58 LJ-SR:DPPC_SOL-DPPC_SOL > 59 Coul-14:DPPC_SOL-DPPC_SOL 60 LJ-14:DPPC_SOL-DPPC_SOL > 61 T-DPPC 62 T-SOL 63 T-LIG 64 Lamb-DPPC > > 65 Lamb-SOL 66 Lamb-LIG > > And I try to remove lines in [bonds], [pairs], [angles] and [ dihedrals ], > but it is the same. > Where is the wrong process? And how could I get the angle and dihedral energy > in the intramolecules? > > Thanks for your any comments. > You're decomposing PME electrostatics. That produces garbage values for quantities that have little meaning, like it says in the thread I suggested you read the whole of. I'm going to stop helping :-) Mark > > Best, > > Chia-yun > > > 2011/3/14 Mark Abraham > > > > > > > > On 14/03/11, "C.Y. Chang" wrote: > > > > > > Hi, > > > > > > I try to calculate hydrogen bond (HB) energy. > > > The g_energy does not have this term. > > > And I find the g_hbond function in Gromacs. > > > But the HB energy calculation is not in g_hbond. > > > > > > > > > > > There's good reasons for this. How would you define the "HB energy" in > > terms of the kind of information accessible to MD simulations? > > > > > > > > > > Therfore, I also try to dump the .ndx file including the HB_donor, > > > HB_acceptor and HB_system from g_hbond, and perfrom the grompp > > > > > > But there is a error msg, > > > > > > Atom 17380 in multiple Energy Mon. groups > > > > > > > > > Look up energy groups in the manual - start of section 3.3. Your .mdp file > > is defining an illegal combination of atoms and energy monitor groups. > > > > > > > > > Another problem is about calculating the intramolecular energy e.g. > > > 1,4-nonbonded, van der waal, electrostatic etc. of the ligand in lipid > > > layer-ligand complex system. > > > > > > > > > I could set up the energy_grp and calculate energy between the ligand > > > group and the lipid layer group. > > > But I need the intramolecular energy in the groups. > > > How should I deal with these problems? > > > > > > > > > > > An inter-group energy doesn't mean anything much, so don't bother. Please > > read the whole of this thread > > http://lists.gromacs.org/pipermail/gmx-users/2010-November/055687.html > > > > > > Mark > > > > -- > > > > gmx-users mailing list gmx-users@gromacs.org > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > >
Re: [gmx-users] Energy calculation
Hi, I try to calculate the Hbond in the ligand and remove the duplicate atoms in the .ndx file dumped from g_hbond. This is the contents in the .ndx file. [ HBD ] 17385 17382 17422 17419 17459 17456 17496 17493 17533 17530 [ HBA ] 17367 17375 17381 17384 17387 17388 17400 17404 17412 17418 17421 17424 17425 17437 17441 17449 17455 17458 17461 17462 17474 17478 17486 17492 17495 17498 17499 17511 17515 17523 17529 17532 17535 17536 17548 And then, I perfrom the grompp. It shows the error msg. Fatal error: atoms 17366 and 17367 in charge group 1 of molecule type 'LIG' are in different energy groups How should I deal with the problem? On the other side, I read the information in the web page ( http://www.mail-archive.com/gmx-users@gromacs.org/msg34617.html) I remove the lines in the [bonds] region in .top files. But I still get these terms 1 Angle2 G96Angle 3 Proper-Dih. 4 Ryckaert-Bell. 5 Improper-Dih.6 LJ-147 Coulomb-14 8 LJ-(SR) 9 Disper.-corr. 10 Coulomb-(SR)11 Coul.-recip.12 Position-Rest. 13 Potential 14 Kinetic-En. 15 Total-Energy16 Temperature 17 Pres.-DC18 Pressure19 Constr.-rmsd20 Box-X 21 Box-Y 22 Box-Z 23 Volume 24 Density 25 pV 26 Enthalpy27 Vir-XX 28 Vir-XY 29 Vir-XZ 30 Vir-YX 31 Vir-YY 32 Vir-YZ 33 Vir-ZX 34 Vir-ZY 35 Vir-ZZ 36 Pres-XX 37 Pres-XY 38 Pres-XZ 39 Pres-YX 40 Pres-YY 41 Pres-YZ 42 Pres-ZX 43 Pres-ZY 44 Pres-ZZ 45 #Surf*SurfTen 46 Mu-X47 Mu-Y48 Mu-Z 49 Coul-SR:LIG-LIG 50 LJ-SR:LIG-LIG 51 Coul-14:LIG-LIG 52 LJ-14:LIG-LIG 53 Coul-SR:LIG-DPPC_SOL54 LJ-SR:LIG-DPPC_SOL 55 Coul-14:LIG-DPPC_SOL56 LJ-14:LIG-DPPC_SOL 57 Coul-SR:DPPC_SOL-DPPC_SOL 58 LJ-SR:DPPC_SOL-DPPC_SOL 59 Coul-14:DPPC_SOL-DPPC_SOL 60 LJ-14:DPPC_SOL-DPPC_SOL 61 T-DPPC 62 T-SOL 63 T-LIG 64 Lamb-DPPC 65 Lamb-SOL66 Lamb-LIG And I try to remove lines in [bonds], [pairs], [angles] and [ dihedrals ], but it is the same. Where is the wrong process? And how could I get the angle and dihedral energy in the intramolecules? Thanks for your any comments. Best, Chia-yun 2011/3/14 Mark Abraham > > > On 14/03/11, *"C.Y. Chang" * wrote: > > Hi, > > I try to calculate hydrogen bond (HB) energy. > The g_energy does not have this term. > And I find the g_hbond function in Gromacs. > But the HB energy calculation is not in g_hbond. > > > There's good reasons for this. How would you define the "HB energy" in > terms of the kind of information accessible to MD simulations? > > > Therfore, I also try to dump the .ndx file including the HB_donor, > HB_acceptor and HB_system from g_hbond, and perfrom the grompp > But there is a error msg, > > Atom 17380 in multiple Energy Mon. groups > > > Look up energy groups in the manual - start of section 3.3. Your .mdp file > is defining an illegal combination of atoms and energy monitor groups. > > > Another problem is about calculating the intramolecular energy e.g. > 1,4-nonbonded, van der waal, electrostatic etc. of the ligand in lipid > layer-ligand complex system. > I could set up the energy_grp and calculate energy between the ligand group > and the lipid layer group. > But I need the intramolecular energy in the groups. > How should I deal with these problems? > > > An inter-group energy doesn't mean anything much, so don't bother. Please > read the whole of this thread > http://lists.gromacs.org/pipermail/gmx-users/2010-November/055687.html > > Mark > -- > 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] Energy calculation
On 14/03/11, "C.Y. Chang" wrote: > Hi, > > I try to calculate hydrogen bond (HB) energy. > The g_energy does not have this term. > And I find the g_hbond function in Gromacs. > But the HB energy calculation is not in g_hbond. > There's good reasons for this. How would you define the "HB energy" in terms of the kind of information accessible to MD simulations? > Therfore, I also try to dump the .ndx file including the HB_donor, > HB_acceptor and HB_system from g_hbond, and perfrom the grompp > > But there is a error msg, > > Atom 17380 in multiple Energy Mon. groups > Look up energy groups in the manual - start of section 3.3. Your .mdp file is defining an illegal combination of atoms and energy monitor groups. > Another problem is about calculating the intramolecular energy e.g. > 1,4-nonbonded, van der waal, electrostatic etc. of the ligand in lipid > layer-ligand complex system. > > I could set up the energy_grp and calculate energy between the ligand group > and the lipid layer group. > But I need the intramolecular energy in the groups. > How should I deal with these problems? > An inter-group energy doesn't mean anything much, so don't bother. Please read the whole of this thread http://lists.gromacs.org/pipermail/gmx-users/2010-November/055687.html Mark -- 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] Energy calculation problem with molecule leaving the box
On 4/02/2011 1:05 AM, Gordan Horvat wrote: I'm doing molecule dynamics of a calixarene in a acetonitrile box with pbc, energy groups defined and npT constant. When I extract interaction energies with g_energy from edr file I expect them to be pretty much constant because I see no significant conformational changes or changes in distance between energy groups and that is true for one part of simulation when the molecule is completely in the box. But when a molecule partially leaves the box energies of interaction for that part which is out of the is box is not calculated (bonded or with other energy groups) and interaction energy sometimes drops to 0.000 for a period of time even though the distance between groups doesn't change. I tried extracting energies through rerunning simulation on trajectories which were converted with -pbc nojump or -pbc mol -center but that gave zero energies all the time. How can I fix this energy calculation problem? So, having run your original simulation with pre-defined energy groups, starting from the mdrun output files, what commands reproduce your observations? Mark -- 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] Energy Calculation
simon sangma wrote: Hi! I want to calculate energy from GROMOS96-GB/SA. What command should be used? g_energy -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/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
