[gmx-users] Energy calculation
C.Y. Chang
chiayun.chang at gmail.com
Thu Mar 17 10:16:13 CET 2011
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 <mark.abraham at anu.edu.au>
>
>
> On 16/03/11, *"C.Y. Chang" * <chiayun.chang at gmail.com> 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 <mark.abraham at anu.edu.au>
>
>>
>>
>> On 14/03/11, *"C.Y. Chang" * <chiayun.chang at gmail.com> 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
>> --
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>
>
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