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Interaction energy
#17386 03/09/08 04:38 PM
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viv Offline OP
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I generated a box with protein, membrane and counterions using Ewald.
All my system is neutral, but now I want to do decomposition of energy from different parts of my system. I want to compute electrostatic energy and forces between any two selections which are not neutral using INTERACTION command.
I found that electrostatic forces are not correct. Do you know how to calculate the electrostatic energy between two selections if they are not neutral using EWALD without using cutt_off.

Thanks,
Victor

Re: Interaction energy
viv #17387 03/10/08 03:08 PM
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What makes you say the energy was wrong? What are you comparing it to as a reference?

Are you trying to include the solvent in the INTE analysis or are you just looking at the intrasolute interactions at this point? A simple coulombic electrostatic treatment with a cutoff should be good enough for post analysis within the protein.

If you are looking at solvent interactions, did you reconstruct the images in your INTE analysis and are you recentering the protein properly?


Joshua Ward Graduate Student Purdue University Department of Medicinal Chemistry and Pharmacology
Re: Interaction energy
jmwict13 #17388 03/10/08 04:23 PM
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The INTEraction command does not support IMAGEs, and therefore it does not support any of the Ewald methods, either.

Re: Interaction energy
jmwict13 #17389 03/10/08 04:39 PM
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I want to analyze my MD trajectory for system which I
obtained with Ewald by decomposition of all my forces in system which I have. Particular, I want to find only unbounded forces (coulomb and vdW) between charge membrane and charge protein. All solvent and counterions I have switched off. For that case we should have interaction
between charged particle near infinitely large surface
from classic point of view, but results are not coincidence
qualitatively and quantitatively.

Thanks, Victor

Re: Interaction energy
rmv #17390 03/10/08 04:53 PM
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Thanks very much for the clarification.
But do you know how correctly to analyze,
say to find forces decomposition from trajectory which we got using Ewald, for that case. I am doubt if using
INTERACTION command with very large cut-off gives the correct force decomposition.
Thanks, Victor

Re: Interaction energy
viv #17391 03/10/08 05:14 PM
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A large cutoff could also cause problems, for the same reason-- no IMAGEs. Anytime some of the atoms are closer than CTOFNB from a cell boundary, some of the atom:atom interactions will be missing from an INTE calc.

If you really want the forces, you'd have to modify the source code to write atomic force trajectory files and then re-run the simulation.

Re: Interaction energy
rmv #17392 03/10/08 06:07 PM
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Many thanks,
Victor.

Re: Interaction energy
rmv #17393 03/10/08 09:15 PM
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Quote:

The INTEraction command does not support IMAGEs, and therefore it does not support any of the Ewald methods, either.




Is this still the case? My INTE command will print out numbers for IMNBvdw and IMELec that are equal to the values printed out by the ENER command.

It does not give any EWALD output, so I am with you there.

I just ask because I initiated a vibrant discussion in a group meeting about whether or not INTE is compatible with Images (me saying it was not) and ultimately lost out by the end when I went back to my desk and tested it myself.


Code:
 CHARMM>     ener
... ...
ENER ENR: Eval# ENERgy Delta-E GRMS
ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ENER CROSS: CMAPs
ENER EXTERN: VDWaals ELEC HBONds ASP USER
ENER IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
ENER EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
---------- --------- --------- --------- --------- ---------
ENER> 0 -22634.53562 0.00000 13.41373
ENER INTERN> 14.82699 33.83666 9.38863 23.28612 5.52573
ENER CROSS> -2.18922
ENER EXTERN> 2346.81491 -20141.28703 0.00000 0.00000 0.00000
ENER IMAGES> 46.06798 -1545.30691 0.00000 0.00000 0.00000
ENER EWALD> 288.10814-163457.27922 159743.67161 0.00000 0.00000
---------- --------- --------- --------- --------- ---------

CHARMM> inte sele all end
SELRPN> 7010 atoms have been selected out of 7010
INTER: Normal Atom Nonbondselected 2643537 from a total of 2643537
VEHEAP> Expanding heap size by 5734400 words.
INTER: Image Nonbond List selected 1021584 from a total of 1021584
INTE ENR: Eval# ENERgy Delta-E GRMS
INTE INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
INTE CROSS: CMAPs
INTE EXTERN: VDWaals ELEC HBONds ASP USER
INTE IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
---------- --------- --------- --------- --------- ---------
INTE> 1 -19209.03615 -3425.49947 11.83351
INTE INTERN> 14.82699 33.83666 9.38863 23.28612 5.52573
INTE CROSS> -2.18922
INTE EXTERN> 2346.81491 -20141.28703 0.00000 0.00000 0.00000
INTE IMAGES> 46.06798 -1545.30691 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------




Just trying to verify that I understand what I am doing as best I can.


Joshua Ward Graduate Student Purdue University Department of Medicinal Chemistry and Pharmacology
Re: Interaction energy
jmwict13 #17394 03/10/08 09:58 PM
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Based on the following from energy.doc--

This command will not work with the selection of images atoms,
or the selection of ST2 waters. All energy terms not listed above will
not be computed. The nonbond list must be generated with the ATOM and VATOM
options. [T.Lazaridis, July 1999: Now INTE can work with the GROUP option]

I had assumed that image atoms would not be included in a double selection such as

inte sele segid L end sele resn TIP3 end

where the 'resn TIP3' selection could imply image waters (it does with some COOR commands). If I change that to

inte sele segid L end sele segid WAT end

which would exclude image waters, the IMNB and IMEL values are the same as those for 'resn TIP3', and they should not be if image atoms were included and excluded as expected from the atom selections.

I do not believe that the image energies reported by INTE are correct or meaningful.


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