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rmv Online Content
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In the output, the IMAGE BYSEG command is commented out, which may be one reason the protein is not placed properly.

All of the extra stuff from CHARMM-GUI tends to complicate problem diagnosis, esp. the vast array of RTF and PARAM files being read.


Rick Venable
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I also used IMAGEing bysegment but it's not showing any centering of protein molecule in water box.

I don't know why there is no contraint on protein for centering in openmm.

Thanks & Regards
Manish Kesherwani

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I suggest you ask the CHARMM-GUI support - they should know how their script is supposed to work.


Lennart Nilsson
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It is possible the script from CHARMM-GUI has not been tested with OpenMM, as the latter is a fairly recent development which requires custom hardware.

Consider setting up a much simpler test case yourself, with just a short peptide in a cube of water, using only the protein parameters with the water_ions stream file.


Rick Venable
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Thanks Rick sir i will try with simple peptide with solvent box.

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Manish Kesherwani

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Thanks sir it's working now with imaging of protein segment during run of dynamics.

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Manish Kesherwani

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Is MMFP actually supported with OpenMM?

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Sir i tried with energy command along with omm then it's giving mmff contribution of energy . but i faced one problem that protein molecule is not coming in center of box during simulation but afer generating trajactory we can align frames with protein molecule then molecule will be in centre. If you have some other solution regarding centering of protein molecule in waterbox please sugggest me. Did you tried simulation with openmm. how was your trajactory.

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As I noted above, in my initial reply--

"It may depend on the values used for @xcen, etc. for the MMFP restraint; I suggest trying w/o restraints and then find the protein center. I found that OpenMM in CHARMM seems to shift the Cartesian coordinates such that the minimum corner of the unit cell is at the origin, instead of the origin being the center. Also, since the OpenMM interface is still somewhat developmental, it's not clear if all of the restraints in CHARMM are fully supported; the documentation does not address the issue."


Rick Venable
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Good Day Sir,

I am running equilibration dynamics in membrane protein using NVIDIA TESLA GPU card(openmm -charmm). when i am using multigpu(more than one gpu) then energy drift is too high around( 1000000 Kcal). Can u specify how we can rectify this.

Please give some suggextion

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