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#33127 - 12/12/13 10:25 AM Re: openmm protein water centering problem [Re: Manish Kesherwan]
Manish Kesherwan Offline
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Registered: 10/22/11
Posts: 50
I used this command for equilibration in NPT using openmm

dyna leap -
restart nstep 1000000 timestp 0.001 -
inbfrq -1 imgfrq -1 ihbfrq 0 ilbfrq 0 -
iunread 11 iunwrite 12 iuncrd 13 -
nsavc 1000 nsavvelo 0 ntrfq 1000 -
nprint 1000 iprfrq 1000 -
firstt @temp finalt @temp twindl -5.0 twindh 5.0 -
ichecw 0 teminc 30.0 ihtfrq 0 ieqfrq 0 -
iasors 1 iasvel 1 iscvel 0 @echeck bycb -
eps 1.0 ctonnb 10.0 ctofnb 12.0 cutnb 16.0 cutim 16.0 vswi -
ewald pmew fftx @fftx ffty @ffty fftz @fftz kappa .34 spline order 6 -
omm langevin gamma 10 - ! turn on openmm, set-up Langevin
prmc pref 1 iprsfrq 25 ! set-up MC barostat at 1 atm, move attempt / 25 steps


Normal CPU run

DYNA CPT leap restart nstep @nstep timestep 0.001 echeck 9999. -
nprint 100 iprfrq 5000 ntrfrq 5000 -
iunrea 11 iunwri 12 iuncrd 13 iunvel -1 kunit -1 -
nsavc 100 nsavv 0 -
PCONS pint pref 1.0 pmass @Pmass pgamma 20.0 -
HOOVER reft @temp tmass 2000.0 tbath @temp firstt @temp

Please help me in running parallel GPU

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#33129 - 12/12/13 02:05 PM Re: openmm protein water centering problem [Re: Manish Kesherwan]
rmv Online   content

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
Since the questions and answers in this post mostly involve the OpenMM interface, it was moved here to this forum.

The energy drift is a function of the numerical precision, and has been shown to be fairly bad when using a GPU with single precision. Mixed precision can improve that somewhat, and double precision is better, but costs more, in terms of time to completion. The env var OPENMM_PRECISION can be used to control the precision.

The default prmc code does not implement an anisotropic pressure tensor, is therefore not appropriate for simulating membrane bilayer based systems. Code has been under development for this, but it does not appear to be in any of the public beta release versions of OpenMM/CHARMM.
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Rick Venable
computational chemist


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#33768 - 04/10/14 12:11 PM Re: openmm protein water centering problem [Re: Manish Kesherwan]
Manish Kesherwan Offline
Forum Member

Registered: 10/22/11
Posts: 50
Thanks for your reply about openmm prmc option for simulating membrane system.
If anisotropic pressure tensor is not supporting then what method can be applied for simulating membrane system.

I am using charmm 37b2.

Please suggest me.

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#33769 - 04/10/14 02:18 PM Re: openmm protein water centering problem [Re: Manish Kesherwan]
rmv Online   content

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
The DOMDEC code in CHARMM (domdec.doc) provides the best combination of speed and accuracy, but what's best for your case may depend both on available hardware and the molecular system.
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Rick Venable
computational chemist


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#37597 - 08/08/19 05:09 AM Re: openmm protein water centering problem [Re: slaw]
Corey Taylor Online   content
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Registered: 07/31/19
Posts: 6
Originally Posted By: slaw
Is MMFP actually supported with OpenMM?


Using the latest version of OpenMM, it doesn't appear to be:

Quote:
***** LEVEL -1 WARNING FROM *****
***** Number of atoms in restraint too large/geometric shape not supported


Where the MMFP block generated by CHARMM-GUI applying a restraint to non-waters looks like this:

Code:
MMFP
GEO rcm sphere -
    Xref @xcen Yref @ycen Zref @zcen XDIR 1.0 YDIR 1.0 ZDIR 1.0 -
    harmonic FORCE 1.0 select .not. ( hydrogen .or. resname TIP3 .or. segid @posid .or. segid @negid ) end
END


My system is a small peptide system (12 AA's) so I doubt size is the issue. When run on CPUs, the peptide is nicely centred in the water box. Commenting out the block means the simulation runs using OpenMM acceleration but the peptide flaps around outside the centred water box.

I note in a more recent post ( CHARMM Forum | How to maintain plane orientation), the suggestion of CONS HARM ABSO as the solution.

So, if I wanted to apply a harmonic constraint as per the manual CONS to mimic effect of the MMFP block, perhaps something like this would do?

Quote:
CONS HARM ABSO 1.0 FORCE 1.0 SELE .not. ( hydrogen .or. resname TIP3 .or. segid @posid .or. segid @negid ) END COMP


Edited by Corey Taylor (08/08/19 05:12 AM)

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#37600 - 08/08/19 11:08 AM Re: openmm protein water centering problem [Re: Manish Kesherwan]
rmv Online   content

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
An issue with that is the suppression of conformational changes; you could just restrain a single atom, e.g. a Calpha near the middle of the sequence.

(I should add that my preference has been to use the Python interface to OpenMM, which is somewhat notable as I've been avoiding Python for years.)
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Rick Venable
computational chemist


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#37601 - 08/09/19 06:38 AM Re: openmm protein water centering problem [Re: Manish Kesherwan]
Corey Taylor Online   content
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Registered: 07/31/19
Posts: 6
Cheers again for the tip - good point re: conformational changes.

And do you mean this (A MD/GCMC OpenMM/XML interface) with respect to the interface?

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#37603 - 08/09/19 11:47 AM Re: openmm protein water centering problem [Re: Manish Kesherwan]
rmv Online   content

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
I'm aware of a couple different python approaches: one using openmmtools, and another from CHARMM-GUI. This seems to be yet another approach, and I'll wager there may be others.
_________________________
Rick Venable
computational chemist


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