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#36320 - 04/24/17 03:20 PM Correct implementation of OpenMM
EArtikis Offline
Forum Member

Registered: 06/01/16
Posts: 3
I was wondering whether I am implementing omm incorrectly in my dynamics script, because I am not noticing a speed-up when compared to my CPU run. I'm using the CHARMM22_cmap forcefield.

...

scalar fbeta set 10 select .not. hydrogen end

prnlev 0
stream "/toppar/gbsw/radius_gbsw.str"
prnlev 5 node 0

gbsw sgamma 0.005 nang 50 conc 5e-2

set ctofnb = 12
calc ctonnb = @ctofnb
calc cutnb = @ctofnb + 2
NBOND atom switch cdie vdw vswitch -
ctonnb @ctonnb ctofnb @ctofnb cutnb @cutnb -

mini sd nstep 100

energy

write psf card name prot.psf
write coor pdb name prot_minimized.pdb

omm on

faster on
shake fast bonh

open unit 1 write form name prot_omm.res
open unit 2 write unform name prot_omm.dcd

dynamics leap start timestep 0.002 -
nstep 25000000 nprint 10000 iprfrq 20000 -
firstt 298 finalt 298 twindl -5.0 twindh 5.0 -
ichecw 0 teminc 0 ihtfrq 0 ieqfrq 0 -
iasors 1 iasvel 1 iscvel 0 -
ilbfrq 0 inbfrq -1 echeck -1 -
iunread 1 iunwrite 1 -
iuncrd 2 nsavc 100 nsavv 0 -
omm langevin gamma 5

open unit 1 write form name prot_omm.res
open unit 2 write unform name prot_omm.dcd

dynamics leap restart timestep 0.002 -
nstep 225000000 nprint 10000 iprfrq 20000 -
firstt 298 finalt 298 twindl -5.0 twindh 5.0 -
ichecw 0 teminc 0 ihtfrq 0 ieqfrq 0 -
iasors 1 iasvel 1 iscvel 0 -
ilbfrq 0 inbfrq -1 echeck -1 -
iunread 1 iunwrite 1 -
nsavc 100 nsavv 0 iuncrd 2 -
omm langevin gamma 5

close unit 1
close unit 2

stop

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#36322 - 04/24/17 04:59 PM Re: Correct implementation of OpenMM [Re: EArtikis]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8079
Loc: 39 03 48 N, 77 06 54 W
The output log file should have clear messages about the OpenMM and GPU usage.

Note that the free version does not include the OpenMM interface.
_________________________
Rick Venable
computational chemist


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#36324 - 04/25/17 09:29 AM Re: Correct implementation of OpenMM [Re: EArtikis]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4614
Loc: ~ 59N, 15E
gbsw is not supported with OpenMM
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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