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#15376 - 08/29/07 01:31 PM Pressure controlling
NMK Offline
Forum Member

Registered: 09/28/06
Posts: 38
I am trying to equillibrate the system which has a top 10A of water fixed and bottom Self assembled monolayers( SAM -fixed) and has a peptide solvated and free to move between ice and SAM.
i used the following script but the pressure seems to be around 500-700 atm. I am using vv2 with PME option
Is the box size wrong. I increased the box size a bit but still the pressure is high.
any idea ?

set a0 44.33
set b0 43.54
set c0 56.46
set theta 90.0

! Setup the image facility for periodic boundary conditions.
crystal define orthorhombic @a0 @b0 @c0 @theta @theta @theta
crystal build noper 0 cutoff 30.0

update inbf -1 ihbf 0 imgfrq 100 imall

image byre sele (.not. segid pep) .and. (.not. segid sam) -
.and. (.not. segid ice) .and. (.not. segid icen) end
image byse sele segid pep end
image fixed sele segid sam end

shake bonh para
define SURFBTM sele segid sam .and. -
(type C2 .or. type H2A .or. type H2B .or. -
type C3 .or. type H3A .or. type H3B .or. -
type C4 .or. type H4A .or. type H4B .or. -
type C5 .or. type H5A .or. type H5B .or. -
type C6 .or. type H6A .or. type H6B .or. -
type C7 .or. type H7A .or. type H7B .or. -
type C8 .or. type H8A .or. type H8B .or. -
type C9 .or. type H9A .or. type H9B .or. -
type C10 .or. type H10A .or. type H10B .or. type H10C) end
define ICETOP sele segid ice .or. segid icen end
cons fix sele SURFBTM .or. ICETOP end

open unit 34 read form name heat.res
open unit 30 writ form name equi.res
open unit 31 writ unform name equi.dcd

THER 1 TREF 310.0 TAU 0.1 SELECT all END
DYNAmics VV2 RESTART TIMEstp 0.002 NSTEP 3000 INBFRQ -1 IHBFRQ -1 IMGFRQ -1 IXTFRQ -1 NSNOS 1 IUNREA 34 IUNWRI 30 IUNCRD 31 IUNLDM -1 IUNVEL -1 NSAVC 10 NSAVV 500 NPRINT 500 IPRFRQ 5000 ISVFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 1000 atom vatom cutnb 14.0 ctofnb 12.0 ctonnb 10.0 -
cdie eps 1.0 vswitch cutim 14.0 wmin 1.0 -
EWALD PMEWald KAPPa 0.34 ORDEr 6 -
FFTX 50 FFTY 50 FFTZ 60 -
QCOR 0.0 -
echeck 1.0e5

#15377 - 08/29/07 02:45 PM Re: Pressure controlling [Re: NMK]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
The pressure fluctuates a great deal, so you need to get an accurate average over an interval of 100 ps or more, using the PRESSI value from the 'AVER PRESS>' lines in the output log file.

Additional notes--

Non-zero value for ISVFRQ are usually not needed, and are not recommended.

ECHECK should not be so large; > 1000 kcal/mol is excessive.


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