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NPAT simulation
#17607 04/01/08 11:36 AM
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mou Offline OP
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dear all,
i want to perform simulation of pure POPC bilayer . To reproduce experimental area per lipid (68 A2),
i do apply increasing surface tension (25,50,75,100 in case of NPgT ensemble)& reached the expected area within 1.7ns.then i extend the simulation further using NPAT ensemble to get constant surface area. The script i am using is as follows:
-----------------------------------------------
set 12 95
set 13 96
label lop13
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
open write card unit 14 name membrane.xtl
crystal define orth 65 64 75 90 90 90
crystal build cutoff 14 noper 0
crystal write card unit 14
crystal define orth 65 64 75 90 90 90
open read unit 14 card name membrane.xtl
crystal read unit 14 card
close unit 14
coor stat
coor stat sele segi mem end
coor stat sele segi sol end
!!
!----------------------------------------------------------------------
! Constraints on membrane
set i 1
label DO_13
!
coor stat mass select ( head .and. resi @i ) end
if ?zave gt 0 set zref = 19.5
if ?zave le 0 set zref = -23.00
MMFP
GEO plane RCM -
xref 0.0 zref @zref yref 0.0 zdir 1.0 -
force 0.0 select head .and. resi @i show end
END
incr i by 1
if i le 128 goto DO_13
!!-----------------image centering--------------------------------------
imag byseg xcen 0.0 ycen 0.0 zcen 0.0 sele .not. resname tip3 end
imag byres xcen 0.0 ycen 0.0 zcen 0.0 sele resname tip3 end
imag byres xcen 0.0 ycen 0.0 zcen 0.0 sele resname popc end
!-----------constraining H-bonds--------------
shake bonh
!---------------in/out put-----------
open read unit 30 card name "rst/po@12.rst
open write unit 31 card name "rst/po@13.rst
open write unit 32 file name "dcd/po@13.dcd
open write unit 33 file name "dvl/po@13.dvl
open write unit 34 card name "ene/po@13.ene
!-----------------dyna NPAT-----------------------
DYNA CPT LEAP RESTRT NSTEP 5000 TIMESTEP 0.002 -
!------------------------------------------------------------
pcons pint pref 1.0 pmzz 2500 pmxx 0.0 pmyy 0.0 -
hoover reft 298.0 tmass 20000.0 -
IPRFRQ 500 IHTFRQ 0 IEQFRQ 0 NTRFRQ 500 -
IUNREA 30 IUNWRI 31 IUNCRD 32 IUNVEL 33 KUNIT 34 -
NPRINT 500 NSAVC 500 NSAVV 500 IHBFRQ 0 INBFRQ 20 -
imgfrq 20 cutimg 14.0 cutnb 14.0 ctofnb 12.0 ctonnb 10.0 -
cdie eps 1.0 vshift -
firstt 298.0 finalt 298.0 teminc 0.0 tstruct 298.0 -
iasors 1 iasvel 1 iscvel 0 ichecw 0 twindh 0.0 twindl -0.0 -
ewald pmew fftx 72 ffty 64 fftz 90 kappa 0.34 spline order 6
!---------------------------------------------------------------
incr 12 by 1
incr 13 by 1
if @13 .le. 1000 goto lop13
stop
---------------------------------------------------------
The problem is that after 50 ps simulation the x,y box dimensions(cross section) are increasing considerably, with decrease in Z dimension(along bilayer normal).What i exactly want is to perform simulation at constant cross section area,where only Z direction is allowed to change.


Please do shed some light on this.
thank you.

Re: NPAT simulation
mou #17608 04/01/08 05:59 PM
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rmv Online Content
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There are a number of possible problems here: a 2 fs timestep (1 fs is highly recommended for constant P), the use of restraints (added forces), and the use of an ORTHorhombic lattice (TETRagonal or HEXAgonal prism are recommended).

Also, is POPC in the fluid phase at 298 K? You need to be well above the melting T for the lipid.

For NPAT, the X and Y sizes should not change at all, and Z should fluctuate in response to pressure changes.

For NPgammaT, each dimension can change, but the volume will be roughly the same, so Z must decrease if X and Y increase. Using TETR lattice requires that a=b, so that X and Y are coupled by symmetry.

Re: NPAT simulation
rmv #25680 10/26/10 04:24 PM
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I have a quick question regarding your comment about being well above the melting T for the lipid; what if the melting T of the lipid is e.g. 323K (DPPC) but I'm interested in physiological temperatures?

Re: NPAT simulation
tbagul #25686 10/26/10 06:33 PM
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rmv Online Content
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Lipid phase behavior is sensitive to composition, water content, and temperature; T should be chosen consistent with the desired phase, lipid composition, and hydration level.

For 310 K (37 C), I suggest using lipids (probably a mixture) which better represent a physiological membrane.

I also suggest a new post for a new question.


Rick Venable
computational chemist

Re: NPAT simulation
rmv #25689 10/26/10 07:12 PM
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Thank you and sorry for not starting a new question.


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