Dear experts,
I am having problem in PBC of my
bilayer system.
The starting structure of bilayer is as
below: "O" is lipid head and "|" is lipid tail
OOOOO
| | | | |
| | | | |
OOOOO
water
OOOOO
| | | | |
| | | | |
OOOOO
After running production for about 7 ns
(I notice from VMD) the lipids from top shift to bottom layer as
below:
| | | | |
OOOOO
water
OOOOO
| | | | |
| | | | |
OOOOO
OOOOO
| | | | |
The input paramters I am using for
this production is as blow:
Dynamic Simulation with Constant
Pressure
&cntrl
imin=0,
irest=1, ntx=5,
nscm=1000, iwrap=1,
ntt=3, gamma_ln=2, temp0=300.0,
ntb=2, ntp=2, pres0=1.0, taup=1.0,
ntc=2, ntf=2,
nstlim=100000, dt=0.001,
ntxo=1, ntwx=500, ntpr=100,
ntwr=-50000,
ntwv=-1,ioutfm=1, ntwe=500,
cut=9
/
This is like the molecule move upwards
or the PBC move downwards. In either case, this kind of shift will
affect my simulation results.
I have changed the nscm=500 but still I
face the same problem.
Is there any option that I should
follow or use to eliminate this problem?
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Tue Dec 25 2012 - 22:30:02 PST
