Dear amber experts
I am simulating glycolipid bilayer system using 1200 lipids and 2500 water all together. As prescribed in AMBER tutorial, I heat the system stepwise in NVT and upon the temperature reaches 353 K, I slowly release the restrain values to zero in NPT ensemble.
I also use PBC and their (initial x, y z ) values at starting structure are 159.3150000 159.2030000 51.5364000.
Upon it finish run in NVT the PBC size become 158.0734034 158.0018952 51.2130288 and after its NPT run this values become 142.5426707 140.5703393 31.6984305.
For NPT run I use the parameters as below:
equi with constant Pressure- fix lipid - move water
&cntrl
imin=0, irest=1, ntx=5,
temp0=353,
ntt=3, gamma_ln=5.0,
ntb=2, ntp=2,
ntc=2, ntf=2,
nstlim=100000, ntwr=-2500,
ntwe=100,
ntwx=100,
ntpr=100,
cut=9,
ntr=0
/
For MD production I use parameters as below:
&cntrl
imin=0, irest=1, ntx=5,
temp0=353,
ntt=3, gamma_ln=5.0,
ntb=2, ntp=2,
ntc=2, ntf=2,
nstlim=100000, ntwr=-50000,
ntwe=100, dt = 0.002, pres0 = 1.0, taup = 2.0,
ntwx=1000,
ntpr = 1000, ntxo = 1, iwrap = 1, nscm = 1000,
cut=9
/
My problem is, once start running MD production, lets say after 0.2ns run, I find (in vmd) the molecules in layer one shift to the other layer.
In other word, the molecule with arrangement tail meet tail (O--- ---O) becomes (---O O---), where the O is the headgroup and (---) is the tail of lipid.
A length of single lipid is about 16.2 Angstrom. I find the water molecules submerge into the head group region.
My question is how to avoid the lipid from one layer shift to other layer? I find the box like moving.
Is there any solution for this?
Appreciate any help.
(I am tying to solve this problem for the past two months but still I don't get a solution)
Thank you.
Regards
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 Sun Dec 23 2012 - 22:00:03 PST
