I have simulated bilayer in water. There are 128 lipid in total and around 600 water molecules on top and bottom of the lipid bilayer.
Up to about 50 to 60 ns the trajectory works fine. Then I find the water molecules shift to one layer more than the other layer.
After that I also notice the layers in the bilayer shift upside down. The water molecules become in the center and the tails of each bilayer pointing upward and bottom of the bilayer.
I used mdinput as below:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Production 300ns constant pressure & zero surface tension
&cntrl
imin=0,
irest=1, ntx=5,
ntt=2, temp0=355.0,
ntxo=1, iwrap=1, nscm=5000,
ntb=2, pres0=1.0,
ntp=3, csurften=3, gamma_ten=0.0, ninterface=2,
ntc=2, ntf=2,
nstlim=100000, dt=0.002,
ntpr=100, ntwr=-50000, ntwx=1000, ntwe=500,
cut=10.0, ioutfm=1
/
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Since I used "iwrap" command, I used "unwrap" command and reimaged the trajectory using commands as below:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
trajin ../$system-MD300-run0900.traj 1 100 5
trajin ../$system-MD300-run1000.traj 1 100 5
unwrap :1-1214
center :1-1214
image center
trajout abc.traj mdcrd
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Can anyone advice me how to treat this trajectory files? I wish I dont want to repeat the simulations. It takes long time to simulation 300 ns.
Hope I get solution to this problem.
Thank you.
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 Mon Mar 10 2014 - 07:30:02 PDT
