Date: Fri, 3 Aug 2018 20:29:19 +0530
Hi All,
I am new to membrane simulation and also in amber. I am using AMBER 12.0
with AMBER 18 tools. The lipid is DMPC. For lipid I have used lipid17 and
for water TIP3P model.
<http://ambermd.org/tutorials/advanced/tutorial16/index.html>
After minimization the box dimension was 70.617000 70.847000 72.789300.
My simulation temperature is 300 K. Now after 70ns production run I notice
that my box dimension is 50.049 81.694 61.070. I am unable to understand
why this change happens. Is it normal behaviour for membrane or not or
there has a any kind of mistake for set up the system? Below, I have shown
the input file for production run, also I have attached the snapshot of the
system after minimization and the corresponding system after it reaches
70ns production run and the graph for varying box dimension.
Input File:
Lipid npt_production 300K
&cntrl
imin=0,
ntx=5,
irest=1,
ntc=2,
ntf=2,
tol=0.0000001,
nstlim=500000,
ntt=3,
gamma_ln=1.0,
temp0=300.0,
ntpr=1000,
ntwr=1000,
ntwx=500,
dt=0.001,
ig=-1,
ntb=2,
ntp=2,
cut=10.0,
ioutfm=1,
ntxo=2,
/
Kindly, help me
Thanks in advance
Somdev Pahari
Research fellow
National Institute of Technology, Rourkela
Odisha
India
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- application/pdf attachment: snap.pdf
(image/jpeg attachment: box_length.jpg)
