Hi All,
I am new to amber. I am using AMBER 12.0 with AMBER 18 tools to simulate a
lipid bilayer system which consists of 128 DMPC bilayer and water
molecules. For lipid I have used lipid17 and for water TIP3P model. I am
following the amber tutorial,
http://ambermd.org/tutorials/
advanced/tutorial16/index.html.
The initial system was setup by using packmol software where the box
dimension is 64.05 A, 64.05 A, 69.2 A. After that I have used ">setbox
dmpc vdw" command and obtained the dimension 70.617000 70.847000
72.789300.
After minimization, I have heated the system up to 200K and do not find any
major deviation in structure. But after heated to 300K I find that the
water molecules tend to leave from water box. I am unable to understand why
this happens. Below, I have shown the input file for heating, also I have
attached the snapshots of the system after minimization and the
corresponding system after it reaches 300 K.
Input File:
Lipid 128 heating 100K-300K
&cntrl
imin=0,
ntx=5,
irest=1,
ntc=2,
ntf=2,
tol=0.0000001,
nstlim=200000,
ntt=3,
gamma_ln=1.0,
ntr=1,
ig=-1,
ntpr=100,
ntwr=10000,
ntwx=100,
dt=0.001,
nmropt=1,
ntb=2,
ntp=2,
taup=2.0,
cut=10.0,
ioutfm=1,
ntxo=2,
/
&wt type='TEMP0', istep1=0, istep2=10000, value1=100.0, value2=110.0 /
&wt type='TEMP0', istep1=10001, istep2=20000, value1=110.0, value2=120.0 /
&wt type='TEMP0', istep1=20001, istep2=30000, value1=120.0, value2=130.0 /
&wt type='TEMP0', istep1=30001, istep2=40000, value1=130.0, value2=140.0 /
&wt type='TEMP0', istep1=40001, istep2=50000, value1=140.0, value2=150.0 /
&wt type='TEMP0', istep1=50001, istep2=60000, value1=150.0, value2=160.0 /
&wt type='TEMP0', istep1=60001, istep2=70000, value1=160.0, value2=170.0 /
&wt type='TEMP0', istep1=70001, istep2=80000, value1=170.0, value2=180.0 /
&wt type='TEMP0', istep1=80001, istep2=90000, value1=180.0, value2=190.0 /
&wt type='TEMP0', istep1=90001, istep2=100000, value1=190.0, value2=200.0 /
&wt type='TEMP0', istep1=100001, istep2=110000, value1=200.0, value2=210.0
/
&wt type='TEMP0', istep1=110001, istep2=120000, value1=210.0, value2=220.0
/
&wt type='TEMP0', istep1=100001, istep2=110000, value1=200.0, value2=210.0
/
&wt type='TEMP0', istep1=110001, istep2=120000, value1=210.0, value2=220.0
/
&wt type='TEMP0', istep1=120001, istep2=130000, value1=220.0, value2=230.0
/
&wt type='TEMP0', istep1=130001, istep2=140000, value1=230.0, value2=240.0
/
&wt type='TEMP0', istep1=140001, istep2=150000, value1=240.0, value2=250.0
/
&wt type='TEMP0', istep1=150001, istep2=160000, value1=250.0, value2=260.0
/
&wt type='TEMP0', istep1=160001, istep2=170000, value1=260.0, value2=270.0
/
&wt type='TEMP0', istep1=170001, istep2=180000, value1=270.0, value2=280.0
/
&wt type='TEMP0', istep1=180001, istep2=190000, value1=280.0, value2=290.0
/
&wt type='TEMP0', istep1=190001, istep2=200000, value1=290.0, value2=300.0
/
&wt type='END' /
Hold lipid fixed
10.0
RES 1 384
END
END
Kindly, help me.
Thanks,
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Received on Thu Jun 21 2018 - 07:30:03 PDT
