The molecules are not out of the box. The periodic boundary conditions
equate, connect, the upper and lower layers of your membrane. In order to
simulate an electrical potential across the membrane, you would need to (A)
simulate two membranes forming a sandwich over one layer of ions that
differs in concentration from the unified top + bottom region of your box,
or (B) recommended, use the electrostatic field simulation tools to impose
a voltage gradient across the membrane. Because the concentration
differences for generating fields in biology are minute, and the numbers of
ions in simulations are so small, you'd need a big box and a long
simulation time to use (A) effectively. But, the molecules are not out of
the box. Just use wrapping in cpptraj if you want to see everything neatly
packed back into the primary unit cell.
Dave
On Thu, Jun 21, 2018 at 10:22 AM somdev pahari <somdevpahari1.gmail.com>
wrote:
> 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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>
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Received on Thu Jun 21 2018 - 08:00:02 PDT
