That's quite a lot of shrinkage, but shrinkage is to be expected after
beginning a simulation when the molecules have been placed to avoid clashes
but not equilibrated against one another. Usually I see about 20%
shrinkage for a protein in water, but the more extensive membrane may be
doing it. There have been a number of bugs fixed regarding the periodic
pair list construction over the years, and while I'm not sure if Amber12
was failing to detect the box shrinking so far that pair list violations
became the norm, I do remember we detected the behavior during a membrane
simulation. Upgrade your Amber distro if possible. Otherwise, the
snapshot you've posted doesn't look unreasonable to me.
Dave
On Fri, Aug 3, 2018 at 11:03 AM somdev pahari <somdevpahari1.gmail.com>
wrote:
> 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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Received on Fri Aug 03 2018 - 08:30:01 PDT
