>From the graph and the input you've shown us, it doesn't look like you are
in trouble from a pair list bug. I'd say carry on with Amber12 until your
distro upgrades, then you'll be able to run faster on newer GPUs and check
your result.
Dave
On Fri, Aug 3, 2018, 5:55 PM Sally Pias <sallypias.gmail.com> wrote:
> Hi Somdev,
>
> Can you post a PDB file of your final structure - or send it to me
> directly? I am not sure I can assess what is going on from the
> two-dimensional image.
>
> Thanks,
> Sally
>
> --
> Sally Pias
> Associate Professor of Chemistry
> Faculty Adjunct, Department of Biology
> New Mexico Tech
> sallypias.gmail.com
>
> On Fri, Aug 3, 2018 at 8:59 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
On Fri, Aug 3, 2018, 5:55 PM Sally Pias <sallypias.gmail.com> wrote:
> Hi Somdev,
>
> Can you post a PDB file of your final structure - or send it to me
> directly? I am not sure I can assess what is going on from the
> two-dimensional image.
>
> Thanks,
> Sally
>
> --
> Sally Pias
> Associate Professor of Chemistry
> Faculty Adjunct, Department of Biology
> New Mexico Tech
> sallypias.gmail.com
>
> On Fri, Aug 3, 2018 at 8:59 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 03 2018 - 15:30:02 PDT
