Seems to me like you could stop the simulation and then restart it. Should
Amber not then regenerate the number of domain decomposition cells to avoid
pair-list violation? This thread:
http://archive.ambermd.org/201612/0340.html suggests that is the case, at
least for amber16.
On Fri, Aug 3, 2018 at 4:22 PM, David Cerutti <dscerutti.gmail.com> wrote:
> >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
>
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Received on Fri Aug 03 2018 - 16:00:01 PDT
