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-- Sally Pias Associate Professor of Chemistry Faculty Adjunct, Department of Biology New Mexico Tech On Fri, Aug 3, 2018 at 6:07 PM, David Cerutti <dscerutti.gmail.com> wrote: > But he's been restarting every 0.5ns so it should be fine. > > On Fri, Aug 3, 2018, 6:50 PM Chris Neale <candrewn.gmail.com> wrote: > > > 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 > > > > > _______________________________________________ > > 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/amberReceived on Fri Aug 10 2018 - 15:30:02 PDT