Actually, using Langevin dynamics, the ig=-1 option would be the only way
to avoid artifacts related to systematic net forces (i.e., a constant
positive value for the ig setting would be completely incorrect in this
case).
On Tue, Sep 19, 2017 at 8:25 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> You can check the manual for what does it mean.
>
> > On Sep 19, 2017, at 9:25 PM, Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
> >
> > Hi Rana,
> >
> > And to use ig=-1 for these runnings, in order to get better samplings.
> >
> > Kind regards,
> > Pengfei
> >
> >> On Sep 16, 2017, at 10:22 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
> >>
> >> Hi,
> >> Breaking down your simulations only means running ten simulations of
> 10ns each restarting from the previous run.
> >> Use nstlim = 5000000 and dt = 0.002.
> >> Best Regards
> >> Elvis Martis
> >> Mumbai, INDIA.
> >>
> >> ________________________________________
> >> From: Rana Rehan Khalid <rrkhalid.umich.edu>
> >> Sent: 17 September 2017 00:37
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] simulation time
> >>
> >> Can you please guide me how i can break simulation for ten runs as you
> >> mention or send me url link.
> >>
> >> Thank you so much sir for your help.
> >>
> >> On Sat, Sep 16, 2017 at 2:34 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> >> wrote:
> >>
> >>> Hi,
> >>> 100 ns is common these days.
> >>> But what I recommend here is, run your MD in parts instead of one
> single
> >>> run.
> >>> Here you can break 100 ns into 10 runs of 10 ns each or 20 runs of 5
> ns
> >>> each.
> >>>
> >>> Best Regards
> >>> Elvis Martis
> >>> Mumbai, INDIA.
> >>>
> >>> ________________________________________
> >>> From: Rana Rehan Khalid <rrkhalid.umich.edu>
> >>> Sent: 17 September 2017 00:01
> >>> To: AMBER Mailing List
> >>> Subject: Re: [AMBER] simulation time
> >>>
> >>> Thanks Elvis. Is this normal practice in MD to run the simulation for
> >>> 50000000 steps?
> >>>
> >>> Regards
> >>>
> >>> On Sat, Sep 16, 2017 at 2:14 PM, Elvis Martis <elvis.martis.bcp.edu.in
> >
> >>> wrote:
> >>>
> >>>> HI
> >>>> all the time scales in the input file are mentioned in ps.
> >>>> For instance dt = 0.002 means 2fs time step.
> >>>> if you want to know the time simulation, then time (ps) = nstlim * dt.
> >>>> for 100 ns = 100000 ps with dt = 0.002 ps your nstlim must be
> 50000000.
> >>>>
> >>>> Best Regards
> >>>> Elvis Martis
> >>>> Mumbai, INDIA.
> >>>>
> >>>> ________________________________________
> >>>> From: Rana Rehan Khalid <rrkhalid.umich.edu>
> >>>> Sent: 16 September 2017 22:22
> >>>> To: AMBER Mailing List
> >>>> Subject: [AMBER] simulation time
> >>>>
> >>>> Hi Everybody
> >>>>
> >>>> If I want to run the simulation in amber for 100ns what would be the
> >>> values
> >>>> of these flags. Actually i am confused between pico and nano.
> >>>>
> >>>> nstlim=50000,
> >>>> dt=0.002, this is for 100ps duration time.
> >>>>
> >>>> nstlim=?? for 50 nenosec
> >>>>
> >>>> Regards
> >>>> _______________________________________________
> >>>> 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/amber
> >
>
>
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Received on Tue Sep 19 2017 - 20:00:02 PDT
