I think jason made a good point, but I expect that allowing the refc to
change for each run is more likely what's going on here. check that first
before doing NVT.
On Tue, Oct 27, 2015 at 1:02 PM, Fabian gmail <fabian.glaser.gmail.com>
wrote:
> So Jason,
>
> Would you recommend to run production with NVT?
>
> The reason I used NPT was the protocol on the tutorial of MMPBSA on amber
> site uses it….
>
> If NVT is good enough, I will switch, since I understand it will also be
> quicker.
>
> Thasnk!!
> Fabian
>
>
>
>
> Dr. Fabian Glaser
> Head of the Structural Bioinformatics section
>
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
> Engineering
> Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
>
> fglaser at technion dot ac dot il
> Tel: +972 4 8293701
> http://bku.technion.ac.il
>
>
> > On 27 Oct 2015, at 6:39 PM, Jason Swails <jason.swails.gmail.com> wrote:
> >
> > I still do not see an image...
> >
> > On Tue, Oct 27, 2015 at 12:10 PM, Fabian gmail <fabian.glaser.gmail.com
> <mailto:fabian.glaser.gmail.com>>
> > wrote:
> >
> >> Yeah I know, but still there is a qualitatively jump that stays stable
> for
> >> each different 5ns simulation, I attach a figure hope you can see it.
> >> Carlos Simmerling explained me what you say that there is jump in time,
> and
> >> restarting I understand also produces some "instantaneous jump in the
> >> restraint energy, which changes the forces and the simulation adjusts
> to a
> >> new average structure with different energy” in Carlos words.
> >>
> >> But still it puzzled me a little, here is the jump please notice it gets
> >> smaller and smaller with simulation time…. but there is a jump specially
> >> after 5ns and 10 ns, there it gets much better.
> >>
> >
> > Restraints with constant pressure are a little weird. To implement
> > constant pressure, what sander/pmemd does is scale the molecule positions
> > slightly (either bringing all of them closer to the center of the box or
> > farther away, depending on whether the pressure needs to be decreased or
> > increased to match the external barostat, respectively).
> >
> > If the restraint positions stay the same, you now have an external force
> > pulling the atoms back to where they *used* to be, thereby opposing the
> > scaling move. I believe that to avoid this, what sander/pmemd does is to
> > scale the restraint coordinates *as well*. So what I think might be
> > happening here is that when you are restarting *with the same restraint
> > coordinate file*, you are also introducing a (very slightly) different
> set
> > of restraint coordinates as sander/pmemd was using at the end of the
> > previous simulation.
> >
> > This will introduce an impulse upon restart (since the restraint force is
> > now a bit different than it was at the end of the previous simulation).
> > Since this is what you say you are seeing (send us pictures! ;)), it
> would
> > seem to me to be a reasonable explanation.
> >
> > You can test this idea in one of two ways:
> >
> > 1. Remove the restraints
> > 2. Remove the barostat
> >
> > If either eliminates the artifact you are seeing, chances are increased
> > that what I described is the culprit (which is less of a problem than
> using
> > restraints for your whole simulation).
> >
> > I plan to use your MMPBSA.py script only starting at 20 or 30 ns for 20
> ns
> >> (2000 frames) is that good enough?
> >>
> >
> > You will probably get the same results using 200 frames over 20 ns than
> > 2000. MMPBSA.py results converge within a few hundred frames (properly
> > sampled and independent from each other, of course).
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
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Received on Tue Oct 27 2015 - 10:30:05 PDT
