Does the list accept images?
I attached it several times…..
I will send it to your personal mail too,
Thanks a lot to everybody for the answers.
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 - 10:00:04 PDT
