Re: [AMBER] Negative dihedral angle n glycan simulation

From: Rajarshi Roy <phd1701171011.iiti.ac.in>
Date: Sat, 27 Apr 2019 07:50:08 +0530

Thank you very much for your time and your detail explanation.

On Sat, Apr 27, 2019 at 6:41 AM Lachele Foley <lf.list.gmail.com> wrote:

> Again, sorry to be so long.
>
> You asked:
> "As you told that dihedral terms are just correction term to other
> bonded parameters I do not get that point. As per my understanding, bonded
> terms are comprised of bond vibration, angle and dihedral terms. So how
> this dihedral term becomes a correction term to this?"
>
> The dihedral term is a way to capture certain subtle effects of
> electronic structure, for example certain geometric phenomena often
> ascribed to "lone pairs", which are not explicitly modeled for 1-4
> interactions in Class I force fields. "Lone pair" effects are modeled
> for 1-2 and 1-3 interactions via the bond and angle terms. But, for
> 1-4 interactions, these phenomena may not be properly modeled by the
> combination of bond, angle, van der Waals and charge-charge
> interactions. The dihedral term provides a mechanism for improving
> the model. As such, most of the energy giving rise to a 1-4
> interaction is usually captured by the non-dihedral terms for the
> relevant atoms. The dihedral term merely provides an energy
> correction.
>
> The paper below is focused on carbohydrates - where these effects are
> very important - but the principles discussed are very general. It's
> written for a scientifically literate, but non-specialist audience, so
> it should be easily accessible to anyone on this list. It describes
> these phenomena, dihedrals ("torsion" terms), Class I force fields,
> etc.
>
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4270206/
>
> On Thu, Apr 11, 2019 at 1:01 PM Rajarshi Roy <phd1701171011.iiti.ac.in>
> wrote:
> >
> > Hi Irfan,
> > Thank you for your concern. I am running my simulation only in cuda using
> > pmemd.cuda module. This issue not because of the gamd simulation. The
> > conventional MD simulation is also showing negative dihedral energy as
> same
> > as the gamd simulation. I also try the aMD simulation to check. First few
> > steps of aMD, no dihedral boost was added to the simulation where
> dihedral
> > energy is negative. But after that, it becomes positive and boost
> potential
> > also appear. I had no clue about this behaviour in aMD. I really confuse
> > and worried about my simulation that is it working properly or not. Any
> > kind of suggestion would be appreciated and again thank you for your
> help.
> >
> > On Thu, Apr 11, 2019 at 10:15 PM Rajarshi Roy <phd1701171011.iiti.ac.in>
> > wrote:
> >
> > > Dear Mam,
> > > I want to thank you for your generous reply. I already discussed with
> the
> > > Gamd guys and they send for negative dihedral energy instead of dual
> boost
> > > we can a use total potential energy boost only. I have a question from
> your
> > > reply. As you told that dihedral terms are just correction term to
> other
> > > bonded parameters I do not get that point. As per my understanding,
> bonded
> > > terms are comprised of bond vibration, angle and dihedral terms. So how
> > > this dihedral term becomes a correction term to this? Maybe it is a
> silly
> > > question to ask but really want to clarify my doubts.
> > > Thank you again for your valuable time.
> > >
> > > On Thu, Apr 11, 2019 at 5:15 PM Irfan Alibay <
> irfan.alibay.lists.gmail.com>
> > > wrote:
> > >
> > >> Hi,
> > >>
> > >> Just to add to this, we looked into this (or at least a very similar)
> > >> issue
> > >> with negative dihedral energies when running aMD simulations some time
> > >> ago.
> > >> Unfortunately, I forgot to report it as it was towards the end of my
> PhD.
> > >> As far as I know, the aMD code will work as expected with negative
> > >> dihedral
> > >> energies when using the CPU version of pmemd (do you find that this in
> > >> indeed the case for you too Rajarshi?).
> > >>
> > >> However they do not in pmemd.cuda. This seems to be due to a missing
> > >> bitwise xor (checking against INT_MAX) when doing uint to double
> > >> conversions after downloading the energies from the device in the aMD
> > >> routines of gpu.cpp.
> > >> Fixing this appears to resolve the problem. I am unsure about GaMD,
> but it
> > >> appears that a similar thing might also be happening.
> > >>
> > >> I can probably create a diff patch for it, if more code details are
> > >> needed.
> > >>
> > >> Many thanks,
> > >>
> > >> Irfan Alibay
> > >> Postdoctoral Research Associate
> > >> Department of Biochemistry
> > >> The University of Oxford
> > >>
> > >>
> > >>
> > >> On Wed, Apr 10, 2019 at 8:14 PM Lachele Foley <lf.list.gmail.com>
> wrote:
> > >>
> > >> > Replying to the list so this info is more generally available in
> case
> > >> > others wonder.
> > >> >
> > >> > The files look ok best I can tell without digging really deeply.
> The
> > >> > GLYCAM force field does have some negative amplitudes in the
> dihedral
> > >> > terms. So, it is certainly possible to have negative dihedral
> values.
> > >> > This is a small effect, and the presence of protein or other
> residues
> > >> > usually make it so that the overall values are negative. But, this
> > >> > file is just an oligosaccharide in water. Water has no dihedrals,
> so
> > >> > no dihedral terms. And, the specific oligosaccharide contains some
> of
> > >> > the atom types that can have negative values in their associated
> > >> > dihedrals. I didn't check every dihedral individually (because
> that's
> > >> > a lot of work), but I think it's ok that you have negative DIHED
> > >> > values. If you're really worried, try using parmtop utilities in
> > >> > AmberTools too look closely at all the dihedrals. Those tools work
> > >> > well.
> > >> >
> > >> > Maybe ask the gamd folks if they can make it possible for negative
> > >> > dihedral energies not to cause trouble?
> > >> >
> > >> > It might not be a problem anyway. Consider the amount of the effect
> > >> > compared to what gamd does. If you are trying to increase sampling,
> > >> > you're probably already messing with the energy function. If the
> > >> > DIHED values are small compared to other bonded energies, it might
> not
> > >> > make a lot of difference to the outcome, depending on exactly what
> > >> > gamd is doing. Keep in mind that dihedral energies are just
> > >> > corrections to the other bonded terms, at least in the GLYCAM
> > >> > philosophy.
> > >> >
> > >> > On Tue, Apr 9, 2019 at 1:32 PM Lachele Foley <lf.list.gmail.com>
> wrote:
> > >> > >
> > >> > > Send it to my personal email (lf.list.gmail.com).
> > >> > >
> > >> > > On Tue, Apr 9, 2019 at 3:56 AM Rajarshi Roy <
> phd1701171011.iiti.ac.in
> > >> >
> > >> > wrote:
> > >> > > >
> > >> > > > Dear Mam,
> > >> > > > Did you receive the topology file? In amber mailing list is not
> > >> > allowing me
> > >> > > > to send those files because of the size issue.
> > >> > > >
> > >> > > > On Tue, Apr 9, 2019 at 9:13 AM Rajarshi Roy <
> > >> phd1701171011.iiti.ac.in>
> > >> > > > wrote:
> > >> > > >
> > >> > > > > Dear Mam,
> > >> > > > > I am not still able to figure it out. I am simulating a
> > >> proteoglycan
> > >> > chain
> > >> > > > > only. So there is no protein part. My chain just consists of
> > >> dermatan
> > >> > > > > sulphate only. Please check my topology and coordinate files.
> I am
> > >> > not able
> > >> > > > > to find any error or discrepancy in output files or by
> > >> visualization.
> > >> > > > > Thank you in advance
> > >> > > > >
> > >> > > > > On Mon, Apr 8, 2019 at 9:20 PM Lachele Foley <
> lf.list.gmail.com>
> > >> > wrote:
> > >> > > > >
> > >> > > > >> Also... I'm pretty sure they shouldn't be negative. So, I
> might
> > >> > need
> > >> > > > >> a lot of details.
> > >> > > > >>
> > >> > > > >> If you already figured it out, just let us know.
> > >> > > > >>
> > >> > > > >> On Mon, Apr 8, 2019 at 11:24 AM Lachele Foley <
> lf.list.gmail.com
> > >> >
> > >> > wrote:
> > >> > > > >> >
> > >> > > > >> > Sorry to take so long to respond. There's lots going on.
> > >> > > > >> >
> > >> > > > >> > Can you tell me more molecular details about your system?
> > >> > > > >> > Specifically, how large is the 'proteo' part and how large
> is
> > >> the
> > >> > > > >> > 'glycan' part? Feel free to send the input prmtop and
> inpcrd
> > >> to
> > >> > me
> > >> > > > >> > (to just me is fine). Thanks!
> > >> > > > >> >
> > >> > > > >> > On Tue, Apr 2, 2019 at 7:05 AM Rajarshi Roy <
> > >> > phd1701171011.iiti.ac.in>
> > >> > > > >> wrote:
> > >> > > > >> > >
> > >> > > > >> > > Dear AMBER user and developers,
> > >> > > > >> > > I am trying to simulate a proteoglycan structure using
> > >> > conventional
> > >> > > > >> > > molecular dynamics technique. Everything seems to be
> fine in
> > >> the
> > >> > > > >> output
> > >> > > > >> > > file where only the dihedral energy is showing a negative
> > >> > value. So
> > >> > > > >> why am
> > >> > > > >> > > I getting the negative value in dihedral energy? Is
> there any
> > >> > > > >> discrepancy
> > >> > > > >> > > in my system?
> > >> > > > >> > > Secondly, when I am trying to simulate the same system
> using
> > >> > amd or
> > >> > > > >> gamd in
> > >> > > > >> > > dual boost mode, but dihedral boost potential remains
> zero
> > >> > throughout
> > >> > > > >> our
> > >> > > > >> > > simulation. As discussed in the gamd archive it is
> because of
> > >> > the
> > >> > > > >> negative
> > >> > > > >> > > dihedral energy.
> > >> > > > >> > > So is it an error to get negative dihedral energy or can
> I
> > >> use
> > >> > the
> > >> > > > >> single
> > >> > > > >> > > potential boost in amd or gamd technique?
> > >> > > > >> > > It will be beneficial for me if you clarify all these
> doubts.
> > >> > > > >> > > Thank you in advance!
> > >> > > > >> > >
> > >> > > > >> > > --
> > >> > > > >> > > *with regards*
> > >> > > > >> > >
> > >> > > > >> > > *Rajarshi Roy*
> > >> > > > >> > >
> > >> > > > >> > >
> > >> > > > >> > > *PhD Research Scholar*
> > >> > > > >> > >
> > >> > > > >> > > *Biosciences and Biomedical Engineering*
> > >> > > > >> > >
> > >> > > > >> > > *Indian Institute of Technology, Indore*
> > >> > > > >> > > *India*
> > >> > > > >> > > _______________________________________________
> > >> > > > >> > > AMBER mailing list
> > >> > > > >> > > AMBER.ambermd.org
> > >> > > > >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > > >> >
> > >> > > > >> >
> > >> > > > >> >
> > >> > > > >> > --
> > >> > > > >> > :-) Lachele
> > >> > > > >> > Lachele Foley
> > >> > > > >> > CCRC/UGA
> > >> > > > >> > Athens, GA USA
> > >> > > > >>
> > >> > > > >>
> > >> > > > >>
> > >> > > > >> --
> > >> > > > >> :-) Lachele
> > >> > > > >> Lachele Foley
> > >> > > > >> CCRC/UGA
> > >> > > > >> Athens, GA USA
> > >> > > > >>
> > >> > > > >> _______________________________________________
> > >> > > > >> AMBER mailing list
> > >> > > > >> AMBER.ambermd.org
> > >> > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > > >>
> > >> > > > >
> > >> > > > >
> > >> > > > > --
> > >> > > > > *with regards*
> > >> > > > >
> > >> > > > > *Rajarshi Roy*
> > >> > > > >
> > >> > > > >
> > >> > > > > *PhD Research Scholar*
> > >> > > > >
> > >> > > > > *Biosciences and Biomedical Engineering*
> > >> > > > >
> > >> > > > > *Indian Institute of Technology, Indore*
> > >> > > > > *India*
> > >> > > > >
> > >> > > >
> > >> > > >
> > >> > > > --
> > >> > > > *with regards*
> > >> > > >
> > >> > > > *Rajarshi Roy*
> > >> > > >
> > >> > > >
> > >> > > > *PhD Research Scholar*
> > >> > > >
> > >> > > > *Biosciences and Biomedical Engineering*
> > >> > > >
> > >> > > > *Indian Institute of Technology, Indore*
> > >> > > > *India*
> > >> > > > _______________________________________________
> > >> > > > AMBER mailing list
> > >> > > > AMBER.ambermd.org
> > >> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > >
> > >> > >
> > >> > >
> > >> > > --
> > >> > > :-) Lachele
> > >> > > Lachele Foley
> > >> > > CCRC/UGA
> > >> > > Athens, GA USA
> > >> >
> > >> >
> > >> >
> > >> > --
> > >> > :-) Lachele
> > >> > Lachele Foley
> > >> > CCRC/UGA
> > >> > Athens, GA USA
> > >> >
> > >> > _______________________________________________
> > >> > 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
> > >>
> > >
> > >
> > > --
> > > *with regards*
> > >
> > > *Rajarshi Roy*
> > >
> > >
> > > *PhD Research Scholar*
> > >
> > > *Biosciences and Biomedical Engineering*
> > >
> > > *Indian Institute of Technology, Indore*
> > > *India*
> > >
> >
> >
> > --
> > *with regards*
> >
> > *Rajarshi Roy*
> >
> >
> > *PhD Research Scholar*
> >
> > *Biosciences and Biomedical Engineering*
> >
> > *Indian Institute of Technology, Indore*
> > *India*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


-- 
*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*India*
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Received on Fri Apr 26 2019 - 19:30:02 PDT
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