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
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Received on Fri Apr 26 2019 - 18:30:03 PDT
