Re: [AMBER] Negative dihedral angle n glycan simulation

From: Rajarshi Roy <phd1701171011.iiti.ac.in>
Date: Thu, 11 Apr 2019 22:15:11 +0530

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
> >
> _______________________________________________
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>


-- 
*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*India*
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Received on Thu Apr 11 2019 - 10:00:03 PDT
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