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*
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Received on Thu Apr 11 2019 - 10:30:03 PDT
