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*
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Received on Tue Apr 09 2019 - 01:00:03 PDT
