From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Aug 07 2017 - 07:18:28 CDT

You can obtain up-to-date CHARMM topology files at:
http://mackerell.umaryland.edu/charmm_ff.shtml

These files are readable from the PSFGen utility:
http://www.ks.uiuc.edu/Research/namd/2.12/ug/node15.html

On Mon, Aug 7, 2017 at 12:07 AM, <t.shivam_at_iitg.ernet.in> wrote:

>
>
> > On Sun, Aug 6, 2017 at 10:30 PM, <t.shivam_at_iitg.ernet.in> wrote:
> >
> >>
> >>
> >> > On Sun, Aug 6, 2017 at 10:51 AM, <t.shivam_at_iitg.ernet.in> wrote:
> >> >
> >> >> Dear vmd users,
> >> >>
> >> >> I have a protein solvated in a water box whose net charge is
> >> >> 7.999999954365194, so when i am using autoionize to neutralize my
> >> system
> >> >> it is showing a charge of -4.563480615615845e-8, i also tried to add
> >> 8
> >> >> chlorine ions instead of going for neutralize option (anyway its more
> >> or
> >> >> less the same thing), so please kindly help me with this problem.
> >> >>
> >> >
> >> > ​there is no problem with autoionize. the problem is between your
> >> chair
> >> > and
> >> > your computer.​ you are doing floating point math here​​, so
> >> -4.5e-8
> >> > is
> >> > essentially zero and most certainly zero when rounded to the precision
> >> at
> >> > which partial charges are specified in the CHARMM force field.
> >> >
> >> > axel.
> >>
> >>
> >> this might sound funny to you but previously i have solvated my protein
> >> in
> >> a smaller box but the charge of the protein is same
> >> (7.999999954365194)so
> >> at that when i neutralized my system, vmd was showing a perfect
> >> zero(0.0),
> >>
> >
> > ​this is not funny. it only shows, that ​you seem unaware of the
> > idiosyncrasies of doing math with floating point numbers.
> >
> >
> >> so i saved the files of the ionized system, but after that i also
> >> created
> >> a bigger box, and now when i am neutralizing it, it is showing
> >> -4.563480615615845e-8, and the strangest part is that when i am checking
> >> my previous system (smaller box showing charge 0.0) it is also showing
> >> -4.563480615615845e-8,why is that happening?i agree that the value
> >> -4.563480615615845e-8 is almost zero.
> >>
> >
> > ​this is happening, because you are doing floating point math (and are
> > outputting results with a precision that exceeds the precision of
> > storage).
> > VMD stores charges as float, and quite a few numbers cannot be
> represented
> > exactly with floating point representations.​
> >
> > i suggest you study the following two blog posts:
> > http://blog.reverberate.org/2014/09/what-every-computer-
> programmer-should.html
> > http://blog.reverberate.org/2016/02/06/floating-point-
> demystified-part2.html
> >
> > p
> > ​lease keep in mind, the origin of the non-exactly-zero is the summing
> > of
> > the partial charges which results in not-exactly-eight. just what do you
> > get, when you subtract 8 from 7.999999954365194 ?? there is no mystery at
> > all here.
> >
> > axel.
> >
> >
> >> regards
> >> shivam
> >> >
> >> >
> >> >>
> >> >> regards
> >> >> shivam
> >> >>
> >> >>
> >> >
> >> >
> >> > --
> >> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> > College of Science & Technology, Temple University, Philadelphia PA,
> >> USA
> >> > International Centre for Theoretical Physics, Trieste. Italy.
> >> >
> >>
> >>
> >
> >
> > --
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> > College of Science & Technology, Temple University, Philadelphia PA, USA
> > International Centre for Theoretical Physics, Trieste. Italy.
> >
>
> yes sir i was unaware of it, i am quite novice to the computational world,
> thanks for your suggestions and the link, i have one follow up question
> regarding the same, since i have obtained the psf of my protein using opls
> topology, but autoionize is using charmm topology to generate the psf
> files will it create problem in my simulations since i wish to use oplsAA
> force field for my simulations,if yes how can i use opls topology to add
> ions to my system.
>
> regards
> shivam
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin