Hi,
As stated in the manual, the output from the vector command is ’Vx Vy
Vz Ox Oy Oz’ where V denotes vector coordinates and ’O’ denotes origin
coordinates. If you want magnitude as well specify the 'magnitude'
keyword - see the manual for full details.
-Dan
On Wed, Jan 2, 2019 at 11:39 PM Fulbabu Sk <phd1701171005.iiti.ac.in> wrote:
>
> Dear all,
> In the output data file, there are 7 columns, but I don't identify which
> one is dipole moment column.
> Please clarify the 7 columns.
>
>
>
>
>
> ***************
> Kind regards
>
> *Md Fulbabu Sk*
>
>
>
> *Ph.D. Research ScholarDiscipline of BioSciences and Biomedical Engineering
> (BSBE)Indian Institute of Technology Indore (IITI), India*
> Computational BioPhysics Group IITI (Kar's Lab)
> <https://iitibsbeparimalkar.wixsite.com/biophysics>
>
>
> On Thu, Jan 3, 2019 at 7:16 AM Xiaocong Wang <wangxiaocong.outlook.com>
> wrote:
>
> > Thank you very much!
> >
> > Dividing by 0.2082 is correct.
> >
> > Best regards,
> >
> > Xiao
> >
> >
> >
> > ________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: Thursday, January 3, 2019 2:52:13 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Calculated dipole moment in AMBER
> >
> > Hi,
> >
> > > I read one post, which says the unit for dipole moment calculated from
> > AMBER cpptraj is not Debye(D). And, the code for calculating dipole moment
> > may be out-dated.
> >
> > CPPTRAJ (like the rest of Amber) uses the AKMA unit system, so charge
> > is in electrons and length is in Angstroms, meaning the dipole is in
> > units of e * Ang; you'll have to convert to get to Debye (I believe
> > the conversion is dividing by ~ 0.2082 but you should double check).
> >
> > The output format of 'dipole' command is outdated - the 'vector
> > dipole' code is fine.
> >
> > -Dan
> >
> > On Wed, Jan 2, 2019 at 10:22 AM Xiaocong Wang <wangxiaocong.outlook.com>
> > wrote:
> > >
> > > Dear all,
> > > I used cpptraj to calculate the dipole moment for a sugar. But, the
> > value is very different from that calculated in QM.
> > > Codes are as follows:
> > >
> > > trajin sugar.rst7
> > > vector v1 :1-2 dipole out sugar_dipole.txt
> > > go
> > >
> > > I read one post, which says the unit for dipole moment calculated from
> > AMBER cpptraj is not Debye(D). And, the code for calculating dipole moment
> > may be out-dated.
> > > Can I get some help on this issue?
> > > Thank you very much!
> > > Best,
> > > Xiao
> > >
> > > _______________________________________________
> > > 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
> > _______________________________________________
> > 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 03 2019 - 05:30:03 PST
