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 The output format of 'dipole' command is outdated - the 'vector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
>
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Received on Wed Jan 02 2019 - 21:00:02 PST
