VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Jun 21 2018 - 10:03:44 CDT

Hi Bargeen,

the *_qm.psf is used to visualize the
​ ​
dcd file generated by NAMD containing the QM region only. This file is
easily generated, by loading the psf and pdb of your entire system, make an
atom selection with your QM regions only, and then save the psf file as
"$sel writepsf outputfilename.psf" .

Best

João

On Thu, Jun 21, 2018 at 9:50 AM SM Bargeen A Turzo <
s.turzo_at_vikes.csuohio.edu> wrote:

> Hi João,
>
>
> Thank you for that. I was also wondering if I need to adjust the
> *_qm-input.psf as well.
>
>
> -Bargeen
> ------------------------------
> *From:* João Ribeiro <jribeiro_at_ks.uiuc.edu>
> *Sent:* Wednesday, June 20, 2018 6:06:36 PM
> *To:* SM Bargeen A Turzo
> *Cc:* Vmd l; Marcelo C. R. Melo
> *Subject:* Re: vmd-l: Atom Selections in QwikMD
>
> Dear Bargeen,
>
> You are not missing anything, QwikMD currently selects the entire residue
> when preparing QM regions including protein and nucleic residues to make
> sure that no charge groups is broken creating QM regions with fractional
> charges, and to keep the total charge of the system constant.
>
> You can find more information at
> http://www.ks.uiuc.edu/Research/qmmm/#LACCG. One can always edit the
> *_qm-input.pdb that defines the qm region (beta column) and the QM-MM bonds
> (occupancy column) to meet their needs. Make sure that you updated the
> total charge in *.conf file as well, if needed or course.
>
> We are evaluating ways of changing this behavior without introducing
> errors.
>
> Best
>
> João
>
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> http://www.ks.uiuc.edu/~jribeiro/
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
> 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851