From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Thu Dec 02 2021 - 11:05:25 CST
Hi Jing Liang,
This may be related to a difference in atom numbering between VMD and NAMD,
one being one-based and the other zero-based, so the atom numbers would be
shifted by 1. However, it is hard to say without knowing more about your
system.
Do you mind sharing a minimal example and the steps you are taking with
QwikMD?
Regarding the description for the qmLinkElement parameter, it should get
the two indices for the QM and MM atoms involved in the QM-MM bond, as well
as the element string. If there is only one QM-MM bond in your simulation,
you will not need to pass the atom numbers, just the element.
Best,
Marcelo
On Thu, 2 Dec 2021 at 04:25, jing liang <jingliang2015_at_gmail.com> wrote:
> Hi,
>
> I don't understand well the description of the parameter qmLinkElement
> from the documentation page:
> https://www.ks.uiuc.edu/Research/namd/2.14/ug/node90.html#47512
>
> It looks to me that when there are two or more bonds I need to pass the
> atom numbers of the MM atoms involved. Are these atom numbers obtained from
> the *psf file?
>
> I used QwikMD for setting the simulation and when I look at the value that
> this parameter got it says:
>
> #QMLinkElement "18 38 Cl"
>
> but the numbers 18 and 38 don't correspond to the atom numbers in the psf
> file of the atoms involved in the bond.
>
> I wonder how the numbers 18 and 38 are obtained? What they are?
>
> thank you
>
>
>
>
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