From: Alex Balaeff (abalaeff_at_polarisqb.com)
Date: Sat Aug 29 2020 - 09:29:48 CDT
Zhihong:
My suggestion is to harmonically restrain the QM atom rather than to keep
it fixed. If you want to limit the movement of your QM molecule around the
simulation cell, the effect is going to be the same. See
https://www.ks.uiuc.edu/Research/namd/2.14/ug/node29.html , "Position
restraint"
Also I suggest to keep the QM region PDB and the restraint PDB as two
separate files. Makes it easier to change things if needed (e.g., if you
need to gradually lift the harmonic restraint).
Best,
Alexander.
On Sat, Aug 29, 2020 at 8:53 AM 辛志宏 <xzhfood_at_njau.edu.cn> wrote:
> Dear ALL,
> An ERROR occured when I run QM/MM by NAMD, the error information and the
> QM region setup as follows:
>
> 。。。。。。。。。。。。。。。。。。。
>
> ERROR: QM atom cannot be fixed in space!
> FATAL ERROR: Error processing QM information.
>
>
>
> QM region setup:
>
> set allatoms [atomselect top all]
> $allatoms set beta 0
> $allatoms set occupancy 0
> set QM [atomselect top "resid 75 76 77 144 193 238 268 299 4231"]
> $QM set beta 1
> $QM set occupancy 1
> $allatoms writepdb YZZ-namd-QM.pdb
>
>
>
> Any suggestion will be much appreciate for fixing the issue, thank you in
> advance.
>
>
> Zhihong XIn
>
>
>
-- ----- Dr. Alexander Balaeff * Polaris Quantum Biotech www.PolarisQB.com <http://www.PolarisQB.com>* (919)-270-5772
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:09 CST