Re: qmmm simulation and question for md analysis

From: Francesco Pietra (
Date: Mon Apr 20 2020 - 05:16:02 CDT

Hi Maryam
Did you submit the general dcd or QMonly.dcd?


On Mon, Apr 20, 2020 at 11:02 AM M. A <> wrote:

> Dear al,
> Hi
> For learning qmmm simulation I tried to repeat the related tutorial and it
> was executed correctly.
> Now I have a question:
> Actually in addition qm analysis for atoms of QM region, I want to check
> thermodynamic properties of residues around QM region. So after simulation
> and in any part of simulation for example Minimization, Annealing or QMMM,
> I uploaded structure files(CBM_QM_QwikMD.pdb and CBM_QM_QwikMD.psf) and dcd
> files for analyzing thermodynamic properties like energy, temperature or
> RMSD .... with NAMD PLOT plugin or other plugins of vmd, but after
> uploading log file there was nothing in multiplot window and this window
> was empty. while log file shows that simulation is completed and there is
> data of energy and pressure.
> do you know what the problem is?
> I am grateful for your help.
> best regards
> --
> Maryam Atabay
> Ph.D in Nano Computational Chemistry
> Department of Physics, Sharif University of Technology

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