qmmm simulation and question for md analysis

From: M. A (matabay2010_at_gmail.com)
Date: Mon Apr 20 2020 - 03:59:45 CDT

Dear al,
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

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:08 CST