From: s.bora erdemli (serdemli_at_ku.edu.tr)
Date: Wed Jul 20 2005 - 15:05:03 CDT
I performed MD simulations with 200 a.a. protein in NVT emsemble at 300 K. Protein is sovated with a TIP 3 water molecules by means of VMD. I used PBC and PME.
After a long minimiation period, I ran the program during 6ns simulation time.
my problem is with the energy output. I did not decide my energy values are correct or not. I am suspicious about order of magnitude. For simulation expressed above, the total energy of the complex was order of 10^5 and so was electrostatics which appered to be dominant .
are there any problem with my data? does anybody know a paper which reports energies of a NAMD simulation ?
thank you very much in advance
Sabri Bora Erdemli
Research and Teaching Asistant
Computational Sciences and Engineering
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