From: s.bora erdemli (serdemli_at_ku.edu.tr)
Date: Mon Jul 11 2005 - 11:20:15 CDT
Hi;
I did molecular dynamics with a protein complex which has 200 residue total and solvated with TIP3 water molecules. It was added counterions in order to neutralize the system. (NVT ensemble, T = 310 K)
My question is the following;
when I looked at the energy output, the order of magnitude of the TOTAL energy is 10^4. It seems strange to me when comparing with the literature. Is it normal? or In order to compare with the literature, Do I have to some kind of neutralization?
sincerely
Sabri Bora Erdemli
Research and Teaching Asistant
KOC UNIVERSITY
Computational Sciences and Engineering
Koc Universitesi pk.218 34550
sariyer/Istanbul TURKEY
tel no: 02123381736
05326512523
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