From: sabri bora erdemli (serdemli_at_ku.edu.tr)
Date: Thu Jul 07 2005 - 09:07:44 CDT
By using namddat I averaged van der Waals energies of my protein - protein complexes, and the sign of the average and the all the energies used in calculating averages were (+) positive.
When I was looking for it in the literature, I came across with numbers which are negatives(-).
Is there anything wrong, or this is depend on something else, I mean the sign of Van der Walls ?
ps. I did simulate a homodimer which has 200 aa. total. It was solvated and added counterions. I used NVT ensemble and CHARMM_27 parameters....
Sabri Bora Erdemli
Research and Teaching Asistant
Computational Sciences and Engineering
Koc Universitesi pk.218 34550
tel no: 902123381736
URL : home.ku.edu.tr/~serdemli
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