From: Boyang Wang (pkuwangboyang_at_yahoo.com.cn)
Date: Thu Jul 07 2005 - 13:23:52 CDT
Hi. I guess that you can try to make a quite long DNA and make the length of the box very close to the length of DNA and apply periodic boundary condition.
You could freeze the DNA chain and make it longer to save time.
That's my guess.
SABRI BORA ERDEMLI <SERDEMLI_at_KU.EDU.TR> 写道：
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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