AMBER Archive (2004)

Subject: AMBER: nrespa=2

From: Marsita M (marsitam_at_hotmail.com)
Date: Tue Dec 21 2004 - 09:19:58 CST

hi everyone

i have a question to ask and hope to get some answers

it's regarding nrespa in the ctrl lists.

is it okay to use nrespa=2 for vacuo simulation using distance dependent
dielectric constant? because i know it is acceptable to use in implicit and
explicit solvent simulation, but i have never heard (i'm still new in MD) of
ppl using nrespa=2 in vacuo. i need to know whether it will cause some
instability to the system since the long range forces is not calculated
every single steps.

and another question, how come the starting energy of my MD simulation
(Nstep=0) and the final energy of the minimized structure (the input rst
file to the MD run) are different?

starting energy for MD (Nstep=0) = 6624 kcal/mol
final energy after minimization = -3.2678E+03 kcal/mol

how come they are so hugely different?
for the minimization, i used constant dielectric with dielc=1
and for the MD, i used distance dependent dielectric, dielc=4, thats the
only difference between the runs, is is because of different types of
dielectric being used?

hope anybody can help me

thanks

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