Dear All,
How is the force calculated during the simulated molecular dynamics?
I'm running SMD in conjunction with Jarzynski relationship.
The dist_vs_t file gives four columns. I was trying to the equation given by
Klaus Schulten's PNAS article referred in AMBER 11 manual to calculate the
force. But I cannot reproduce the force column using
x0(t) and x and v=0.04 angstrom/ps and time step 0.002 ps.
Any suggestions will be helpful.
Thanks and regards
Sai
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Received on Wed Aug 31 2011 - 16:30:02 PDT
