From: Ramesh Cheerla (cheerla.ramesh1_at_gmail.com)
Date: Tue Oct 09 2012 - 09:01:52 CDT
Dear NAMD users,
I am performing simulations of a polymer crystal in NAMD, the
forcefield that I have considered for these simulation has the Vdw
interactions in buckingham format, I am making use of tabulated potentials
for this purpose.
I have generated table with a spacing(dr) of 0.01 and tried to run
minimization but there is no change in the position of atoms and potential
energy, So to see the dependence of potential energy on spacing(dr) I have
made simple tests by varying "dr". By doing so I have understood that
even for a small change of "dr" also there is a large change in potential
energy.
Here i am summarizing the potential energies that I have obtained for each
"dr"
*dr(spacing) PE(kcal/mol) *
0.010500 0.1385
0.010570 0.1404
0.010571 9999999999.9999
0.010572 9999999999.9999
0.010573 0.1394
0.010575 9999999999.9999
0.010580 0.1372
0.010590 9999999999.9999
0.010600 0.1431
0.010700 9999999999.9999
0.010900 9999999999.9999
0.011000 0.1426
How can I account for this large change in potenmtial energy even for a
small change in spacing, I have used table interpretation type as "cubic"
(tableInterpType cubic) in my configuration file.
Can anybody explain the reason for this large change? Is the tabulated
potential in NAMD is very sensitive to the spacing or is this a limitation
in NAMD ?
Thank you in advance.
-- Regards, Ramesh,
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