From: Ramesh Cheerla (cheerla.ramesh1_at_gmail.com)
Date: Tue Oct 02 2012 - 10:17:47 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, is there any
option in NAMD for handling buckingham potentials other than using tables.
As I have tried with the tables, if I do minimization
with the tabulated buckingham potentials, energy is not changing after
the first step of minimization and no movement in the position of atoms. If
I try to run equilibration with the output of this minimization, simulation
is crashing in second step itself by giving the following errors:
ERROR: Atom 2229 velocity is -4754.04 -400.092 -37998.6
(limit is 10000)
ERROR: Atom 5535 velocity is 5033.54 173.554 38130.6
(limit is 10000)
ERROR: Atoms moving too fast; simulation has become
I have used following protocol for tabulated potentials:
1) Generated tables with a spacing of 0.01 angstroms and all the
constants(A,B & C) required for calculation of potential energy and force
are taken in NAMD convention i.e (kcal/mol and Angstroms). and used
following formulas for calculation of potential energy and force:
2) I have included following options in my configuration file:
3) Finally I have included "NBTABLE" option in CHARMM parameter file
which I am using.
Moreover in parameter file I have tried to remove the sigma and epsilon
entries for the atom types for which I am using tables but it is giving
the error "no Vdw parameters for atom type" , why NAMD is giving this
error though I am specifying the interactions in NBTABLE ?
Am I making any mistake in using tabulated potentials ?.
Can anybody please help me in this regard,
Thank you in advance.
-- Regards, Ramesh.
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