Hi,
I am trying to run pmemd using AMOEBA parameters (which I have
previously done succesfully), where the DMSO molecule has an additional
'M' site defined at the lone pair position.
While I have been able to generate the inpcrd and prmtop files using
/amoeba_parm, /after one step in a pmemd NPT simulation, all the
velocity dependent properties are NaN, while all the potential energy
values are fine.
NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = NaN PRESS
= NaN
Etot = NaN EKtot = NaN EPtot =
-22940.5513
BOND = 226.9192 ANGLE = 597.6138 DIHED =
-226.2797
1-4 NB = 550.2788 1-4 EEL = 0.0000 VDWAALS =
1424.3225
EELEC = -21829.1325 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = NaN VIRIAL = NaN VOLUME =
140608.0000
EPOLZ = -3684.2734
Dipole convergence: rms = 0.469E-04 iters = 14.00
Density =
0.6981
When I run the system using tinker programs, including /dynamic/, the
system propagates succesfully. I have previously generated inpcrd and
prmtop files with AMOEBA parameters (using /amoeba_parm) /for other
systems that ran succesfully with pmemd, the only difference this time
is the M site.
This site has a mass of 1, and bond and angle constraints to maintain
its position, but zero everything else, which are explicitly listed out.
(vdw, torsions, multipoles, polarizability).
I also tried restarting in pmemd using the /.dyn /output from a tinker
dynamic run, which had the same problem as above.
Is there some way to fix this? It doesn't seem like the M site is
defined any differently than any other atoms, except for all the zeroed
parameters.
Thanks very much,
Maggie Johnson
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Received on Fri Dec 05 2008 - 15:58:15 PST
