Dear Amber,
I am doing a simulation of RNA with NaCl salt. I am able to do MD without
fail for 100mM, 200mM and 500mM but when I increase the salt to 1000mM,
the simulations fails in the initial stage. SANDER output says:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 1.9954E+12 Cl- 1079
BOND = 109.1329 ANGLE = 941.2407 DIHED =
529.7401
VDWAALS = NaN EEL = NaN HBOND =
0.0000
1-4 VDW = 518.6927 1-4 EEL = -1686.6642 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
100 NaN NaN 0.0000E+00 P 1
BOND = NaN ANGLE = 101106.7185 DIHED =
353.8000
VDWAALS = -1004.0093 EEL = NaN HBOND =
0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = NaN
EAMBER = NaN
the initial structure looks fine and inputs are all correct. This problem
is arising only when I increase NaCl concentration to 1000mM. Any
suggestion/help would be highly appreciated.
Regards,
Santosh
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Received on Thu Oct 28 2010 - 06:00:02 PDT
