Hi,
I was trying to simulate a protein in implicit solvent environment. i have
first minimized the structure and then tried to carry out a production MD
in implicit solvent using the following input parameters:
*hca MD Generalised Born, 12 angstrom cut off &cntrl imin = 0, ntb = 0,
igb = 1, ntpr = 500, ntwx = 500, ntt = 3, gamma_ln = 1.0, tempi = 300.0,
temp0 = 300.0, nstlim = 100000, dt = 0.002, cut = 12.0 /*
but as soon as I start the simulation the structure started to collapse.
Here I am annexing a copy of the output file:
*vlimit exceeded for step 496; vmax = **********vlimit exceeded for
step 497; vmax = **********vlimit exceeded for step 498; vmax =
**********vlimit exceeded for step 499; vmax = ********** NSTEP =
500 TIME(PS) = 1.000 TEMP(K) =********* PRESS = 0.0 Etot
= NaN EKtot = 19874662.4076 EPtot =
NaN BOND = 852405.4613 ANGLE = 94829.9606 DIHED =
8798.7961 1-4 NB = 71329408.5341 1-4 EEL = 11302.8746 VDWAALS =
************** EELEC = -18466.3455 EGB = NaN
RESTRAINT =
0.0000 ------------------------------------------------------------------------------vlimit
exceeded for step 500; vmax = **********vlimit exceeded for step 501;
vmax = **********vlimit exceeded for step 502; vmax = **********vlimit
exceeded for step 503; vmax = **********vlimit exceeded for step 504;
vmax = **********vlimit exceeded for step 505; vmax = **********vlimit
exceeded for step 506; vmax = **********vlimit exceeded for step 507;
vmax = **********vlimit exceeded for step 508; vmax = **********vlimit
exceeded for step 509; vmax = ***********
Please help me out
*.*
With regards,
Avik Bhattacharjee
IIT KGP
INDIA*.*
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Received on Sat Apr 16 2016 - 10:00:05 PDT
