Hello,
I am trying to do classical MD simulation with a Fe(III)-OH metalloenzyme
system having 40000 atoms (including water molecule) . I run minimisation
with 5000 steepest descent and 10000 conjugate gradient steps restrainning
the active site with a restraint value of 20 kcal mol-1 A-2 .The system
then gently annealed from 0 to 300 K for 50 ps with the same constraint
followed by a 1ns of density equilibration under an NTP ensemble at a
target temperature of 300 K and a target pressure of 1.0 atm using ntt=3
and Berendsen barostat with a collision frequency of 2ps with a restraint
of 10 kcal mol-1 A-2. Thereafter I reduced the restraint weight in 5 steps
i.e with a restraint of 8, 6, 4, 2, 0. But I find some errors like "vlimit
exceeded for step" . The error message is as follows,
vlimit exceeded for step 5804; vmax = 32.7330
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 2333 4822 4823
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Can you please tell me how do I solve this type of problem?
--
Asmita Sen
C/o- Dr. Gopalan Rajaraman
Junior Research Fellow (CSIR)
Department of Chemistry
IIT Bombay, Powai,
Mumbai- 400076, India
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Received on Thu Mar 01 2018 - 06:00:05 PST
