Hello,
I am new to amber. I have set my system following the tutorials and the
mailing list. In my study, I want to perform QM/MM calculations and only
want to compare energies of the same system with the different redox state
of a cofactor.
Initially, I have set my system, assigned parameters for cofactors and run
MM minimization to relax the system. Input min.in file is as follows:
Minimize
&cntrl
imin=1,
maxcyc=10000,
ncyc=15000,
ntmin=1
cut=12.0,
ntb=0,
ntr=0,
&end
The final output of minimization is as follows:
NSTEP ENERGY RMS GMAX NAME NUMBER
10000 -1.7204E+04 1.9128E-01 6.5236E+00 FE 12904
BOND = 535.2363 ANGLE = 2384.2104 DIHED =
10119.0373
VDWAALS = -7876.9128 EEL = -62106.5349 HBOND =
0.0000
1-4 VDW = 3235.9670 1-4 EEL = 36504.6003 RESTRAINT =
0.0000
So, my question is, can I consider that my system is relaxed sufficiently
with this GMAX value? or I have to check the parameters or another thing
for Fe to further lower the GMAX?
What should be the values of GMAX or RMS to consider the fully minimized
system?
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Received on Thu Oct 17 2019 - 07:00:03 PDT
