Dear all
we are running a MD simulation on a protein-drug complex in octahedron water box, the complex was minimized with periodic boundaries, restraining all the residues (1-388).
Minmizaiton input file:
Stage 1 - minimisation
&cntrl
imin = 1,
maxcyc = 1000,
ncyc = 500,
ntb = 1,
ntr = 1,
cut = 10.0
/
Hold the comp fixed
500.0
RES 1 388
END
END
The starting energy 7.1251E+10 and final energy after minimzation is -8.1747E+04 The initial structure and minimized structure has 0.6 ang deviation.
During heating, we got an error
"Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 526 1048 1049 "
with the input file mentioned below
Stage 1 - Heating
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000,
dt = 0.002
ntpr = 100,
ntwx = 100,
ntwr = 1000
/
Keep comp fixed with weak restraints
10.0
RES 1 388
END
END
Then we have changed, dt = 0.001 and the heating is taken place without any error, but the structure is distorting too much (kindly see the attached figure). We appreciate your suggestions and comments.
Thank you in advance.
With regards
Vahid
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Received on Wed Jul 15 2015 - 22:30:02 PDT
