Hello,
I am doing regular MD simulations of 4 identical sugar chains. Each of
these chains should have the C1-C2-C3-C4 dihedral angle in one of the
sugars restrained. The contents of the restraints file are therefore:
&rst iat = 3, 18, 16, 13,
r1 = -58, r2 = -57, r3 = -37, r4 = -36,
rk2 = 32.0, rk3 = 32.0, &end
&rst iat = 201, 216, 214, 211,
r1 = -58, r2 = -57, r3 = -37, r4 = -36,
&end
&rst iat = 399, 414, 412, 409,
r1 = -58, r2 = -57, r3 = -37, r4 = -36,
&end
&rst iat = 597, 612, 610, 607,
r1 = -58, r2 = -57, r3 = -37, r4 = -36,
&end
If now run these simulations and compare with simulations without
restraints, I get a difference by a factor of 3. The input file is just
standard in my opinion:
&cntrl
imin=0,
ntx=5,
irest=1,
nstlim=250000000,
dt=0.004,
ntf=2,
ntc=2,
temp0=300.0,
ntpr=25000,
ntwx=25000,
cut=10.0,
ntb=2,
ntp=1,
barostat=2,
ntt=3,
gamma_ln=1.0,
nmropt=1,
ig=-1,
/
&wt type='END' /
DISANG=rst.pucker
Has anybody seen this before? Where could be the issue?
Best regards and thank you in advance,
Richard
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Received on Wed Jan 26 2022 - 06:30:02 PST
