Dear AMBER support,
I have been struggling with a problem I've been having with a thermodynamic integration calculation.
I have a molecule with a little over 50 atoms, and I am perturbing a small part of it (O-COCH3) to (O-
CH3). According to advice from AMBER, I am dividng the calculation into four parts: Appearing and
disappearing atoms (ie the uncoupling of Van Der Waals interactions), and charging and uncharging
atoms which have appeared or disappeared. I am having trouble with the calculations where I
decouple Van Der Waals interactions because the RMS fluctuations in DV/DL which I am getting are
way too high (average over 3 kcal/mol). I am doing this using 9 values of clambda as described in
the manual.
Here is my infile:
First equilibration:
&cntrl
imin = 0,
ntx = 1, irest = 0, ntr = 1,
ntpr = 100, ntwr = 100, ntwx = 5000, ntwe = 5000,
ntf = 2, ntb = 2, cut = 10,
nstlim = 500000, dt = .002, ntc = 2,
tempi = 0.0, temp0 = 298.0, ntt = 1,
tautp = 2.0, ntp = 1,
icfe = 1, clambda = 0.33787, klambda = 6,
&end
Restraining region
10.0
RES 1 1
END
END
Then:
&cntrl
imin = 0,
ntx = 5, irest = 1, ntr = 1, iwrap=1,
ntpr = 100, ntwr = 100, ntwx = 5000, ntwe = 5000,
ntf = 2, ntb = 2, cut = 10,
nstlim = 2500000, dt = .002, ntc = 2,
tempi = 298.0, temp0 = 298.0, ntt = 1,
tautp = 1.0, ntp = 1,
icfe = 1, clambda = 0.33787, klambda = 6,
&end
Restraining region
10.0
RES 1 1
END
END
My guess was that this was because the frcmod file I used for the dummy atoms wasn't consistent
with the force field for the analogous real atoms, but I can't see my mistake. Here is a my frcmod:
remark goes here
MASS
D2 1.008
D4 12.01
D5 16.00 same as O
BOND
D5-c 648.0 1.214 same as c-o
c-D4 328.3 1.508 same as c-c3
D4-D2 337.3 1.092 same as c3-hc
ANGLE
D5-c-os 76.2 122.43 same as o-c-os
D5-c-D4 68.0 123.11 same as c3-c-o
D4-c-os 69.3 111.96 same as c3-c-os
c-D4-D2 47.2 109.68 same as c-c3-hc
D2-D4-D2 39.4 108.35 same as hc-c3-hc
DIHE
X-c -D4-X 0 0.000 0.000 0.000 same as X -c -c3-X
X-c -c3-X 0 0.000 0.000 0.000 same as X -c -c3-X
IMPROPER
NONBON
D2 1.0000 0.0000
D4 1.0000 0.0000
D5 1.0000 0.0000 ATTN, need revision
I was wondering if anyone else has had a similar problem, and discovered what was going wrong?
I would really appreciate any helpful suggestions anyone has on this.
Thanks in advance,
Holly Freedman
--
Department of Physics, University of Alberta
Edmonton CANADA
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Received on Wed Jul 04 2007 - 06:07:07 PDT
