I am trying to do a TI calculation using AMBER 10's softcore
potentials feature but am getting odd results, and was hoping someone
might know what has gone wrong here.
I am mutating a T:A base pair to A:A in a short DNA:RNA hybrid. The
softcore region includes both bases of the base pair in question, 28
atoms total. After 2000 steps of minimization, I attempt to heat the
system from 100 K (assigned velocities) to 300 K using the mdin file
below. The temperature of the softcore region tends to stay > 500 K
and every few thousand steps suddenly jumps up to some insane number
(sometimes > 10000 K) and a bunch of vlimit errors are produced. The
base pair being alchemically mutated flies apart, distorting the rest
of the structure.
This happens at all clambdas I've tried. When I minimize and heat
either configuration without TI, it remains stable.
Would anyone be able to give a clue as to what I'm doing wrong?
Thanks,
--Tom
Heating sample mdin:
&cntrl
imin=0, ntx=1, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
nscm=5000,
ntf=1, ntc=1,
ntb=1, ntp=0,
nstlim=50000, t=0.0, dt=0.001,
cut=9.0,
tempi=100.0, ntt=3, gamma_ln=3, ig=12345,
ntr=0, nmropt=1,
icfe=1, ifsc=1,
clambda=0.33787,
crgmask=':7.N1,C6,H6,C5,C7,H71,H72,H73,C4,O4,N3,H3,C2,O2',
scmask=':7.N1,C6,H6,C5,C7,H71,H72,H73,C4,O4,N3,H3,C2,O2 |
:19.N9,C8,H8,N7,C5,C6,N6,H61,H62,N1,C2,H2,N3,C4',
&end
Heating from 100 to 300 K
&wt type='TEMP0', istep1=0, istep2=10000, value1=100.0, value2=300.0, &end
&wt type='TEMP0', istep1=10001, istep2=50000, value1=300.0, value2=300.0, &end
&wt type='END', &end
(crgmask and scmask are adjusted appropriately for the other configuration)
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Received on Mon May 25 2009 - 01:13:48 PDT
