AMBER Archive (2009)

Subject: [AMBER] Strange high temperature in softcore TI

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Sun May 24 2009 - 20:54:43 CDT

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_at_N1,C6,H6,C5,C7,H71,H72,H73,C4,O4,N3,H3,C2,O2',
scmask=':7_at_N1,C6,H6,C5,C7,H71,H72,H73,C4,O4,N3,H3,C2,O2 |
:19_at_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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