AMBER Archive (2009)

Subject: Re: [AMBER] Strange high temperature in softcore TI

Date: Sun May 24 2009 - 21:26:28 CDT


this sounds like atoms in the TI region are crashing into each other,
causing the high temperatures and structural distortions. Odd that you
dont see that when you run without TI, though...

Always a good thing to try is to test your runs with a smaller TI region
and make it subsequently bigger until you reach a point were problems
occur. Say only make the one base that actualy changes softcore.

Kind Regards,


On Sun, May 24, 2009 9:54 pm, Tom Joseph wrote:
> 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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Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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