AMBER Archive (2009)

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

From: Tom Joseph (
Date: Sun May 24 2009 - 22:20:20 CDT

Thanks very much! Reducing the number of softcore atoms by only
including one base seems to have helped.

Attempting to do the alchemy in one shot (rather than removing
charges/mutating/adding charges as in your tutorial), even with the
reduced softcore region, results in vlimit errors and sander crashing.
I wanted to do this in hopes that the electrostatics would "stabilize"
the van der Waals interactions, which alone give a relatively high

I know even 14 atoms is a decently large change, but why should
leaving the electrostatics on during the mutation cause such problems,
since they are scaled by lambda?


On Sun, May 24, 2009 at 10:26 PM, <> wrote:
> Hi,
> 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,
> Thomas
> 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)
>> _______________________________________________
>> AMBER mailing list
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
> _______________________________________________
> AMBER mailing list

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