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
RMSD for DV/DL.
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?
Thanks,
--Tom
On Sun, May 24, 2009 at 10:26 PM, <steinbrt.rci.rutgers.edu> 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.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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
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>
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Received on Mon May 25 2009 - 01:14:20 PDT
