I have only ran 160 ns with ff14SBonlysc+gb8 so far but even with that
the RMSD of the Ub is 5 AA. Yes, and for most of my simulations the
structure changes a lot during equilibration. I was referring to this
paper while constructing input files:"Routine Microsecond Molecular
Dynamics Simulations with AMBER
on GPUs. 1. Generalized Born"
But is there another paper which provides more specifics about how to
handle the equilibration process? Should I keep the coordinates fixed by
harmonic constraints?
Thanks!
Nihal Korkmaz
On 10/14/14, 7:19 PM, Carlos Simmerling wrote:
> Are you saying that you get the same behavior with both combinations?
> That's somewhat surprising, since these gb models are really different.
>
> Simulations with gb can be very sensitive to equilibration - did you follow
> a published protocol?
> On Oct 14, 2014 4:50 PM, "Nihal Korkmaz" <enihalkorkmaz.gmail.com> wrote:
>
>> Dear all,
>>
>> I have been running ff99SBnmr+gb7 and ff14SBonlysc+gb8 simulations. For
>> only alpha helical systems I do not have any problems. However, with
>> proteins that also contain B-sheets I observe high RMSD values and loss
>> of secondary structure, mostly B-sheets. This is not only happening
>> after simulating for a long time but I observe a steady increase in
>> RMSD. For Ubiquitin monomer, I have 5 AA Calpha-RMSD at 70 ns, it
>> reaches up to 10.5 AA and the Ub fold is lost.
>>
>> I am wondering if anyone experienced the same and has a suggestion to
>> fix this.
>>
>> This is my input file:
>> &cntrl
>> imin=0, ntb=0, ntx=5, irest=1,
>> ntpr=1000, ntwr=10000000, ntwx=1000, ntwe=5000,
>> nstlim=10000000, dt=0.001,
>>
>> ntt=3, temp0=300.00, tempi=300.00,
>> ig=-1, tautp=1, gamma_ln=20,
>>
>> ntc=2, tol=0.00001, ntf=2,
>> dielc=1, cut=9999, rgbmax=12,
>> igb=8, gbsa=0,
>> saltcon=0.15, ioutfm=1, nscm=100,
>> &end
>>
>> Thanks
>>
>> --
>> E.N. Korkmaz
>> UW-Madison, Biophysics Program
>>
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>>
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Received on Tue Oct 14 2014 - 19:00:02 PDT
