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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 14 2014 - 17:30:02 PDT
