Thank you for your reply.
Basically I have two proteins in complex. One is 59 aa long and the other
one is 179 aa long. The crystal structure of the complex is available. I
did the following procedure for simulations:
Minimize with restraints (solute fixed):
&cntrl
imin=1,
maxcyc=10000,
ncyc=5000,
ntx=1
ntb=1,
ntr=1,
ntpr=1000,
ntwx=0,
cut=10.0,
/
Hold the solute fixed
50.0
RES 1 238
END
Minimize the whole system (no restraints):
&cntrl
imin=1,
maxcyc=10000,
ncyc=5000,
ntr=0,
ntb=1
ntpr=100,
ntwx=0,
cut=10.0,
/
Heating:
Heat
&cntrl
imin=0,
ntx=1,
ntxo=2,
ioutfm=1,
irest=0,
nstlim=500000,
dt=0.002,
ntf=2,
ntc=2,
tempi=0.0,
temp0=300.0,
ntpr=1000,
ntwx=1000,
ntwr=10000,
cut=10.0,
ntb=1,
ntp=0,
ntr=0,
ntt=3,
gamma_ln=1.0,
ig=-1,
/
&wt TYPE='TEMP0', istep1=0, istep2=500000,
value1=0.1 value2=300.0, /
&wt TYPE='END' /
Production:
&cntrl
imin=0,
irest=1,
ntx=5,
ntxo=2,
ioutfm=1,
nstlim=30000000,
dt=0.002,
ntf=2,
ntc=2,
temp0=300.0,
ntpr=1000,
ntwx=10000,
ntwr=10000,
cut=10.0,
ntb=2,
pres0=1.0
ntp=1,
taup=2.0
ntr=0,
ntt=3,
gamma_ln=1.0,
ig=-1,
/
I am looking for some papers as per your suggestion but Does anything
stands out to you that I may have been missing here that might be causing
RMSD fluctuation?
Thanks again for your time and concern!!!
On Fri, Mar 11, 2016 at 8:49 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> If you simulate complexes, make sure to look at the imaging commands. But
> that probably isn't the case here. I would look carefully at your
> equilibration protocol, which you did not tell us. A good protocol often
> consists of multiple steps, including minimization, heating, use of
> restraints and more. The details depend on the source of your structure, if
> all atoms were well resolved, and more.
>
> Since we can't really design a good protocol for your system, I suggest
> looking at papers where people do careful equilibration on systems similar
> to yours, with similar challenges. Adapt their protocol.
>
> If you do decide to ask here for more help, tell us more about your initial
> structure,and all of the details of each step of your equilibration.
> On Mar 11, 2016 8:41 PM, "Arati Paudyal" <apsilwal123.gmail.com> wrote:
>
> > Dear all,
> >
> > I just finished a 1 ns heating and a 60 ns production simulation. But
> when
> > I processed the RMSD I feel like it is too high. I know the fluctuation
> > from 1-3 angstron is expected but mine looks like it is over 4 sometimes.
> > Could you please explain what might have gone wrong during simulation? IS
> > there anything I can do to avoid such fluctuation during simulation? I
> > used exactly same input and time to run another simulation with a
> different
> > protein complex and rmsd was a lot lower in that case. I know it depends
> on
> > the system but if I could understand if there is anything I can do to
> > improve this it would be of great help. Can I even use any of these
> frames
> > to process mmpbsa script?
> >
> > Rmsd input:
> >
> > trajin heat.rmsd
> > trajin equil.rmsd
> > reference x.inpcrd
> > rms reference out backbone.rmsd .CA,C,N
> >
> >
> > [image: Inline image 1]
> >
> >
> > If I remove equil.mdcrd an donly do trajin heat.mdrcd, rmsd is alot lower
> > but I can see it is increasing towards the end. So I think it is
> > fluctuating more during equilibrium stage. Following is the one only with
> > heat.mdcrd
> >
> >
> > [image: Inline image 2]
> >
> >
> >
> >
> > Thank you all in advance for your time!!!
> >
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 11 2016 - 18:30:03 PST
