I have never had good success with such a simplistic protocol, maybe it
works for others. There should be density equilibration, slow reduction of
restraints and so on. My group outs the full equilibration protocol in all
of our work, so if you want an example you could look at our recent
publications.
On Mar 11, 2016 9:07 PM, "Arati Paudyal" <apsilwal123.gmail.com> wrote:
> 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!!!
> > >
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> > >
> > >
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Received on Sat Mar 12 2016 - 03:30:05 PST
