Conformational changes that have a long time scale? It's difficult for a
single number to characterize the behaviour of such a complex system.
Perhaps you can visualize the trajectory and see if anything obvious jumps
out at you when the RMSd takes off.
Good luck!
Jason
On Fri, Jan 7, 2011 at 1:32 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody,
>
> I'm sure that some of you must have made a similar observation.
>
> Following equilibration, and during the production run the backbone rmsd of
> the protein is drifting. I'm attaching two snapshots for easy reference. The
> equilibration run was over 6ns and the production run over 14ns. The md.infiles are identical.
>
> Any ideas regarding this behaviour?
>
> Many thanks
>
> George
>
> EQUILIBRATION: md.in
>
> heat 3ogn-3og
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=1000000,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=2, ntp=1, taup=2.0,
> ntpr=1000, ntwx=1000,
> ntt=3, gamma_ln=2.0, ig=-1,
> temp0=300.0,
> /
> ================
> PRODUCTION: md.in
>
> heat 3ogn-3og
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=1000000,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=2, ntp=1, taup=2.0,
> ntpr=5000, ntwx=5000,
> ntt=3, gamma_ln=2.0, ig=-1,
> temp0=300.0,
> /
>
>
>
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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Jan 07 2011 - 11:00:03 PST
