Hi,
When dealing with molecules that have separated during the course of a
simulation due to wrapping (such as when 2 strands of DNA separate), I
often find I have to do more than 1 set of center/image commands to
get things back together - it makes sense if you think about it for a
bit, but I know that I personally find it hard to wrap my mind around
the idea of imaging sometimes (no pun intended I swear).
I'm assuming that 1-368 includes both monomers, so that 1-184 is
monomer 1 and 185-368 is monomer 2. I'm also assuming you have a
truncated octahedral box (hence use of the 'familiar' keyword). Try
this:
center :1-184 origin mass
image center origin familiar
center :1-368 origin mass
image center origin familiar
I would run a short (i.e. trajin B7noWATnoNa200nsvsbound.mdcrd.gz 1 1)
test run with these commands (along with a trajout) to see if the
imaging was performed correctly before you run the larger calculation.
Let me know if you have any more problems. Good luck!
-Dan
On Wed, Jul 6, 2011 at 12:14 PM, Daniel Scott <dscott5.nd.edu> wrote:
> Hi all,
> I spotted problems while analyzing an MD simulation of a heterodimeric
> protein, where the rmsd distance versus a reference structure had
> intermittent spikes. At one of those time frames, I took a snapshot
> pdb which confirmed that the molecule was drifting outside the box. As one
> monomer was more outside the primary box than the other, this monomer was
> moved to the other side of the primary box, separating it from the other
> monomer. This explains the rmsd spikes, yet i am using the "center" and
> "image" commands that I thought would prevent this problem from happening in
> the first place. The reference I am fitting to ("B7complextleap.pdb") is
> also centered in the box, so this adds to my confusion! Specifically, my
> job script was:
>
> ------------------------------------------------------------------------------------------------------------
> trajin B7noWATnoNa200nsvsbound.mdcrd.gz
> center :1-368 mass
> image center :1-368 bymask familiar
> reference B7complextleap.pdb
> rms reference out B7vsbound200ns.rms :1-368.CA,C,N
> atomicfluct out B7bfactorN200ns.apf .N byatom bfactor
> atomicfluct out B7bfactorCA200ns.apf .CA byatom bfactor
> atomicfluct out B7bfactorC200ns.apf .C byatom bfactor
> atomicfluct out B7bfactorO200ns.apf .O byatom bfactor
> trajout B7noWATnoNa200nsvsboundnoorigin.mdcrd nobox
> ------------------------------------------------------------------------------------------------------------
>
> Please give any advice on how to eliminate this box-shifting problem.
>
> Thanks,
> Dan Scott
> Grad student, University of Notre Dame
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Received on Wed Jul 06 2011 - 10:30:03 PDT
