Ah, Carlos was going to suggest that this is an imaging issue most likely.
If the topology file has the different monomeric units listed as different
molecules in the topology file (which it most likely does if they're NOT
covalently bound), then the wrapping subroutine *may* move a monomer to the
other side of the periodic box.
You will see the archive flooded with examples of this if you search for
"iwrap" in the Amber mailing archive. You can visualize this easily by
loading your trajectories in VMD, and you'll see different monomers appear
to jump around.
You can fix this via the "center" and "image" commands in ptraj.
For each monomer, add 2 lines to your ptraj file like this:
center :1-28 mass origin
image origin center (familiar)
where familiar is used for an octahedral box. My suggested modifications to
your ptraj script are listed below:
> I used ptraj with the following input file:
>
>
> trajin g1tetra_prod_mdx1
> trajin g1tetra_prod_mdx2
>
center :1-28 mass origin
image origin familiar
center :1-56 mass origin
image origin familiar
center :1-84 mass origin
image origin familiar
center :1-112 mass origin
image origin familiar
rms first out g1tetra_rms_1_112.dat :1-112 .CA, C, N
> strip :WAT
> go
>
>
Based on your mask, it appears as though you're either omitting the last
monomer, or there are only 4. In any case, add another 2 lines to the above
if you need to move all 5 monomers back to the box.
Hope this helps,
Jason
>
>
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Wed, March 23, 2011 6:15:58 PM
> Subject: Re: [AMBER] odd output from rms measurement
>
>
> We need to know how this was calculated.
>
> On Mar 23, 2011 5:56 PM, "Chris Chris" <alpharecept.yahoo...
> _______________________________________________
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>
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Mar 23 2011 - 19:00:03 PDT
