your restraint weight is very weak.
it will calculate the non-fit rmsd for atoms in
the rmsmask, but will do no best fit.
when you use ptraj and do an alignment, then
you already have something different from what
you asked sander to do. try to use ptraj to calculate
the rmsd without any fitting at all.
alternatively, use a much stronger restraint
weight and see if the agreement in rmsd improves.
it could be something else, but I am guessing it
is the extremely weak restraint in sander as compared
to actual alignment in ptraj.
On 9/22/07, Ilyas Yildirim <yildirim.pas.rochester.edu> wrote:
>
> Dear Amber Users,
>
> I am having trouble understanding how the RMSD is calculated in targetted
> MD simulations. I have the following input file:
> ------------ tgtmd.in ------------------------
> TMD: NMR->XRAY; target rmsd 3.267; resid 1-2,8-11,17-18 restrained
> &cntrl
> imin = 0, ntx = 5, nstlim = 1200000, irest=1,
> dt = 0.002, ntc = 2, ntf = 2, tol = 0.000001,
> tempi = 300.0, temp0 = 300.0,
> scee = 1.2, cut = 99.9,
> ntpr = 50, ntwx = 50, ntwr = 50,
> ntb = 0, ntt = 1, tautp = 0.5, ntp = 0,
> igb = 1, nscm = 0, nmropt = 0,
> ntr = 1, restraint_wt=0.02,
> restraintmask=":1-2,8-11,17-18",
> itgtmd = 1, tgtrmsd = 3.267, tgtmdfrc = 1.0,
> tgtrmsmask="(:3-7,12-16)",
> /
> -----------------------------------
> What this script does is it restraints the residues 1-2,8-11,17-18
> with a restraint weight of 0.02. While doing that, implicitly, it aligns
> the system with respect to restraintmask.
>
> Then, the rmsd is calculated for the residues 3-7,12-16. At each
> step, "Current RMSD from reference" is printed out. I could not figure out
> how this 'Current RMSD from reference' is calculated. When I extract that
> particular snapshot from the trajectory and use ptraj (first aligning the
> residues 1-2,8-11,17-18 and then calculating the rmsd of residues
> 3-7,12-16), I get pretty different result.
>
> 1. Is there a mistake the way I describe/understand the above input file?
> 2. Does TMD follow a different alignment algorithm?
>
> Thanks in advance for your responses.
>
> Best,
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> = Department of Chemistry - =
> = University of Rochester - =
> = Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
> = http://www.pas.rochester.edu/~yildirim/ =
> ---------------------------------------------------------------
>
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Received on Sun Sep 23 2007 - 06:07:55 PDT
