I doubt that it is related to the removal of CM motion.
you haven't said what your system is- could it be that you
have more than 1 molecule of solute (like a DNA
duplex) where one monomer has been imaged? Have you visually
checked the dynamics of the system to make sure that all
molecules (if more than 1) stay together?
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
Gustavo Pierdominici Sottile wrote:
> Hi,
> I am writing because when I use ptraj using the following commands:
> ptraj ggg.top
> traj.in ...mdcr
> rms first mass out rms.out time 0.5
> go
>
> The file rms.out looks like this
> 0.50 0.00000
> 1.00 0.54404
> 1.50 0.58151
> 2.00 0.61220
> 2.50 4.50474
> 3.00 33.04290
> 3.50 33.04551
> 4.00 33.04471
> 4.50 33.07805
> 5.00 33.07316
> 5.50 33.38253
> 6.00 44.47040
> 6.50 44.66780
> 7.00 44.37050
> 7.50 44.46267
>
> The point where the rms goes up has a coincident point in the
> dynamics where appears the following message:
> KE Trans = 1.7116 KE Rot = 0.0553 C.O.M. Vel = 0.004397
>
> Translational and rotational motion removed
>
> KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
> There is something rare because the rms file says that there exists an
> rms of 44 between the last and the first structure. If I see them and
> they are very similar, moreover, I calculate the rms and the result is
> 0.8. Perhaps there is something wrong that I canīt see
> Thanking in advance
> Gustavo
>
> ~
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Received on Wed Feb 16 2005 - 13:53:00 PST
