I said I do NOT think it is CM motion removal. This is described in the
manual (NSCM). I think it is possible that it is imaging of your 2 chains.
Please view all of the structures, not just first and last. It is important
to know what your molecule is doing, not just to read values output by
a program. If it is imaging, this is not a "big problem" as you say but it
is normal. Please check the iwrap section of the manual and also read about
the image command in ptraj.
===================================================================
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 have already written about the problem with the rms and I was
> asked if I have a duplex. The answer is yes. the system is composed of
> two polipeptide chains and 6000 water molecules. The number of atoms
> is 30000. You told me that the problem could be the removel of the CM
> motion. What does it mean? I havenīt seen the dynamics but the first
> and the last structure look nice. It would be strange there exists a
> big problem in the middle
> Thanks in advance
> Gustavo
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Received on Wed Feb 16 2005 - 14:53:00 PST
