AMBER Archive (2005)

Subject: AMBER:

From: Gustavo Pierdominici Sottile (gsottile_at_unq.edu.ar)
Date: Wed Feb 16 2005 - 06:22:59 CST

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

~

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu