AMBER Archive (2005)

Subject: AMBER: ptraj

From: Gustavo Pierdominici Sottile (gsottile_at_unq.edu.ar)
Date: Fri Feb 18 2005 - 08:58:37 CST

Hi,
   I am writing due to a problem of those that is difficult to find the
causes. When analyzing a trajectory with ptraj the rms that was obtained was
like this:
1.0 0.1
5.0 0.7
...
50.0 0.7
...
145.0 0.7
150.0 344.0
155.0 344.0
160.0 354.0
I could not explain why in such a small time there was a sudden explosion.
This was not the case. The problem was that in configuration number 56 the
trajectory file had lines like this:
 1) 53.832 35.095 25.884 40.759 34.347 25.658 41.421 35.387 26.722
41.142
 2) 84.440 49.617 31.167 84.757 50.407 30.811 83.836 39.229 18.752
13.027 39.000 17.789 13.163 38.429 19.181 12.502 40.111
In each line of the file there are 10 numbers (as in 1)) but in the next
there are 17 numbers (2))
So, ptraj reads something out of phase. After this wrong line,
configurations restart to be OK again. But in other moment the same kind of
line appears.
Reading the output file, I see that there is no problem with the energy.
Moreover the .crd file that is written temporary also has no problem.
I think that this is a problem of connection of this cluster but I am not
certain. What do you think?
Do you think that this problem in the trajectory file affects other things?
If someone has had this problem, please write me.
Thanking in advance
Gustavo

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