AMBER: blows up

From: Gustavo Pierdominici Sottile <>
Date: Tue, 15 Feb 2005 16:11:43 -0300

Hi ,
    I have a problem and canīt practice a dynamic. The starting structure
was the system (a protein 7000 atoms and water molecules 23000 atoms) at 300
K with constraints on CA atoms. Then I practiced various 10 ps dynamics so
as to take out the constraints slowly. 20, 15, 10 5, 3, 1, 0.1, 0.001. In
every of these short dynamics if I use ptraj , trajin .crd, rms first mass
out ---.crd time 0.5;
the output was half of the total time with a rms of 0.8 and then a sudden
blow that make it rise to 30.0 being there till the end. It made me no
matters because when I saw the first and the last structure, they were very
similar in all cases. (in all cases I saw the structures without water)
The problem appears when I start the dynamic without constraints. When it
arrives to 26 ps a message appears saying vlimit exceded...... and it
I send you two outputs, the one that explotes is the restart from the other.
Pd1: when the .top was done with leap, a warning appeared saying that the
total charge of the system is -27.00 , but I thought it was a common thing.
Pd2: all the rms that I did with ptraj were as I described above. They also
were performed adding strip : WAT, but the results were the same.
Pd3: I used tip3 model and in a tutorial it is said that bond length must be
fix. Could it be the problem? Is it possible that the explicit solvent
molecules ar the cause of the rise in energy?
Thanking in advance

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Received on Tue Feb 15 2005 - 19:53:00 PST
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