On Mon, Jul 26, 2010, Siddharth Rastogi wrote:
>
> I am doing an MD simulation study of my protein+water system.
> I minimized the whole system (all heavy atoms + backbone atoms + CA atoms
> restrained) first and then proceeded for the trajectory production.
> However, after 10 ns of trajectory production, I couldn't move further. The
> mdout file shows that "vlilmit exceeded for step 0; vmax = 1132.4370"
This sounds like the error happens on the very first step of a restart(?)
And, since you seem to be running things in 1ns "chunks", is it correct
to say that you have run 9 or 10 chunks so far, and then see the problem?
It sounds like there might be something wrong with the restart file, or
perhaps something bad happened right near the end of the chunk right before
the one that failed. You could run a one-step minimization, and check the
energy reported there vs. the last energy reported in the previous md.
And, of course, visualize your trajectory to see if you can spot any problems.
Your input file looks fine to me, but you might try setting ntx=7 -- I can't
remember exactly when we changed the code to read the box information from
the restart file, even when ntx=5.
....dac
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Received on Mon Jul 26 2010 - 18:30:04 PDT
