On Wed, Oct 10, 2012, Jitesh Doshi wrote:
> I am running minimization in three steps, with PBC on,
> 1. all atoms restrained
> 2. only protein backbone atoms restrained
> 3. all atoms free
>
> all with 2500 steepest descent and 5000 conjugate gradient steps.
>
> and then moving to run heating and equilibration with following input
Make sure the energy at step 0 of the dynamics matches the last step of
minimization. Make sure that checkoverlap (in ptraj) reports no bad contacts.
Run a short (serial) simulation with ntpr=1, ntwx=1, nstlim=100. Visualize
your trajectory and look for suspicious behavior.
You have a big system, and this may not be easy. If there is any non-standard
part of your setup (not just ordinary amino acids...) look in that region
first.
...dac
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Received on Wed Oct 10 2012 - 04:30:06 PDT
