On Thu, Apr 13, 2017, Jorgen Simonsen wrote:
>
> I am having an issue with the temperature after I have slowly heated up the
> system:
It's not clear from your eamil what the "issue" is with temperature.
>
> NSTEP = 0 TIME(PS) = 100.000 TEMP(K) = 440.42 PRESS = -621.5
If you start a simulation with randomized velocities in Amber, the first (or
zeroth) step will have an apparent temperature that is too high, because the
randomization procedure does not take account of SHAKE. This is correct
itself after a very small number of steps.
> ***** Processor 0
> ***** System must be very inhomogeneous.
> ***** Readjusting recip sizes.
> In this slab, Atoms found: 1415 Allocated: 1412
It's not clear if this stopped your run, or is just an informative message.
If you have not yet carried out constant pressure equilibration, try that with
a short serial run; you can go back to parallel runs after your system has
a density close to the final one.
Of course, the above "inhomogeneous" message might signal a real problem:
visualize your system to look for problems. Use the checkoverlap command in
cpptraj or the checkValidity command in parmed to see if there are common
problems with your setup.
....dac
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Received on Thu Apr 13 2017 - 05:00:02 PDT
