RE: "the error of movement of atoms"

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Mar 01 2019 - 16:21:35 CST

Its probably *not* your minimization. 10000 steps is more than I typically minimize for. Instead, take a look at the troubleshooting advice: https://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting Do any of the atoms appear out of place in VMD?

-Josh

On 2019-03-01 14:08:01-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
hello everybody,
At first, I have to say the number of atoms of my simulation is 140000.
And after running the first stage of simulation that means minimization at 10000 steps in order to check the error before running a full simulation,
but at the next stage ( temp & pressure coupling ) an error appears in the log file that says some of the atoms with related numbers are unstable and moving too fast, why?
I think it's because of the short time of minimization, am I right? if not, please guide me.

Regards,
soroush

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