RE: "the error of movement of atoms"

From: soroush ziaei (
Date: Thu Mar 14 2019 - 03:36:25 CDT

Hello mr.joshua,
at the first solution that related to increasing dimensions of the periodic box in order to allow each atom's radius to wrap around easily...
I have to say in some cases, this method doesn't work, why?
is it necessary to add the margin parameter in the config file in order to correct dimensions in all vectors?
meanwhile, the amount of cutoff was chosen 12 angstroms (default)...
is it necessary to reduce this amount in order to reduce interaction in the edge of the box?

best regards,

From: Vermaas, Joshua
Sent: Saturday, March 2, 2019 1:51 AM
Subject: RE: namd-l: "the error of movement of atoms"

Its probably *not* your minimization. 10000 steps is more than I typically minimize for. Instead, take a look at the troubleshooting advice: Do any of the atoms appear out of place in VMD?

On 2019-03-01 14:08:01-07:00 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.

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