Stéphane Téletchéa wrote:
While switching from NVT to NPT, i'm crashing my simulation.
The error message seen is (repeated 10 times, then mdrun aborts):
#####
Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20
-1.59647e+20 -1.59647e+20
Correcting invalid box:
old box (3x3):
old box[ 0]={-9.82630e+20, 0.00000e+00, -0.00000e+00}
old box[ 1]={ 0.00000e+00, -8.90833e+20, -0.00000e+00}
old box[ 2]={ 0.00000e+00, 0.00000e+00, -1.12456e+21}
new box (3x3):
new box[ 0]={-9.82630e+20, 0.00000e+00, -0.00000e+00}
new box[ 1]={ 0.00000e+00, -8.90833e+20, -0.00000e+00}
new box[ 2]={ 0.00000e+00, 8.90833e+20, -1.12456e+21}
.....
-------------------------------------------------------
Program mdrun_lam, VERSION 3.3.1
Source code file: ns.c, line: 265
Fatal error:
Box was shifted at least 10 times. Please see log-file.
-------------------------------------------------------
#####
I've searched in the archives this could be related to a non
sufficiently equilibrated system, but the first 20ps NVT run fine, so i
presume there's either a problem in the way i'm doing it (thus the
RFC-like question from the other message) or i'm missing something obvious.
Since i've tried to eliminate many errors and still get these errors
after different trials (removing shuffle and sort, generating or not
velocities while switching from pr1 to pr2, i've also tried the
"unconstrained_start=yes").
You will want to use unconstrained_start=yes in any restart of a
simulation using constraints with which you're attempting to be exact.
If you have any pointer, i'll be very happy to read it ...
I'm still looking at my setup system (protein in a water/spc solvent) in
order to find where is my error, but since the NVT run seems ok
(analysing precisely it at the moment, but no visual problem neither any
hint in the logs), i'm willing to understand why the switch to NPT fails.
As I think DvdS is hinting, if your box volume is such that the system
is of the wrong size, then a sudden switch to NpT with a short time
constant will cause a big perturbation to the system. This can break
stuff. Check pressures, densities and volumes. To fix, either use a long
time constant with NpT (and wait a while), or choose the volume with
editconf so as to get the right outcome for the switch to NpT.
Mark
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