[gmx-users] Strange error from my simulation

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 21 21:25:57 CEST 2007

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.


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