[gmx-users] Strange error from my simulation

Tsjerk Wassenaar tsjerkw at gmail.com
Mon May 21 22:54:14 CEST 2007


And if you're at it, also change your temperature coupling...(check
the archives).

Tsjerk

On 5/21/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623



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