[gmx-users] Pressure error in MD relating to [FILE nsgrid.c, LINE 218]

Gale, Ella ella.gale at imperial.ac.uk
Thu May 11 20:49:46 CEST 2006


I have been getting the following funky error.

"Step 2  Warning: pressure scaling more than 1%, mu: 1.02018 1.02018 1.02018

Step 3  Warning: pressure scaling more than 1%, mu: 8.80037e+07 8.80037e+07 8.80037e+07

Step 4  Warning: pressure scaling more than 1%, mu: 4.6015e+10 4.6015e+10 4.6015e+10
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]"

What I am doing is simulating a gold surface with some thioalkanes bonded to it, the box is periodic as I want to simulate a unit cell, and the thioalkane chains cross the perioidic boundary conditions and wrap back round. From reading the old posts to the list about this error I know that one of the causes could be that one of my coordinates is possibly NAN or my atoms are too close. 

I've checked that every atom is within the box at the start, and I've looked at the structure to check nothing overlaps. The weird thing is that I can minimise the system, the error only appears when I do an MD run. 

Any ideas?

Incidentally, does anyone know how close atoms can get before this error arises? I'm modelling my system with all the hydrogens included, could this be causing the problem? The other thing I thought was that I might be running foul of some limit on the number of decimal places in the .gro file. I've set it up with 6 dp, and upped that to 14 at the end of the minimisation (I want to do NMA). How many decimal places does gromacs read the .gro file to?

Any help would be much appreciated.


Ella Gale
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