[gmx-users] nsgrid error

istvan at kolossvary.hu istvan at kolossvary.hu
Tue Dec 23 23:56:02 CET 2003


I am experimenting with NVE simulations using the simplest possible system; 
alanine dipeptide in a 3x3x3 nm SPC box with PBC and PME. I tried a great 
many different constraint settings (LINCS, SHAKE, none), but I don't seem to 
be able to generate a reasonable 1 ns trajectory even with a 1 fs time step. 
The system blows up with even lyncs-order=12 and 1 fs time step. SHAKE seems 
more stable, but visually the peptide hydrogens look weird. Similarly, with 
no constraint at all, as the simulation approaches 1 ns the methyl hydrogens 
on the ACE and NAC caps form a reversed umbrella (like in high winds) around 
the carbon atom. On the other hand, running the same simulation in NPT is 
perfectly fine. When Gromacs gives up on the NVE simulations the following 
error message appears followed by a segmentation fault (the only difference 
is the time and the serial number of the water): 

Constraint error in algorithm Lincs at step 246494 

t = 492.988 ps: Water molecule starting at atom 944 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates
Large VCM(group Protein):     -2.33346,     -5.83257,      9.18551, ekin-cm: 
Fatal error: ci = -2147483648 should be in 0 .. 215 [FILE nsgrid.c, LINE 

I am using Gromacs version 3.1.4 and I thought that it was simple enough to 
run NVE on the alanine dipeptide, but I proved to be wrong. 

Any thoughts? 

Many thanks, 

  Istvan Kolossvary 

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