[gmx-users] program crashed

[Dongsheng Zhang]

On Wed, 2006-07-05 at 15:11 +1000, Mark Abraham wrote:
> > Mark,
> >
> > Thank you for your reply. When I checked step38885.pdb, I found a
> > polymer chain in my system fall apart (bond broken). If I visualize the
> > trajectory. it is fine till step38000 (last frame in my trr file).
> 
> OK... bonds don't just "break" in MD simulations. Bonded potentials don't
> allow for it, and often bond-length constraint algorithms are being used
> anyway.
 That is what I expect. However I find some atoms are far away from
others from step38885.pdb even though I have used all-bonds constraint.
Do you have any idea what's going on? Thank you for your help!


The following is part of my pdb file:

ATOM   1183 HH31 PPO B  40     -63.880  12.235  23.304  1.00  0.00
ATOM   1184 HH32 PPO B  40     -69.011   3.629  46.672  1.00  0.00
ATOM   1185 HH33 PPO B  40    -144.627  84.477  51.559  1.00  0.00
ATOM   1186  CH  PPO B  40     -51.713   0.381   2.039  1.00  0.00
ATOM   1187  HH  PPO B  40    -110.463  36.603  -0.242  1.00  0.00
ATOM   1188  CH2 PPO B  40     -38.759  29.954  26.664  1.00  0.00
ATOM   1189 HH21 PPO B  40     -28.084  28.831  32.811  1.00  0.00
ATOM   1190 HH22 PPO B  40     -28.802  16.898  37.557  1.00  0.00
ATOM   1191  O   PPO B  40     -32.030  16.986  38.515  1.00  0.00



Dongsheng


>  If you're not using such algorithms, it might be helpful to look
> at the time evolution of the bond length of the bond that breaks. I have
> heard of weird cases where some resonance got established in the system
> eventually leading to some catastrophic failure (think Tacoma Narrows
> Suspension Bridge!) - if so then the time evolution should show such
> behaviour. I can't explain the KE doubling though...
> 
> Mark
> 
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