[gmx-users] Can I set only a part of a molecule into freeze group?

[谭宏伟(Hongwei Tan)]

Hi, Dear Gromacs users,
I am interesting in the interaction between some kind of protein and
ice crystal. I hoped to observe the process of the protein binding to
the ice crystal. I have to fix the water molecules in the ice crystal
during the simulation to avoid the ice framework exploding. If I set
the whole ice including all the H and O atoms in the waters into the
freeze gourp, all things are ok .But if I only set the O atoms of the
water in the ice into the Freeze group, simulation would crash and the
log file says that:

  t = 0.824 ps: Water molecule starting at atom 3385 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
Large VCM(group rest):      0.00150,     -0.01327,     -0.00626,
ekin-cm:  2.51588e+00
Large VCM(group rest):      0.00629,      0.00795,     -0.00216,
ekin-cm:  1.24285e+00
Large VCM(group rest):     -0.01347,      0.01582,      0.00515,
ekin-cm:  5.29648e+00
Large VCM(group rest):      0.00745,     -0.00744,     -0.00052,
ekin-cm:  1.28536e+00
Large VCM(group rest):      0.00728,     -0.00595,      0.00223,
ekin-cm:  1.07953e+00

Step 1003, time 1.003 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 10530269184.000000 (between atoms 478 and 479) rms 675239232.000000
bonds that rotated more than 30 degrees:

Is there any one who had met the same situation? Or the Gromacs
program couldn't simulation the strange system like this one?
Anyway, thank you in advance!



--
Sincerely
Hongwei Tan
Department of Chemistry
Beijing Normal University
Beijing China 100875




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