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

谭宏伟(Hongwei Tan) hongwei.tan at 163.com
Wed Nov 30 16:08:18 CET 2005

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!

Hongwei Tan
Department of Chemistry
Beijing Normal University
Beijing China 100875

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