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

[Hongwei Tan]

Thank you.
If I move the constraints on the ice during the simulation, do you think the problem could be solved? Or there is better method to handle such situation?      






-----原始邮件-----
发件人:"zjim" 
发送时间:2005-12-01 09:29:53
收件人:"hongwei tan" 
抄送:(无)
主题:Re: [gmx-users] Can I set only a part of a molecule into freeze group?



Dear Tan
 
Such situation may be caused by the bad contacts which contributes to the huge force that make your system unstable (the system seems to be crashed),when you freeze all H2O atoms, the sructure of the ice crystal keeps same as the beginning,so the bad contacts will not happen. While, when only the O atom is set as freezing group, the water can rotate  freely while the O atom is fixed, i think this is the cause of bad contacts take place. other, as the ice is stable under 273 K (1 atm), the temperature may be also considered.



 



-----原始邮件-----
发件人:"谭宏伟(Hongwei Tan)" 
发送时间:2005-11-30 23:08:18
收件人:gmx-users at gromacs.org
抄送:(无)
主题:[gmx-users] Can I set only a part of a molecule into freeze group?






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

E-mail: hongwei.tan at 163.com
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