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

[jinming]

If you move the constraits, I think the problem will be solved,but i am a bit worried about the structure of ice crystal is still kept well as the MD simulation proceeds.If it is ok, would you please tell me the result. I am rather interesting in it. 
  ----- Original Message ----- 
  From: Hongwei Tan 
  To: gmx-users at gromacs.org 
  Sent: Thursday, December 01, 2005 9:53 AM
  Subject: Re: Re: [gmx-users] Can I set only a part of a molecule into freeze group?


  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?      





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    -----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.




     


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      -----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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