<P>Thank you.</P>
<P>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? <BR><BR><BR></P>
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<BR>-----原始邮件-----<BR>发件人:"zjim" <FIT_TONE@163.COM><BR>发送时间:2005-12-01 09:29:53<BR>收件人:"hongwei tan" <HONGWEI.TAN@163.COM><BR>抄送:(无)<BR>主题:Re: [gmx-users] Can I set only a part of a molecule into freeze group?<BR><BR><BR>
<P>Dear Tan</P>
<P> </P>
<P>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.</P>
<P><BR><BR><BR> </P>
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<BR>-----原始邮件-----<BR>发件人:"谭宏伟(Hongwei Tan)" <HONGWEI.TAN@163.COM><BR>发送时间:2005-11-30 23:08:18<BR>收件人:gmx-users@gromacs.org<BR>抄送:(无)<BR>主题:[gmx-users] Can I set only a part of a molecule into freeze group?<BR><BR><BR><BR><BR><BR><BR>Hi, Dear Gromacs users,<BR>I am interesting in the interaction between some kind of protein and<BR>ice crystal. I hoped to observe the process of the protein binding to<BR>the ice crystal. I have to fix the water molecules in the ice crystal<BR>during the simulation to avoid the ice framework exploding. If I set<BR>the whole ice including all the H and O atoms in the waters into the<BR>freeze gourp, all things are ok .But if I only set the O atoms of the<BR>water in the ice into the Freeze group, simulation would crash and the<BR>log file says that:<BR><BR> t = 0.824 ps: Water molecule starting at atom 3385 can not be settled.<BR>Check for bad contacts and/or reduce the timestep.Wrote pdb files with<BR>previous and current coordinates<BR>Large VCM(group rest): 0.00150, -0.01327, -0.00626,<BR>ekin-cm: 2.51588e+00<BR>Large VCM(group rest): 0.00629, 0.00795, -0.00216,<BR>ekin-cm: 1.24285e+00<BR>Large VCM(group rest): -0.01347, 0.01582, 0.00515,<BR>ekin-cm: 5.29648e+00<BR>Large VCM(group rest): 0.00745, -0.00744, -0.00052,<BR>ekin-cm: 1.28536e+00<BR>Large VCM(group rest): 0.00728, -0.00595, 0.00223,<BR>ekin-cm: 1.07953e+00<BR><BR>Step 1003, time 1.003 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 10530269184.000000 (between atoms 478 and 479) rms 675239232.000000<BR>bonds that rotated more than 30 degrees:<BR><BR>Is there any one who had met the same situation? Or the Gromacs<BR>program couldn't simulation the strange system like this one?<BR>Anyway, thank you in advance!<BR><BR><BR><BR>--<BR>Sincerely<BR>Hongwei Tan<BR>Department of Chemistry<BR>Beijing Normal University<BR>Beijing China 100875<BR><BR><BR><SPAN></SPAN><BR><!-- footer --><BR><BR><BR><BR><BR>
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