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<DIV><FONT size=2>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. </FONT></DIV>
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<DIV style="FONT: 9pt 宋体">----- Original Message ----- </DIV>
<DIV style="BACKGROUND: #e4e4e4; FONT: 9pt 宋体; font-color: black"><B>From:</B>
<A title=hongwei.tan@163.com href="mailto:hongwei.tan@163.com">Hongwei Tan</A>
</DIV>
<DIV style="FONT: 9pt 宋体"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 9pt 宋体"><B>Sent:</B> Thursday, December 01, 2005 9:53
AM</DIV>
<DIV style="FONT: 9pt 宋体"><B>Subject:</B> Re: Re: [gmx-users] Can I set only a
part of a molecule into freeze group?</DIV>
<DIV><BR></DIV>
<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>
<DIV style="BORDER-BOTTOM: #999 1px solid"></DIV><BR><FONT
style="FONT-SIZE: 14px" color=black>想 要 一 个 快 n 倍 的 免 费 邮 箱 吗 ?
</FONT><BR><A style="FONT-SIZE: 12px; COLOR: blue; LINE-HEIGHT: 160%"
href="http://www.126.com/help/126fab.htm" target=_blank>126 专 业 电 子 邮 局 ——
全 球 领 先 的 中 文 邮 箱 带 你 进 入 极 速 之 旅 </A><!-- CoreMail Version 2.5 Copyright (c) 2002-2005 www.mailtech.cn --></BLOCKQUOTE><BR><!-- footer --><BR><BR><BR><BR><BR>
<DIV style="BORDER-BOTTOM: #999 1px solid"></DIV><BR><FONT
style="FONT-SIZE: 14px" color=black>绝 无 广 告 的 网 易 新 一 代 电 子 邮 箱</FONT>
<BR><A style="FONT-SIZE: 12px; COLOR: blue; LINE-HEIGHT: 160%"
href="http://www.188.com/index.htm?mailsite=163&mailpos=20051128&num=A"
target=_blank>国 际 顶 级 杀 毒 反 垃 圾 引 擎,豪 华 带 宽 创 新 web 技 术——真 正 的 行 家 首 选 !
</A><!-- CoreMail Version 2.5 Copyright (c) 2002-2005 www.mailtech.cn --></BLOCKQUOTE><BR><BR><BR><BR><SPAN>--------------------------<BR>Hongwei
Tan<BR>Department of Chemistry<BR>Beijing Normal University<BR>Beijing China
100875<BR><BR>E-mail: <A
href="mailto:hongwei.tan@163.com">hongwei.tan@163.com</A><BR></SPAN><BR><!-- footer --><BR><BR><BR><BR><BR>
<DIV style="BORDER-BOTTOM: #999 1px solid"></DIV><BR><FONT
style="FONT-SIZE: 14px" color=black>想 要 一 个 快 n 倍 的 免 费 邮 箱 吗 ? </FONT><BR><A
style="FONT-SIZE: 12px; COLOR: blue; LINE-HEIGHT: 160%"
href="http://www.126.com/help/126fab.htm" target=_blank>126 专 业 电 子 邮 局 —— 全 球
领 先 的 中 文 邮 箱 带 你 进 入 极 速 之 旅 </A>
<P>
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