<P>Dear Jinming:</P>
<P> We optimized the whole system including ice and protein again with conjugated gradient method to a lower force,and set the include option in the mdp file to FLEXIBLE to move the constraints. The problem seems to be solved. <BR></P>
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<BR>-----原始邮件-----<BR>发件人:gmx-users-request@gromacs.org<BR>发送时间:2005-12-01 14:32:24<BR>收件人:gmx-users@gromacs.org<BR>抄送:(无)<BR>主题:gmx-users Digest, Vol 20, Issue 2<BR><BR><BR><PRE style="WIDTH: 100%; WHITE-SPACE: normal; WORD-WRAP: break-word"><P>Date: Mon, 31 Jan 2005 14:35:36 +0800<BR>From: "jinming" <<A href="mailto:fit_tone@163.com">fit_tone@163.com</A>><BR>Subject: Re: Re: [gmx-users] Can I set only a part of a molecule into<BR> freeze group?</P><P>
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@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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