<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><BR>Dear Sir : In fact, these structures were initially centered within the same coordinate system as your Gromacs Tutorials .<BR><BR><A class=plink href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" rel=nofollow target=_blank><IMG class=pimg border=0 alt=4 src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"></A><BR><BR>--- <B>10年4月12日，周一, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> 写道：<BR>
<BLOCKQUOTE style="BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT: 5px; MARGIN-LEFT: 5px"><BR>发件人: Justin A. Lemkul <jalemkul@vt.edu><BR>主题: Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl<BR>收件人: "Gromacs Users' List" <gmx-users@gromacs.org><BR>日期: 2010年4月12日,周一,下午9:07<BR><BR>
<DIV class=plainMail><BR><BR>xi zhao wrote:<BR>> <BR>> my procesure:<BR>> 1. cat cgprotein cgmembrane>system.gro (using Martini force field)<BR><BR>Were these structures initially centered within the same coordinate system? By your description, it sounds like these two components are simply not placed properly. There is a membrane protein tutorial linked from the Gromacs Tutorials page that guides you through constructing an atomistic membrane protein system using InflateGRO. You might find it useful.<BR><BR>-Justin<BR><BR>> 2 perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat<BR>> 3. grompp_d -f em.mdp -c system_inflated.gro -p topol.top -o system_inflatedem.tpr (with strong postion restraint)<BR>> 4. mdrun<BR>> 5 in the system_inflatedem.gro , the protein and membrane separate each other.<BR>> please help me !<BR>> <BR>> 4 <<A
href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" target=_blank>http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844</A>><BR>> <BR>> --- *10年4月12日，周一, Justin A. Lemkul /<<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>>/* 写道：<BR>> <BR>> <BR>> 发件人: Justin A. Lemkul <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>><BR>> 主题: Re: [gmx-users] construct CG membrane protein and CG membrane<BR>> and inflategro.pl<BR>> 收件人: "Discussion list for GROMACS users" <<A
href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>> 日期: 2010年4月12日,周一,下午8:42<BR>> <BR>> <BR>> <BR>> xi zhao wrote:<BR>> ><BR>> ><BR>> > Dear Gromacs users:<BR>> > I use inflateGRO.pl to insert CG protein in to CG POPC membrane,<BR>> but when carryied EM with Strong POStion REStraint, the protien and<BR>> membrane were apart. Please help me!<BR>> <BR>> What does "apart" mean? If you want free help, you have to make it<BR>> easy to help you. That means thorough descriptions of what you're<BR>> doing, what you're seeing, and if
necessary, posting images online<BR>> (not as attachments!) for us to take a look. The InflateGRO method<BR>> should generate a configuration that has molecules separated by a<BR>> large amount of space, but if there is something else wrong you'll<BR>> have to provide a better description.<BR>> <BR>> -Justin<BR>> <BR>> > 4<BR>> <<A href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" target=_blank>http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844</A><BR>> <<A
href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" target=_blank>http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844</A>>><BR>> ><BR>> ><BR>> > <BR>> -- ========================================<BR>> <BR>> Justin A. Lemkul<BR>> Ph.D. Candidate<BR>> ICTAS Doctoral Scholar<BR>> MILES-IGERT Trainee<BR>> Department of Biochemistry<BR>> Virginia Tech<BR>> Blacksburg, VA<BR>> jalemkul[at]vt.edu | (540) 231-9080<BR>> <A
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR>> <BR>> ========================================<BR>> -- gmx-users mailing list <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank>http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org</A>><BR>> <A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>> Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A>
before<BR>> posting!<BR>> Please don't post (un)subscribe requests to the list. Use the www<BR>> interface or send it to <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A><BR>> <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" target=_blank>http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org</A>>.<BR>> Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php" target=_blank>http://www.gromacs.org/mailing_lists/users.php</A><BR>> <BR>> <BR>> <BR><BR>-- ========================================<BR><BR>Justin A. Lemkul<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>MILES-IGERT Trainee<BR>Department of
Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]vt.edu | (540) 231-9080<BR><A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR><BR>========================================<BR>-- gmx-users mailing list <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org"
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