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<B><SPAN style="FONT-WEIGHT: bold">From:</SPAN></B> "gmx-users-request@gromacs.org" <gmx-users-request@gromacs.org><BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> gmx-users@gromacs.org<BR><B><SPAN style="FONT-WEIGHT: bold">Sent:</SPAN></B> Thu, August 12, 2010 2:32:17 AM<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> gmx-users Digest, Vol 76, Issue 59<BR></FONT><BR>Send gmx-users mailing list submissions to<BR> <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><BR>To subscribe or unsubscribe via the World Wide Web, visit<BR> http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>or, via email, send a message with subject or body 'help' to<BR> <A href="mailto:gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A><BR><BR>You can reach the person managing the list
at<BR> <A href="mailto:gmx-users-owner@gromacs.org" ymailto="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</A><BR><BR>When replying, please edit your Subject line so it is more specific<BR>than "Re: Contents of gmx-users digest..."<BR><BR><BR>Today's Topics:<BR><BR> 1. g_rms question (udi)<BR> 2. mdrun : error (Nilesh Dhumal)<BR> 3. Re: mdrun : error (Justin A. Lemkul)<BR> 4. need help (Anamika Awasthi)<BR> 5. Re: need help (Mark Abraham)<BR> 6. Re: g_rms question (Tsjerk Wassenaar)<BR> 7. trying to install gromacs on linux single processor<BR> (Anamika Awasthi)<BR><BR><BR>----------------------------------------------------------------------<BR><BR>Message: 1<BR>Date: Thu, 12 Aug 2010 00:39:03 +0300<BR>From: udi <<A href="mailto:udi_zel@012.net.il" ymailto="mailto:udi_zel@012.net.il">udi_zel@012.net.il</A>><BR>Subject: [gmx-users] g_rms
question<BR>To: <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>Message-ID: <000001cb399d$9e2dee10$da89ca30$@net.il><BR>Content-Type: text/plain; charset="us-ascii"<BR><BR>Hi gromacs users,<BR><BR>I'm simulating a protein that consists of 5 domains. I have calculated the<BR>whole protein's backbone RMSD by entering '4' twice.<BR><BR>Now, I would like to calculate the contribution of every domain i.e. if the<BR>whole protein's RMSD in the first frame is 1nm, then how is this 1nm<BR>distributed between the 5 domains.<BR><BR>I have created 5 groups in the index file of the backbone of every domain<BR>and calculated the RMSD by first entering '4' in order to fit the whole<BR>backbone and entered the domains backbone groups in the second entry. (5<BR>different calculations). The problem is that the values I get from the<BR>domains do not add up to the whole backbone RMSD values!!! What am
doing<BR>wrong? <BR><BR><BR><BR>Thanks from advanced<BR><BR>Chears<BR><BR><BR><BR>Udi <BR><BR>-------------- next part --------------<BR>An HTML attachment was scrubbed...<BR>URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100812/e2049fd7/attachment-0001.html<BR><BR>------------------------------<BR><BR>Message: 2<BR>Date: Wed, 11 Aug 2010 20:43:05 -0400<BR>From: "Nilesh Dhumal" <<A href="mailto:ndhumal@andrew.cmu.edu" ymailto="mailto:ndhumal@andrew.cmu.edu">ndhumal@andrew.cmu.edu</A>><BR>Subject: [gmx-users] mdrun : error <BR>To: <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>Message-ID:<BR> <<A href="mailto:9bfc32c21b990b64977354fe7b803a7c.squirrel@webmail.andrew.cmu.edu" ymailto="mailto:9bfc32c21b990b64977354fe7b803a7c.squirrel@webmail.andrew.cmu.edu">9bfc32c21b990b64977354fe7b803a7c.squirrel@webmail.andrew.cmu.edu</A>><BR>Content-Type:
text/plain;charset=iso-8859-1<BR><BR>Hello,<BR>I am trying to do equilibration for my system (solvent + solute). I am<BR>geting the following error. If I run solvent and solute molecules<BR>separately, its run well. For mixture I am getting following error.<BR>What this error means.<BR><BR>Fatal error:<BR>1 of the 22334 bonded interactions could not be calculated because some<BR>atoms involved moved further apart than the multi-body cut-off distance<BR>(0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for<BR>pairs and tabulated bonds also see option -ddcheck<BR><BR>NIlesh<BR><BR><BR><BR>------------------------------<BR><BR>Message: 3<BR>Date: Wed, 11 Aug 2010 20:48:52 -0400<BR>From: "Justin A. Lemkul" <<A href="mailto:jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>><BR>Subject: Re: [gmx-users] mdrun : error<BR>To: Discussion list for GROMACS users <<A href="mailto:gmx-users@gromacs.org"
ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>Message-ID: <<A href="mailto:4C6344F4.8020009@vt.edu" ymailto="mailto:4C6344F4.8020009@vt.edu">4C6344F4.8020009@vt.edu</A>><BR>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<BR><BR><BR><BR>Nilesh Dhumal wrote:<BR>> Hello,<BR>> I am trying to do equilibration for my system (solvent + solute). I am<BR>> geting the following error. If I run solvent and solute molecules<BR>> separately, its run well. For mixture I am getting following error.<BR>> What this error means.<BR>> <BR>> Fatal error:<BR>> 1 of the 22334 bonded interactions could not be calculated because some<BR>> atoms involved moved further apart than the multi-body cut-off distance<BR>> (0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for<BR>> pairs and tabulated bonds also see option -ddcheck<BR>> <BR><BR>Search the list archive. This has been
asked and answered several times, so <BR>you'll likely find something useful. Also, take mdrun's advice and read about <BR>the options it's telling you.<BR><BR>-Justin<BR><BR>> NIlesh<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]<A href="http://vt.edu/" target=_blank>vt.edu</A> | (540) 231-9080<BR>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR><BR>========================================<BR><BR><BR>------------------------------<BR><BR>Message: 4<BR>Date: Thu, 12 Aug 2010 12:09:50 +0530<BR>From: Anamika Awasthi <<A href="mailto:aawasthi28@gmail.com" ymailto="mailto:aawasthi28@gmail.com">aawasthi28@gmail.com</A>><BR>Subject: [gmx-users] need help<BR>To: <A href="mailto:gmx-users@gromacs.org"
ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>Message-ID:<BR> <AANLkTinqNjmg=z626T6XuAm4RvRP+zC01stohW2+<A href="mailto:7GuG@mail.gmail.com" ymailto="mailto:7GuG@mail.gmail.com">7GuG@mail.gmail.com</A>><BR>Content-Type: text/plain; charset="iso-8859-1"<BR><BR>Dear gromacs user,<BR><BR> I want to install gromacs new version on my linux system. can u all please<BR>guide me,<BR><BR><BR>Thanking u in advance<BR><BR>Anamika<BR>-------------- next part --------------<BR>An HTML attachment was scrubbed...<BR>URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100812/d63d74d8/attachment-0001.html<BR><BR>------------------------------<BR><BR>Message: 5<BR>Date: Thu, 12 Aug 2010 16:51:53 +1000<BR>From: Mark Abraham <<A href="mailto:mark.abraham@anu.edu.au" ymailto="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</A>><BR>Subject: Re: [gmx-users] need help<BR>To: Discussion list for
GROMACS users <<A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>Message-ID: <<A href="mailto:fbb4be4c2c0c2.4c6426a9@anu.edu.au" ymailto="mailto:fbb4be4c2c0c2.4c6426a9@anu.edu.au">fbb4be4c2c0c2.4c6426a9@anu.edu.au</A>><BR>Content-Type: text/plain; charset="us-ascii"<BR><BR><BR><BR>----- Original Message -----<BR>From: Anamika Awasthi <<A href="mailto:aawasthi28@gmail.com" ymailto="mailto:aawasthi28@gmail.com">aawasthi28@gmail.com</A>><BR>Date: Thursday, August 12, 2010 16:41<BR>Subject: [gmx-users] need help<BR>To: <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><BR>> Dear gromacs user,<BR>> <BR>> I want to install gromacs new version on my linux system. can u all please guide me,<BR><BR>The GROMACS installation guide can be found on the GROMACS webpage :-) There's a ton of other useful information there,
please be sure to search it and the rest of the web before asking questions. You'll make much faster progress that way! :-)<BR><BR>Mark<BR><BR>-------------- next part --------------<BR>An HTML attachment was scrubbed...<BR>URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100812/9987e742/attachment-0001.html<BR><BR>------------------------------<BR><BR>Message: 6<BR>Date: Thu, 12 Aug 2010 09:23:05 +0200<BR>From: Tsjerk Wassenaar <<A href="mailto:tsjerkw@gmail.com" ymailto="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</A>><BR>Subject: Re: [gmx-users] g_rms question<BR>To: Discussion list for GROMACS users <<A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>Message-ID:<BR> <AANLkTi=8NnB+p_p+0S+<A href="mailto:ck-HVAuxE_a6VjDLZi4kMoJaO@mail.gmail.com"
ymailto="mailto:ck-HVAuxE_a6VjDLZi4kMoJaO@mail.gmail.com">ck-HVAuxE_a6VjDLZi4kMoJaO@mail.gmail.com</A>><BR>Content-Type: text/plain; charset="windows-1252"<BR><BR>Hi Udi,<BR><BR>Square the numbers... It's Root Mean Square Deviation, right? But roots<BR>don't add up like that.<BR><BR>Cheers,<BR><BR>Tsjerk<BR><BR>On Aug 12, 2010 12:02 AM, "udi" <<A href="mailto:udi_zel@012.net.il" ymailto="mailto:udi_zel@012.net.il">udi_zel@012.net.il</A>> wrote:<BR><BR>Hi gromacs users,<BR><BR>I’m simulating a protein that consists of 5 domains. I have calculated the<BR>whole protein’s backbone RMSD by entering ‘4’ twice.<BR><BR>Now, I would like to calculate the contribution of every domain i.e. if the<BR>whole protein’s RMSD in the first frame is 1nm, then how is this 1nm<BR>distributed between the 5 domains.<BR><BR>I have created 5 groups in the index file of the backbone of every domain<BR>and calculated the RMSD by first entering ‘4’ in
order to fit the whole<BR>backbone and entered the domains backbone groups in the second entry. (5<BR>different calculations). The problem is that the values I get from the<BR>domains do not add up to the whole backbone RMSD values!!! What am doing<BR>wrong?<BR><BR><BR><BR>Thanks from advanced<BR><BR>Chears<BR><BR><BR><BR>Udi<BR><BR>--<BR>gmx-users mailing list <A href="mailto: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 http://www.gromacs.org/search before posting!<BR>Please don't post (un)subscribe requests to the list. Use the<BR>www interface or send it to <A href="mailto:gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read
http://www.gromacs.org/mailing_lists/users.php<BR>-------------- next part --------------<BR>An HTML attachment was scrubbed...<BR>URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100812/f975352e/attachment-0001.html<BR><BR>------------------------------<BR><BR>Message: 7<BR>Date: Thu, 12 Aug 2010 15:01:31 +0530<BR>From: Anamika Awasthi <<A href="mailto:aawasthi28@gmail.com" ymailto="mailto:aawasthi28@gmail.com">aawasthi28@gmail.com</A>><BR>Subject: [gmx-users] trying to install gromacs on linux single<BR> processor<BR>To: <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>Message-ID:<BR> <AANLkTikpAN3JbMSSU67WPRoo0zntCKrpgvBrD51YF+<A href="mailto:By@mail.gmail.com" ymailto="mailto:By@mail.gmail.com">By@mail.gmail.com</A>><BR>Content-Type: text/plain; charset="iso-8859-1"<BR><BR>hello all,<BR><BR>I am trying to install new version
of gromacs on linux single processor,<BR>getting this error<BR>./configure --enable-threads --enable-float<BR>checking build system type... x86_64-unknown-linux-gnu<BR>checking host system type... x86_64-unknown-linux-gnu<BR>checking for a BSD-compatible install... /usr/bin/install -c<BR>checking whether build environment is sane... configure: error: newly<BR>created file is older than distributed files!<BR>Check your system clock<BR>-------------- next part --------------<BR>An HTML attachment was scrubbed...<BR>URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100812/f8c1fd48/attachment.html<BR><BR>------------------------------<BR><BR>-- <BR>gmx-users mailing list<BR><A href="mailto: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><BR>End of gmx-users Digest, Vol 76, Issue 59<BR>*****************************************<BR></DIV></DIV></div><br>
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