________________________________ From: "gmx-users-requ...@gromacs.org" <gmx-users-requ...@gromacs.org> To: gmx-users@gromacs.org Sent: Thu, August 12, 2010 2:32:17 AM Subject: gmx-users Digest, Vol 76, Issue 59 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. g_rms question (udi) 2. mdrun : error (Nilesh Dhumal) 3. Re: mdrun : error (Justin A. Lemkul) 4. need help (Anamika Awasthi) 5. Re: need help (Mark Abraham) 6. Re: g_rms question (Tsjerk Wassenaar) 7. trying to install gromacs on linux single processor (Anamika Awasthi) ---------------------------------------------------------------------- Message: 1 Date: Thu, 12 Aug 2010 00:39:03 +0300 From: udi <udi_...@012.net.il> Subject: [gmx-users] g_rms question To: gmx-users@gromacs.org Message-ID: <000001cb399d$9e2dee10$da89ca...@net.il> Content-Type: text/plain; charset="us-ascii" Hi gromacs users, I'm simulating a protein that consists of 5 domains. I have calculated the whole protein's backbone RMSD by entering '4' twice. Now, I would like to calculate the contribution of every domain i.e. if the whole protein's RMSD in the first frame is 1nm, then how is this 1nm distributed between the 5 domains. I have created 5 groups in the index file of the backbone of every domain and calculated the RMSD by first entering '4' in order to fit the whole backbone and entered the domains backbone groups in the second entry. (5 different calculations). The problem is that the values I get from the domains do not add up to the whole backbone RMSD values!!! What am doing wrong? Thanks from advanced Chears Udi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100812/e2049fd7/attachment-0001.html ------------------------------ Message: 2 Date: Wed, 11 Aug 2010 20:43:05 -0400 From: "Nilesh Dhumal" <ndhu...@andrew.cmu.edu> Subject: [gmx-users] mdrun : error To: gmx-users@gromacs.org Message-ID: <9bfc32c21b990b64977354fe7b803a7c.squir...@webmail.andrew.cmu.edu> Content-Type: text/plain;charset=iso-8859-1 Hello, I am trying to do equilibration for my system (solvent + solute). I am geting the following error. If I run solvent and solute molecules separately, its run well. For mixture I am getting following error. What this error means. Fatal error: 1 of the 22334 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck NIlesh ------------------------------ Message: 3 Date: Wed, 11 Aug 2010 20:48:52 -0400 From: "Justin A. Lemkul" <jalem...@vt.edu> Subject: Re: [gmx-users] mdrun : error To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4c6344f4.8020...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Nilesh Dhumal wrote: > Hello, > I am trying to do equilibration for my system (solvent + solute). I am > geting the following error. If I run solvent and solute molecules > separately, its run well. For mixture I am getting following error. > What this error means. > > Fatal error: > 1 of the 22334 bonded interactions could not be calculated because some > atoms involved moved further apart than the multi-body cut-off distance > (0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for > pairs and tabulated bonds also see option -ddcheck > Search the list archive. This has been asked and answered several times, so you'll likely find something useful. Also, take mdrun's advice and read about the options it's telling you. -Justin > NIlesh > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 4 Date: Thu, 12 Aug 2010 12:09:50 +0530 From: Anamika Awasthi <aawasth...@gmail.com> Subject: [gmx-users] need help To: gmx-users@gromacs.org Message-ID: <aanlktinqnjmg=z626t6xuam4rvrp+zc01stohw2+7...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear gromacs user, I want to install gromacs new version on my linux system. can u all please guide me, Thanking u in advance Anamika -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100812/d63d74d8/attachment-0001.html ------------------------------ Message: 5 Date: Thu, 12 Aug 2010 16:51:53 +1000 From: Mark Abraham <mark.abra...@anu.edu.au> Subject: Re: [gmx-users] need help To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <fbb4be4c2c0c2.4c642...@anu.edu.au> Content-Type: text/plain; charset="us-ascii" ----- Original Message ----- From: Anamika Awasthi <aawasth...@gmail.com> Date: Thursday, August 12, 2010 16:41 Subject: [gmx-users] need help To: gmx-users@gromacs.org > Dear gromacs user, > > I want to install gromacs new version on my linux system. can u all please >guide me, 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! :-) Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100812/9987e742/attachment-0001.html ------------------------------ Message: 6 Date: Thu, 12 Aug 2010 09:23:05 +0200 From: Tsjerk Wassenaar <tsje...@gmail.com> Subject: Re: [gmx-users] g_rms question To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <aanlkti=8nnb+p_p+0s+ck-hvauxe_a6vjdlzi4kmo...@mail.gmail.com> Content-Type: text/plain; charset="windows-1252" Hi Udi, Square the numbers... It's Root Mean Square Deviation, right? But roots don't add up like that. Cheers, Tsjerk On Aug 12, 2010 12:02 AM, "udi" <udi_...@012.net.il> wrote: Hi gromacs users, I’m simulating a protein that consists of 5 domains. I have calculated the whole protein’s backbone RMSD by entering ‘4’ twice. Now, I would like to calculate the contribution of every domain i.e. if the whole protein’s RMSD in the first frame is 1nm, then how is this 1nm distributed between the 5 domains. I have created 5 groups in the index file of the backbone of every domain and calculated the RMSD by first entering ‘4’ in order to fit the whole backbone and entered the domains backbone groups in the second entry. (5 different calculations). The problem is that the values I get from the domains do not add up to the whole backbone RMSD values!!! What am doing wrong? Thanks from advanced Chears Udi -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100812/f975352e/attachment-0001.html ------------------------------ Message: 7 Date: Thu, 12 Aug 2010 15:01:31 +0530 From: Anamika Awasthi <aawasth...@gmail.com> Subject: [gmx-users] trying to install gromacs on linux single processor To: gmx-users@gromacs.org Message-ID: <aanlktikpan3jbmssu67wproo0zntckrpgvbrd51yf...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" hello all, I am trying to install new version of gromacs on linux single processor, getting this error ./configure --enable-threads --enable-float checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... configure: error: newly created file is older than distributed files! Check your system clock -------------- next part -------------- An HTML attachment was scrubbed... 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