Re: [gmx-users] Re: do_dssp
Yes , I am using the correct options for dssp. But still I am getting the same error. On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/04/2012 10:25 AM, bharat gupta wrote: Hi, I am trying to plot the ss content using the do_dssp command , but I am getting the following error :- Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 /dev/null 2 /dev/null I am using the DSSPold version. What could be the possible reason for such an error ?? Many of them. Start by making sure you're following the advice of do_dssp -h. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: do_dssp
On 5/04/2012 4:16 PM, bharat gupta wrote: Yes , I am using the correct options for dssp. But still I am getting the same error. What does invoking /usr/local/bin/dsspcmbi say? Mark On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 5/04/2012 10:25 AM, bharat gupta wrote: Hi, I am trying to plot the ss content using the do_dssp command , but I am getting the following error :- Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 /dev/null 2 /dev/null I am using the DSSPold version. What could be the possible reason for such an error ?? Many of them. Start by making sure you're following the advice of do_dssp -h. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: do_dssp
*This is the output : [root@BHARATPC ~]# /usr/local/bin/dssp bash: /usr/local/bin/dssp: Permission denied I have already set the pat for dssp in .bashrc using export command , I don't know why this error is there. Is it due to renaming dsspcmbi to dssp ?? * On Thu, Apr 5, 2012 at 4:08 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/04/2012 4:16 PM, bharat gupta wrote: Yes , I am using the correct options for dssp. But still I am getting the same error. What does invoking /usr/local/bin/dsspcmbi say? Mark On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/04/2012 10:25 AM, bharat gupta wrote: Hi, I am trying to plot the ss content using the do_dssp command , but I am getting the following error :- Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 /dev/null 2 /dev/null I am using the DSSPold version. What could be the possible reason for such an error ?? Many of them. Start by making sure you're following the advice of do_dssp -h. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: do_dssp
On 5/04/2012 5:16 PM, bharat gupta wrote: /This is the output : [root@BHARATPC ~]# /usr/local/bin/dssp / Don't run as root except for installing software, unless you like rebuilding your computer from the ground up. /bash: /usr/local/bin/dssp: Permission denied / Possibly you didn't give execute permission on some file or other. This is not a GROMACS problem, but rather a problem with how you have done your dssp installation. Consult its documentation. / I have already set the pat for dssp in .bashrc using export command , I don't know why this error is there. Is it due to renaming dsspcmbi to dssp ?? / You have now reported testing a command different from the one you reported that you had instructed do_dssp to use. So it is hard for me to believe your assertion that you are following the advice in do_dssp -h correctly with a correct version of DSSP. Mark // On Thu, Apr 5, 2012 at 4:08 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 5/04/2012 4:16 PM, bharat gupta wrote: Yes , I am using the correct options for dssp. But still I am getting the same error. What does invoking /usr/local/bin/dsspcmbi say? Mark On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 5/04/2012 10:25 AM, bharat gupta wrote: Hi, I am trying to plot the ss content using the do_dssp command , but I am getting the following error :- Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 /dev/null 2 /dev/null I am using the DSSPold version. What could be the possible reason for such an error ?? Many of them. Start by making sure you're following the advice of do_dssp -h. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: do_dssp
Ok now after downloading the latest version of dssp, and giving right permissions and after executing the /usr/local/bin/dssp command I am getting the following output :- [root@BHARATPC peptide2]# /usr/local/bin/dssp DSSP options: -h [ --help ] Display help message -i [ --input ] argInput file -o [ --output ] arg Output file, use 'stdout' to output to screen -v [ --verbose ] Verbose output -d [ --debug ] argDebug level (for even more verbose output) Examples: To calculate the secondary structure for the file 1crn.pdb and write the result to a file called 1crn.dssp, you type: dssp.exe -i 1crn.pdb -o 1crn.dssp On Thu, Apr 5, 2012 at 4:23 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/04/2012 5:16 PM, bharat gupta wrote: *This is the output : [root@BHARATPC ~]# /usr/local/bin/dssp * Don't run as root except for installing software, unless you like rebuilding your computer from the ground up. *bash: /usr/local/bin/dssp: Permission denied * Possibly you didn't give execute permission on some file or other. This is not a GROMACS problem, but rather a problem with how you have done your dssp installation. Consult its documentation. * I have already set the pat for dssp in .bashrc using export command , I don't know why this error is there. Is it due to renaming dsspcmbi to dssp ?? * You have now reported testing a command different from the one you reported that you had instructed do_dssp to use. So it is hard for me to believe your assertion that you are following the advice in do_dssp -h correctly with a correct version of DSSP. Mark * * On Thu, Apr 5, 2012 at 4:08 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/04/2012 4:16 PM, bharat gupta wrote: Yes , I am using the correct options for dssp. But still I am getting the same error. What does invoking /usr/local/bin/dsspcmbi say? Mark On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/04/2012 10:25 AM, bharat gupta wrote: Hi, I am trying to plot the ss content using the do_dssp command , but I am getting the following error :- Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 /dev/null 2 /dev/null I am using the DSSPold version. What could be the possible reason for such an error ?? Many of them. Start by making sure you're following the advice of do_dssp -h. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Another do_dssp problem
Dear Gromacs gurus, Forgive me for starting another topic on do_dssp. I encountered a somewhat different problem with the program. The environment and dssp permission setup are (supposedly) OK, but the dssp stuck at frame 0. do_dssp -f md.trr -s md.tpr -e 200 ... Selected 5: 'MainChain' There are 566 residues in your selected group Opening library file /usr/local/gromacs-3.3.3/share/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up ddd9M9eN to ./#ddd9M9eN.1# And it just stayed there forever (1 hour and counting on a 2.7 GHz machine). I am using the old dssp (dsspcmbi) and (as directed) compiled it using GCC and CC (neither worked). Running dssp executable never gives any problem. Any ideas? Thanks. -- Clement Angkawidjaja, PhD. G30 Assistant Professor Chemistry-Biology Combined Major Program International College, Osaka University 1-30 Machikaneyama-cho Toyonaka, Osaka 560-0043, Japan http://www.icou.osaka-u.ac.jp/cbcmp/ Tel. +81-6-6850-5952 Fax +81-6-6850-5961 Laboratory of Molecular Biotechnology Graduate School of Engineering, Osaka University 2-1 Yamadaoka U1E-804 Suita, Osaka 565-0871, Japan http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html Tel/Fax +81-6-6879-4157 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] how to change the timestamp of a xtc file
Hi, A quick question, how can I change the .xtc file which beginning at 0, end at 1 ns to beginning at 5ns and end at 6ns. Thanks for any suggestions, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Monitoring of Salt bridges during simulation Run
Dear Gromacs Users! I'd like to monitor origin and destabilisation of salt-bridges during simulation time. In particular I want to define some charged residues within selection groups to monitor both of intra-protein as well as protein-protein interactions. In past I've used only g_hbondhttp://manual.gromacs.org/online/g_hbond.htmlutillity to monitor Hbonds within selection. Is there any specified program for such task but with salt-bridges only ? Thanks for help, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Monitoring of Salt bridges during simulation Run
You can use g_saltbr option , http://manual.gromacs.org/online/g_saltbr.html On Thu, Apr 5, 2012 at 5:23 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs Users! I'd like to monitor origin and destabilisation of salt-bridges during simulation time. In particular I want to define some charged residues within selection groups to monitor both of intra-protein as well as protein-protein interactions. In past I've used only g_hbondhttp://manual.gromacs.org/online/g_hbond.htmlutillity to monitor Hbonds within selection. Is there any specified program for such task but with salt-bridges only ? Thanks for help, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Monitoring of Salt bridges during simulation Run
g_saltbr? If you have salt bridges you already know about and want to look at, you can always go with g_dist per pair manually. On 2012-04-05 12:23:02PM +0400, James Starlight wrote: Dear Gromacs Users! I'd like to monitor origin and destabilisation of salt-bridges during simulation time. In particular I want to define some charged residues within selection groups to monitor both of intra-protein as well as protein-protein interactions. In past I've used only g_hbondhttp://manual.gromacs.org/online/g_hbond.htmlutillity to monitor Hbonds within selection. Is there any specified program for such task but with salt-bridges only ? Thanks for help, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] how to change the timestamp of a xtc file
trjcat -settime or trjconv -t0 On 2012-04-05 03:59:44PM +0800, lina wrote: Hi, A quick question, how can I change the .xtc file which beginning at 0, end at 1 ns to beginning at 5ns and end at 6ns. Thanks for any suggestions, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] how to change the timestamp of a xtc file
On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai p...@uab.edu wrote: trjcat -settime or trjconv -t0 Thank you, a further question, a trjcat-ed xtc file, which timestamp like 0-5 0-2 0-5 0-3 ... Are there someway to update them all in the trjcated ones? Thanks ahead, On 2012-04-05 03:59:44PM +0800, lina wrote: Hi, A quick question, how can I change the .xtc file which beginning at 0, end at 1 ns to beginning at 5ns and end at 6ns. Thanks for any suggestions, Best regards, -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] which xtc file should be used for the trjconv command
On Thu, Apr 5, 2012 at 11:50 AM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, In the on-line tutorial on lysozyme (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html), there is a command trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact Will you please consider in that command whether we can change md_1_1.xtc to state.xtc? Yes. I am looking forward to getting your reply. Cheers, Acoot -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Monitoring of Salt bridges during simulation Run
Bharat, Peter thanks for advises I've checked g_saltbr but not found possible definition of the specified regions ( this utility lacks -n index.ndx option). How I could ignore contacts between solvent and protein ? Also what is the real *-t value should I provide ? As I understood this is only Rmin but could I define Rmax cutoff as well? James * 5 апреля 2012 г. 12:36 пользователь Peter C. Lai p...@uab.edu написал: g_saltbr? If you have salt bridges you already know about and want to look at, you can always go with g_dist per pair manually. On 2012-04-05 12:23:02PM +0400, James Starlight wrote: Dear Gromacs Users! I'd like to monitor origin and destabilisation of salt-bridges during simulation time. In particular I want to define some charged residues within selection groups to monitor both of intra-protein as well as protein-protein interactions. In past I've used only g_hbondhttp://manual.gromacs.org/online/g_hbond.htmlutillity to monitor Hbonds within selection. Is there any specified program for such task but with salt-bridges only ? Thanks for help, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] something about tpr file
Hi, suppose I lost original .tpr file, can I get tpr file from the .xtc file ? I mean from the .xtc or trr file, not by re-run grompp to generate tpr file. Thanks ahead, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] how to change the timestamp of a xtc file
On 05/04/12, lina lina.lastn...@gmail.com wrote: On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai p...@uab.edu wrote: trjcat -settime or trjconv -t0 Thank you, a further question, a trjcat-ed xtc file, which timestamp like 0-5 0-2 0-5 0-3 ... Are there someway to update them all in the trjcated ones? I've no idea what you mean, but trjconv -settime is still your friend. Mark Thanks ahead, On 2012-04-05 03:59:44PM +0800, lina wrote: Hi, A quick question, how can I change the .xtc file which beginning at 0, end at 1 ns to beginning at 5ns and end at 6ns. Thanks for any suggestions, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] how to change the timestamp of a xtc file
On Thu, Apr 5, 2012 at 6:07 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 05/04/12, lina lina.lastn...@gmail.com wrote: On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai p...@uab.edu wrote: trjcat -settime or trjconv -t0 Thank you, a further question, a trjcat-ed xtc file, which timestamp like 0-5 0-2 0-5 0-3 ... Are there someway to update them all in the trjcated ones? I've no idea what you mean, but trjconv -settime is still your friend. sorry I didn't say it clearly. Well, I mean several xtc files all starts with 0 but ends with 1 ns, 2 ns, 1 ns I use trjcat -cat combine them together. now I wonder can make the time continuously. from 0 to 4ns. Thanks, Mark Thanks ahead, On 2012-04-05 03:59:44PM +0800, lina wrote: Hi, A quick question, how can I change the .xtc file which beginning at 0, end at 1 ns to beginning at 5ns and end at 6ns. Thanks for any suggestions, Best regards, -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: do_dssp
On 05/04/12, bharat gupta bharat.85.m...@gmail.com wrote: Ok now after downloading the latest version of dssp, This won't work, because the latest version of DSSP is newer than any released version of GROMACS, and they made big changes. This was discussed at length on the list only yesterday... go and find that thread to see how you need to proceed. and giving right permissions and after executing the /usr/local/bin/dssp command I am getting the following output :- [root@BHARATPC peptide2]# /usr/local/bin/dssp By running this program as root, you trusted it not to have a bug that could trash your computer. There is no reason to run that risk. Mark DSSP options: -h [ --help ] Display help message -i [ --input ] argInput file -o [ --output ] arg Output file, use 'stdout' to output to screen -v [ --verbose ] Verbose output -d [ --debug ] argDebug level (for even more verbose output) Examples: To calculate the secondary structure for the file 1crn.pdb and write the result to a file called 1crn.dssp, you type: dssp.exe -i 1crn.pdb -o 1crn.dssp On Thu, Apr 5, 2012 at 4:23 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 5/04/2012 5:16 PM, bharat gupta wrote: This is the output : [root@BHARATPC ~]# /usr/local/bin/dssp Don't run as root except for installing software, unless you like rebuilding your computer from the ground up. bash: /usr/local/bin/dssp: Permission denied Possibly you didn't give execute permission on some file or other. This is not a GROMACS problem, but rather a problem with how you have done your dssp installation. Consult its documentation. I have already set the pat for dssp in .bashrc using export command , I don't know why this error is there. Is it due to renaming dsspcmbi to dssp ?? You have now reported testing a command different from the one you reported that you had instructed do_dssp to use. So it is hard for me to believe your assertion that you are following the advice in do_dssp -h correctly with a correct version of DSSP. Mark On Thu, Apr 5, 2012 at 4:08 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 5/04/2012 4:16 PM, bharat gupta wrote: Yes , I am using the correct options for dssp. But still I am getting the same error. What does invoking /usr/local/bin/dsspcmbi say? Mark On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 5/04/2012 10:25 AM, bharat gupta wrote: Hi, I am trying to plot the ss content using the do_dssp command , but I am getting the following error :- Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 /dev/null 2 /dev/null I am using the DSSPold version. What could be the possible reason for such an error ?? Many of them. Start by making sure you're following the advice of do_dssp -h. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com
Re: [gmx-users] something about tpr file
On 05/04/12, lina lina.lastn...@gmail.com wrote: Hi, suppose I lost original .tpr file, can I get tpr file from the .xtc file ? I mean from the .xtc or trr file, not by re-run grompp to generate tpr file. No Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] how to change the timestamp of a xtc file
On 05/04/12, lina lina.lastn...@gmail.com wrote: On Thu, Apr 5, 2012 at 6:07 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 05/04/12, lina lina.lastn...@gmail.com wrote: On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai p...@uab.edu wrote: trjcat -settime or trjconv -t0 Thank you, a further question, a trjcat-ed xtc file, which timestamp like 0-5 0-2 0-5 0-3 ... Are there someway to update them all in the trjcated ones? I've no idea what you mean, but trjconv -settime is still your friend. sorry I didn't say it clearly. Well, I mean several xtc files all starts with 0 but ends with 1 ns, 2 ns, 1 ns I use trjcat -cat combine them together. now I wonder can make the time continuously. from 0 to 4ns. Read the -h output for trjconv and trjcat and choose wisely. Mark Thanks, Mark Thanks ahead, On 2012-04-05 03:59:44PM +0800, lina wrote: Hi, A quick question, how can I change the .xtc file which beginning at 0, end at 1 ns to beginning at 5ns and end at 6ns. Thanks for any suggestions, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Atom N not found....
rama david wrote: Hi Gromacs friends, When I given the command ... pdb2gmx -f .. -o .. -p .. -ignh I gate the following error.. -- Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1070 Fatal error: atom N not found in buiding block 1ACE while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors When I goes through the detail of the website at http://www.gromacs.org/Documentation/Errors and document I come to know that I have to modify the rtp file, Nowhere in the explanation of the error does it suggest that you should alter the .rtp file in this instance. You have atoms in your structure that are not in the .rtp entry. Specifically, your structure file has an N atom in ACE, but ACE only contains CA, C, and O. The N atom should be the first atom in the next residue, not ACE. -Justin -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Monitoring of Salt bridges during simulation Run
On 05/04/12, James Starlight jmsstarli...@gmail.com wrote: Bharat, Peter thanks for advises I've checked g_saltbr but not found possible definition of the specified regions ( this utility lacks -n index.ndx option). How I could ignore contacts between solvent and protein ? Use trjconv -n and tpbconv -n to create a matching subset of your trajectory and -s input file, and use that as input to g_saltbr. Also what is the real -t value should I provide ? As I understood this is only Rmin but could I define Rmax cutoff as well? Looks like Rmax to me, from g_saltbr -h, but if you experiment, find out and report back it can go into the next version of the documentation (which is never perfect!). Mark James 5 апреля 2012 г. 12:36 пользователь Peter C. Lai p...@uab.edu написал: g_saltbr? If you have salt bridges you already know about and want to look at, you can always go with g_dist per pair manually. On 2012-04-05 12:23:02PM +0400, James Starlight wrote: Dear Gromacs Users! I'd like to monitor origin and destabilisation of salt-bridges during simulation time. In particular I want to define some charged residues within selection groups to monitor both of intra-protein as well as protein-protein interactions. In past I've used only g_hbondhttp://manual.gromacs.org/online/g_hbond.htmlutillity to monitor Hbonds within selection. Is there any specified program for such task but with salt-bridges only ? Thanks for help, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] the different protonation state of HIS
Dear All, For the different protonation state of HIS, what are there 3-letter code for GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me to read? Do we still have any other confusing amino acids? I am looking forward to getting a reply from you. Cheers, Acoot-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: questions about Principal Component Analysis
Dear Tserk and the rest of GROMACS users, Last time I measured the cosine content of different time intervals from the PCs of the whole trajectory. This time I did PCA for each time interval and measured the cc which is the right way I suppose. Maisuradze et al., 2009 claim that a CC value below 0.5 indicates that the protein-water system stops behaving as one with Brownian motions. Yet in none of my time intervals the CC dropped below 0.6. Can this happen for an equilibrated system? It is known that RMSIP can be used to measure the overlap between essential subspaces. My question is can RMSIP help me decide at which point to consider a system equilibrated from a thermodynamical point of view, namely the point at which the system stops doing Brownian motion? Does this point necessarily coincide with that where the RMSD is stabilized? Our protein is co-complexed in another one in the crystal structure, which is believed to hold it in an inactive state. However, we simulate the monomer state, hence we expect a large domain motion to occur in the first few nanosecond. Provided that the first 20ns are considered the time for equilibration, does it make sense to do PCA in this time interval? Thanks in advance for your help. Thomas On 12 March 2012 15:44, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Thomas, Whether or not it makes sense to do PCA on the domain only depends on the question you ask. It may well make sense if you aim at characterizing the intra-domain motions. But be aware that you will view those motions within the context of the rest of the protein. It is quite likely that the internal motions depend on the interaction with the surroundings. Concerning the cosine content, there indeed seems to ba a transition. But that is already evident from your RMSD plot. A lot of stuff is still happening in the second half of the simulation. To see if the last part of your simulation is in a (local) equilibrium, you can calculate the average structure from that part, say the alst 10 or 20 ns, and determine the RMSD against the average. The RMSD should then decrease towards the average and level off or oscillate around it to assure you've reached some sort of equilibrium. On the basis of that you could then decide whether it's worthwhile performing PCA on that part only. Cheers, Tsjerk -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] the different protonation state of HIS
On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, For the different protonation state of HIS, what are there 3-letter code for GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me to read? Do we still have any other confusing amino acids? In pdb2gmx -his you will get something like below 0. H on ND1 only (HSD) 1. H on NE2 only (HSE) 2. H on ND1 and NE2 (HSP) 3. Coupled to Heme (HIS1) Then based on the pka value and the PH, you can make a choice. I am looking forward to getting a reply from you. Cheers, Acoot -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] how to change the timestamp of a xtc file
On 2012-04-05 06:18:34PM +0800, lina wrote: On Thu, Apr 5, 2012 at 6:07 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 05/04/12, lina lina.lastn...@gmail.com wrote: On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai p...@uab.edu wrote: trjcat -settime or trjconv -t0 Thank you, a further question, a trjcat-ed xtc file, which timestamp like 0-5 0-2 0-5 0-3 ... Are there someway to update them all in the trjcated ones? I've no idea what you mean, but trjconv -settime is still your friend. sorry I didn't say it clearly. Well, I mean several xtc files all starts with 0 but ends with 1 ns, 2 ns, 1 ns I use trjcat -cat combine them together. now I wonder can make the time continuously. from 0 to 4ns. use trjcat or trjconv -settime on each individual xtc file to generate the correct starting times for each, then trjcat the corrected trajectories. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] the different protonation state of HIS
On 2012-04-05 08:55:24PM +0800, lina wrote: On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, For the different protonation state of HIS, what are there 3-letter code for This is also somewhat forcefield dependent (and how you name the histidines in the PDB as well). GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me to read? Do we still have any other confusing amino acids? -SH will show up as part of a -SH containing residue (cysteine). pdb2gmx will attempt to ask you about -S-S- bridges correctly if two cysteines are close to each other, use the -ss parameter to pdb2gmx. The manual has a description of how to force a disulfide bridge using specbond.dat if the starting structure is suboptimal... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] the different protonation state of HIS
Dear All, For pdb2gmx, we have -ignh. Does -ignh will always give the correct HIS format at pH 7? Looking forward to getting your reply. Cheers, Acoot From: lina lina.lastn...@gmail.com To: Acoot Brett acootbr...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, 5 April 2012 10:55 PM Subject: Re: [gmx-users] the different protonation state of HIS On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, For the different protonation state of HIS, what are there 3-letter code for GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me to read? Do we still have any other confusing amino acids? In pdb2gmx -his you will get something like below 0. H on ND1 only (HSD) 1. H on NE2 only (HSE) 2. H on ND1 and NE2 (HSP) 3. Coupled to Heme (HIS1) Then based on the pka value and the PH, you can make a choice. I am looking forward to getting a reply from you. Cheers, Acoot -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] the different protonation state of HIS
Acoot Brett wrote: Dear All, For pdb2gmx, we have -ignh. Does -ignh will always give the correct HIS format at pH 7? Strictly speaking, the -ignh option doesn't have anything to do with HIS protonation, it simply ignores H atoms in the input. HIS protonation states are then determined by an algorithm that seeks to maximize the hydrogen bonding network in the structure. Whether or not that necessarily reproduces reality (or completely replicates any protonation states in the original input that had its H atoms ignored) is an exercise for the user and can be changed with -his. -Justin Looking forward to getting your reply. Cheers, Acoot *From:* lina lina.lastn...@gmail.com *To:* Acoot Brett acootbr...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, 5 April 2012 10:55 PM *Subject:* Re: [gmx-users] the different protonation state of HIS On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett acootbr...@yahoo.com mailto:acootbr...@yahoo.com wrote: Dear All, For the different protonation state of HIS, what are there 3-letter code for GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me to read? Do we still have any other confusing amino acids? In pdb2gmx -his you will get something like below 0. H on ND1 only (HSD) 1. H on NE2 only (HSE) 2. H on ND1 and NE2 (HSP) 3. Coupled to Heme (HIS1) Then based on the pka value and the PH, you can make a choice. I am looking forward to getting a reply from you. Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] the different protonation state of HIS
On 2012-04-05 06:19:07AM -0700, Acoot Brett wrote: Dear All, For pdb2gmx, we have -ignh. Does -ignh will always give the correct HIS format at pH 7? -ignh does not do what you think it does. -ignh ignores the original PDB's hydrogen coordinates. Picking the correct histidine protonation at pH 7 is still structure- dependent since either nitrogen can be protonated. The manual for pdb2gmx states the following automatic HIS protonation: For His, this is based on an optimal hydrogen bonding conformation. Hydrogen bonds are defined based on a simple geometric criterium, specified by the maximum hydrogen-donor-acceptor angle and donor-acceptor distance, which are set by -angle and -dist respectively. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] jobs failed
Hello: I am using the following script to run Gromacs in cluster, but it failed: # @ job_name = bm # @ class = kdm-large # @ error = gromacs.info # @ output = gromacs.out # @ environment = COPY_ALL # @ wall_clock_limit = 10:00:00 # @ notification = error # @ job_type = bluegene # @ bg_size = 64 # @ queue mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args -v -s md.tpr -o md.trr -cpo md.cpt -c md.gro -g md-out.log -launch -mode VN -np 256 and here is the log file Back Off! I just backed up md-out.log to ./#md-out.log.1# Getting Loaded... Reading file md.tpr, VERSION 4.5.5 (single precision) Loaded with Money Will use 192 particle-particle and 64 PME only nodes This is a guess, check the performance at the end of the log file Making 3D domain decomposition 8 x 4 x 6 Back Off! I just backed up md.trr to ./#md.trr.2# Back Off! I just backed up traj.xtc to ./#traj.xtc.3# Back Off! I just backed up ener.edr to ./#ener.edr.3# WARNING: This run will generate roughly 3302 Mb of data starting mdrun 'BmEH-complex-POA in water' 5000 steps, 10.0 ps. step 0 NOTE: Turning on dynamic load balancing vol 0.41 imb F 18% pme/F 0.61 step 100, will finish Tue Apr 17 13:49:51 2012 vol 0.42 imb F 12% pme/F 0.60 step 200, will finish Sun Apr 15 23:46:30 2012 vol 0.44 imb F 12% pme/F 0.57 step 300, will finish Sun Apr 15 12:20:49 2012 vol 0.45 imb F 12% pme/F 0.58 step 400, will finish Sun Apr 15 07:01:25 2012 vol 0.48 imb F 12% pme/F 0.57 step 500, will finish Sun Apr 15 03:46:13 2012 vol 0.49! imb F 11% pme/F 0.57 step 600, will finish Sun Apr 15 01:43:05 2012 vol 0.46! imb F 10% pme/F 0.59 step 700, will finish Sun Apr 15 00:01:14 2012 vol 0.42! imb F 10% pme/F 0.58 step 800, will finish Sat Apr 14 22:56:06 2012 vol 0.45! imb F 12% pme/F 0.56 step 900, will finish Sat Apr 14 22:16:49 2012 vol 0.46! imb F 10% pme/F 0.57 step 1000, will finish Sat Apr 14 21:49:10 2012 vol 0.46! imb F 9% pme/F 0.58 step 1100, will finish Sat Apr 14 21:26:04 2012 vol 0.47! imb F 10% pme/F 0.57 step 1200, will finish Sat Apr 14 21:02:35 2012 vol 0.45 imb F 9% pme/F 0.58 step 1300, will finish Sat Apr 14 20:34:22 2012 vol 0.45! imb F 9% pme/F 0.58 step 1400, will finish Sat Apr 14 20:15:54 2012 vol 0.48! imb F 11% pme/F 0.57 step 1500, will finish Sat Apr 14 20:07:48 2012 vol 0.47! imb F 10% pme/F 0.58 step 1600, will finish Sat Apr 14 19:57:46 2012 vol 0.47! imb F 13% pme/F 0.58 step 1700, will finish Sat Apr 14 19:51:47 2012 vol 0.45! imb F 11% pme/F 0.58 step 1800, will finish Sat Apr 14 19:44:37 2012 vol 0.46! imb F 13% pme/F 0.57 step 1900, will finish Sat Apr 14 19:37:10 2012 vol 0.50! imb F 12% pme/F 0.58 step 2000, will finish Sat Apr 14 19:29:20 2012 vol 0.50! imb F 12% pme/F 0.58 step 2100, will finish Sat Apr 14 19:23:00 2012 vol 0.48 imb F 10% pme/F 0.57 step 2200, will finish Sat Apr 14 19:15:43 2012 vol 0.50! imb F 11% pme/F 0.57 step 2300, will finish Sat Apr 14 19:13:30 2012 vol 0.49! imb F 11% pme/F 0.57 step 2400, will finish Sat Apr 14 19:10:14 2012 vol 0.48 imb F 10% pme/F 0.58 step 2500, will finish Sat Apr 14 19:01:51 2012 vol 0.47! imb F 12% pme/F 0.58 step 2600, will finish Sat Apr 14 18:55:11 2012 vol 0.48! imb F 11% pme/F 0.58 step 2700, will finish Sat Apr 14 18:49:47 2012 vol 0.46! imb F 12% pme/F 0.58 step 2800, will finish Sat Apr 14 18:45:32 2012 --- Program mdrun_mpi_bg, VERSION 4.5.5 Source code file: ../../../src/mdlib/domdec.c, line: 2633 Fatal error: Step 2850: The domain decomposition grid has shifted too much in the Z-direction around cell 5 0 2 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Don't Push Me, Cause I'm Close to the Edge (Tricky) Error on node 162, will try to stop all the nodes Halting parallel program mdrun_mpi_bg on CPU 162 out of 256 gcq#8: Don't Push Me, Cause I'm Close to the Edge (Tricky) Abort(-1) on node 162 (rank 162 in comm 1140850688): application called MPI_Abort(MPI_COMM_WORLD, -1) - process 162 Apr 05 13:15:36.667617 BE_MPI (ERROR): The error message in the job record is as follows: Apr 05 13:15:36.667681 BE_MPI (ERROR): killed with signal 6 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Zn Coordination
Dear all, I am relatively new to GROMACS and MD in general. I have gone through various GROMACS tutorials and successfully run a couple of my own simulations but that are pretty simple, i.e. just single chain protein with standard amino acids in SPC/E, not requiring much expert knowledge. I am now dealing with a more involved protein-RNA complex bound to ATP and a Zn ion. I saw that GROMACS recognizes both ZN and ATP among its standard building blocks. My question regards the coordination of the Zn ion. In my crystal structure Zn is coordinated by three cysteines and a histidine residue as is common among nucleic acid binding proteins and is usually, as in my case, only structural and not involved in active site catalysis. Since Zn is already recognized by default in GROMACS, do I need to be concerned about the specifics of the Zn coordination? I read in another thread that it may be quite advanced, possibly requiring some parameterization as stated herehttp://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_species. I also saw this paperhttp://jcp.aip.org/resource/1/jcpsa6/v132/i20/p205101_s1?view=fulltext that discusses Zn coordination but am unsure if it necessarily pertains to my case or if this information has already been incorporated into GROMACS. I'm not particularly interested in the specifics of the Zn site, but in a distant part of the structure, I just don't want to have some weird or drastic effect of the Zn finger unfolding or something along those lines. Is it sufficient to just introduce simple harmonic distant restraints to keep Zn in place? Any advice would be greatly appreciated. Thank you, Tom P.S. I am using the AMBER ff99SB force field after reading up on the advantages and disadvantages of those available to GROMACS relating to protein-nucleic acid complexes. Any advice on this would also be appreciated. -- Thomas D. Grant Graduate Research Assistant Hauptman-Woodward Medical Research Institute 700 Ellicott St. Buffalo, NY 14203 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_hbond
Hello, How can I add chlorin atom as a acceptor in g_hbond. I am using Gromacs VERSION 4.0.7 NIlesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Zn Coordination
Thomas Grant wrote: Dear all, I am relatively new to GROMACS and MD in general. I have gone through various GROMACS tutorials and successfully run a couple of my own simulations but that are pretty simple, i.e. just single chain protein with standard amino acids in SPC/E, not requiring much expert knowledge. I am now dealing with a more involved protein-RNA complex bound to ATP and a Zn ion. I saw that GROMACS recognizes both ZN and ATP among its standard building blocks. My question regards the coordination of the Zn ion. In my crystal structure Zn is coordinated by three cysteines and a histidine residue as is common among nucleic acid binding proteins and is usually, as in my case, only structural and not involved in active site catalysis. Since Zn is already recognized by default in GROMACS, do I need to be concerned about the specifics of the Zn coordination? I read in another thread that it may be quite advanced, possibly requiring some parameterization as stated here http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_species. I also saw this paper http://jcp.aip.org/resource/1/jcpsa6/v132/i20/p205101_s1?view=fulltext that discusses Zn coordination but am unsure if it necessarily pertains to my case or if this information has already been incorporated into GROMACS. I'm not particularly interested in the specifics of the Zn site, but in a distant part of the structure, I just don't want to have some weird or drastic effect of the Zn finger unfolding or something along those lines. Is it sufficient to just introduce simple harmonic distant restraints to keep Zn in place? For simply keeping the Zn ion in place, that is probably sufficient. Any advice would be greatly appreciated. Thank you, Tom P.S. I am using the AMBER ff99SB force field after reading up on the advantages and disadvantages of those available to GROMACS relating to protein-nucleic acid complexes. Any advice on this would also be appreciated. Seems like a reasonable choice. -Justin -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_hbond
Nilesh Dhumal wrote: Hello, How can I add chlorin atom as a acceptor in g_hbond. Either modify the source code (the search_acceptors routine in gmx_hbond.c) or make a dummy structure/topology that lists the Cl atoms as O. The program searches for acceptors by atom name only (O and/or N if using -nitacc), so you can probably trick it into thinking that's what they are. -Justin -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Different results from identical tpr after MD
Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. -- --- *Thanks and Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
Thanks for the reply. * *I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. And also how to believe the statement made by several research papers based on unconverged simulations. On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/**Documentation/Terminology/**Reproducibilityhttp://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: jobs failed
Hello: I am using the following script to run Gromacs in cluster, but it failed: # @ job_name = bm # @ class = kdm-large # @ error = gromacs.info # @ output = gromacs.out # @ environment = COPY_ALL # @ wall_clock_limit = 10:00:00 # @ notification = error # @ job_type = bluegene # @ bg_size = 64 # @ queue mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args -v -s md.tpr -o md.trr -cpo md.cpt -c md.gro -g md-out.log -launch -mode VN -np 256 and here is the log file Back Off! I just backed up md-out.log to ./#md-out.log.1# Getting Loaded... Reading file md.tpr, VERSION 4.5.5 (single precision) Loaded with Money Will use 192 particle-particle and 64 PME only nodes This is a guess, check the performance at the end of the log file Making 3D domain decomposition 8 x 4 x 6 Back Off! I just backed up md.trr to ./#md.trr.2# Back Off! I just backed up traj.xtc to ./#traj.xtc.3# Back Off! I just backed up ener.edr to ./#ener.edr.3# WARNING: This run will generate roughly 3302 Mb of data starting mdrun 'BmEH-complex-POA in water' 5000 steps, 10.0 ps. step 0 NOTE: Turning on dynamic load balancing vol 0.41 imb F 18% pme/F 0.61 step 100, will finish Tue Apr 17 13:49:51 2012 vol 0.42 imb F 12% pme/F 0.60 step 200, will finish Sun Apr 15 23:46:30 2012 vol 0.44 imb F 12% pme/F 0.57 step 300, will finish Sun Apr 15 12:20:49 2012 vol 0.45 imb F 12% pme/F 0.58 step 400, will finish Sun Apr 15 07:01:25 2012 vol 0.48 imb F 12% pme/F 0.57 step 500, will finish Sun Apr 15 03:46:13 2012 vol 0.49! imb F 11% pme/F 0.57 step 600, will finish Sun Apr 15 01:43:05 2012 vol 0.46! imb F 10% pme/F 0.59 step 700, will finish Sun Apr 15 00:01:14 2012 vol 0.42! imb F 10% pme/F 0.58 step 800, will finish Sat Apr 14 22:56:06 2012 vol 0.45! imb F 12% pme/F 0.56 step 900, will finish Sat Apr 14 22:16:49 2012 vol 0.46! imb F 10% pme/F 0.57 step 1000, will finish Sat Apr 14 21:49:10 2012 vol 0.46! imb F 9% pme/F 0.58 step 1100, will finish Sat Apr 14 21:26:04 2012 vol 0.47! imb F 10% pme/F 0.57 step 1200, will finish Sat Apr 14 21:02:35 2012 vol 0.45 imb F 9% pme/F 0.58 step 1300, will finish Sat Apr 14 20:34:22 2012 vol 0.45! imb F 9% pme/F 0.58 step 1400, will finish Sat Apr 14 20:15:54 2012 vol 0.48! imb F 11% pme/F 0.57 step 1500, will finish Sat Apr 14 20:07:48 2012 vol 0.47! imb F 10% pme/F 0.58 step 1600, will finish Sat Apr 14 19:57:46 2012 vol 0.47! imb F 13% pme/F 0.58 step 1700, will finish Sat Apr 14 19:51:47 2012 vol 0.45! imb F 11% pme/F 0.58 step 1800, will finish Sat Apr 14 19:44:37 2012 vol 0.46! imb F 13% pme/F 0.57 step 1900, will finish Sat Apr 14 19:37:10 2012 vol 0.50! imb F 12% pme/F 0.58 step 2000, will finish Sat Apr 14 19:29:20 2012 vol 0.50! imb F 12% pme/F 0.58 step 2100, will finish Sat Apr 14 19:23:00 2012 vol 0.48 imb F 10% pme/F 0.57 step 2200, will finish Sat Apr 14 19:15:43 2012 vol 0.50! imb F 11% pme/F 0.57 step 2300, will finish Sat Apr 14 19:13:30 2012 vol 0.49! imb F 11% pme/F 0.57 step 2400, will finish Sat Apr 14 19:10:14 2012 vol 0.48 imb F 10% pme/F 0.58 step 2500, will finish Sat Apr 14 19:01:51 2012 vol 0.47! imb F 12% pme/F 0.58 step 2600, will finish Sat Apr 14 18:55:11 2012 vol 0.48! imb F 11% pme/F 0.58 step 2700, will finish Sat Apr 14 18:49:47 2012 vol 0.46! imb F 12% pme/F 0.58 step 2800, will finish Sat Apr 14 18:45:32 2012 Check what happens to your volume. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
Well you're really supposed to conduct multiple runs anyway. Remember, a single MD run over a period of time only samples 1 possible trajectory out of the ensemble of possible trajectories... On 2012-04-05 11:38:20PM +0530, bipin singh wrote: Thanks for the reply. * *I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. And also how to believe the statement made by several research papers based on unconverged simulations. On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/**Documentation/Terminology/**Reproducibilityhttp://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
That's an interesting philosophical question. In this case, you'll wind up with a 50 ns trajectory where each configuration is consistent with the thermodynamic ensemble you're approximating. That's as close a definition to realistic as I think is worth worrying about. You'd only need to worry about mdrun not giving you exactly reproducible trajectories to 7 or 8 significant figures of precision in atomic coordinates if, simultaneously, nature behaved completely deterministically, you could observe a molecular system with that degree of precision, and your forcefield was exact; none of those three things are true. That said, 50 ns seems like a very short time to simulate a complex system like protein/DNA/RNA. I'd be very worried about drawing anything other than observations from such a small data set (because you're almost certainly not converged in your sampling, as you allude to in your final question). MZ On Thu, Apr 5, 2012 at 2:08 PM, bipin singh bipinel...@gmail.com wrote: Thanks for the reply. I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. And also how to believe the statement made by several research papers based on unconverged simulations. On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- 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 -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- --- Regards, Bipin Singh -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
But we hope finally no matter which trajectory, a stable protein conformation should be got! As for during the production MD, no significant energy change included. I am looking forward to getting more feedback on this topic. Acoot From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 6 April 2012 4:20 AM Subject: Re: [gmx-users] Different results from identical tpr after MD Well you're really supposed to conduct multiple runs anyway. Remember, a single MD run over a period of time only samples 1 possible trajectory out of the ensemble of possible trajectories... On 2012-04-05 11:38:20PM +0530, bipin singh wrote: Thanks for the reply. * *I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. And also how to believe the statement made by several research papers based on unconverged simulations. On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/**Documentation/Terminology/**Reproducibilityhttp://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- *Regards,* Bipin Singh -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] jobs failed
On 2012-04-05 04:15:00PM +0200, Albert wrote: Your box is violent shrinking too much for the domain decomposition routines to handle. What ensemble and integrator are you running? If normal md, then are you trying to NPT before NVT equilibration? Hello: I am using the following script to run Gromacs in cluster, but it failed: # @ job_name = bm # @ class = kdm-large # @ error = gromacs.info # @ output = gromacs.out # @ environment = COPY_ALL # @ wall_clock_limit = 10:00:00 # @ notification = error # @ job_type = bluegene # @ bg_size = 64 # @ queue mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args -v -s md.tpr -o md.trr -cpo md.cpt -c md.gro -g md-out.log -launch -mode VN -np 256 and here is the log file Back Off! I just backed up md-out.log to ./#md-out.log.1# Getting Loaded... Reading file md.tpr, VERSION 4.5.5 (single precision) Loaded with Money Will use 192 particle-particle and 64 PME only nodes This is a guess, check the performance at the end of the log file Making 3D domain decomposition 8 x 4 x 6 Back Off! I just backed up md.trr to ./#md.trr.2# Back Off! I just backed up traj.xtc to ./#traj.xtc.3# Back Off! I just backed up ener.edr to ./#ener.edr.3# WARNING: This run will generate roughly 3302 Mb of data starting mdrun 'BmEH-complex-POA in water' 5000 steps, 10.0 ps. step 0 NOTE: Turning on dynamic load balancing vol 0.41 imb F 18% pme/F 0.61 step 100, will finish Tue Apr 17 13:49:51 2012 vol 0.42 imb F 12% pme/F 0.60 step 200, will finish Sun Apr 15 23:46:30 2012 vol 0.44 imb F 12% pme/F 0.57 step 300, will finish Sun Apr 15 12:20:49 2012 vol 0.45 imb F 12% pme/F 0.58 step 400, will finish Sun Apr 15 07:01:25 2012 vol 0.48 imb F 12% pme/F 0.57 step 500, will finish Sun Apr 15 03:46:13 2012 vol 0.49! imb F 11% pme/F 0.57 step 600, will finish Sun Apr 15 01:43:05 2012 vol 0.46! imb F 10% pme/F 0.59 step 700, will finish Sun Apr 15 00:01:14 2012 vol 0.42! imb F 10% pme/F 0.58 step 800, will finish Sat Apr 14 22:56:06 2012 vol 0.45! imb F 12% pme/F 0.56 step 900, will finish Sat Apr 14 22:16:49 2012 vol 0.46! imb F 10% pme/F 0.57 step 1000, will finish Sat Apr 14 21:49:10 2012 vol 0.46! imb F 9% pme/F 0.58 step 1100, will finish Sat Apr 14 21:26:04 2012 vol 0.47! imb F 10% pme/F 0.57 step 1200, will finish Sat Apr 14 21:02:35 2012 vol 0.45 imb F 9% pme/F 0.58 step 1300, will finish Sat Apr 14 20:34:22 2012 vol 0.45! imb F 9% pme/F 0.58 step 1400, will finish Sat Apr 14 20:15:54 2012 vol 0.48! imb F 11% pme/F 0.57 step 1500, will finish Sat Apr 14 20:07:48 2012 vol 0.47! imb F 10% pme/F 0.58 step 1600, will finish Sat Apr 14 19:57:46 2012 vol 0.47! imb F 13% pme/F 0.58 step 1700, will finish Sat Apr 14 19:51:47 2012 vol 0.45! imb F 11% pme/F 0.58 step 1800, will finish Sat Apr 14 19:44:37 2012 vol 0.46! imb F 13% pme/F 0.57 step 1900, will finish Sat Apr 14 19:37:10 2012 vol 0.50! imb F 12% pme/F 0.58 step 2000, will finish Sat Apr 14 19:29:20 2012 vol 0.50! imb F 12% pme/F 0.58 step 2100, will finish Sat Apr 14 19:23:00 2012 vol 0.48 imb F 10% pme/F 0.57 step 2200, will finish Sat Apr 14 19:15:43 2012 vol 0.50! imb F 11% pme/F 0.57 step 2300, will finish Sat Apr 14 19:13:30 2012 vol 0.49! imb F 11% pme/F 0.57 step 2400, will finish Sat Apr 14 19:10:14 2012 vol 0.48 imb F 10% pme/F 0.58 step 2500, will finish Sat Apr 14 19:01:51 2012 vol 0.47! imb F 12% pme/F 0.58 step 2600, will finish Sat Apr 14 18:55:11 2012 vol 0.48! imb F 11% pme/F 0.58 step 2700, will finish Sat Apr 14 18:49:47 2012 vol 0.46! imb F 12% pme/F 0.58 step 2800, will finish Sat Apr 14 18:45:32 2012 --- Program mdrun_mpi_bg, VERSION 4.5.5 Source code file: ../../../src/mdlib/domdec.c, line: 2633 Fatal error: Step 2850: The domain decomposition grid has shifted too much in the Z-direction around cell 5 0 2 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Don't Push Me, Cause I'm Close to the Edge (Tricky) Error on node 162, will try to stop all the nodes Halting parallel program mdrun_mpi_bg on CPU 162 out of 256 gcq#8: Don't Push Me, Cause I'm Close to the Edge (Tricky) Abort(-1) on node 162 (rank 162 in comm 1140850688): application called MPI_Abort(MPI_COMM_WORLD, -1) - process 162 Apr 05 13:15:36.667617 BE_MPI (ERROR): The error message in the job record is as follows: Apr 05 13:15:36.667681 BE_MPI (ERROR): killed with signal 6 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] Different results from identical tpr after MD
Here I want to talk on the time length of production MD. I have a professor on computational biology. She said for MD only several ps is enough. I have the expereince to run production MD for several ns, and I have got stable conformation. But I am sure for some protein system, even a 50 ns MS will not give the stable conformation, thus maybe the results are not reproducible. I am not sure whether my explaination is suitable to you. Cheers, Acoot From: Matthew Zwier mczw...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 6 April 2012 4:24 AM Subject: Re: [gmx-users] Different results from identical tpr after MD That's an interesting philosophical question. In this case, you'll wind up with a 50 ns trajectory where each configuration is consistent with the thermodynamic ensemble you're approximating. That's as close a definition to realistic as I think is worth worrying about. You'd only need to worry about mdrun not giving you exactly reproducible trajectories to 7 or 8 significant figures of precision in atomic coordinates if, simultaneously, nature behaved completely deterministically, you could observe a molecular system with that degree of precision, and your forcefield was exact; none of those three things are true. That said, 50 ns seems like a very short time to simulate a complex system like protein/DNA/RNA. I'd be very worried about drawing anything other than observations from such a small data set (because you're almost certainly not converged in your sampling, as you allude to in your final question). MZ On Thu, Apr 5, 2012 at 2:08 PM, bipin singh bipinel...@gmail.com wrote: Thanks for the reply. I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. And also how to believe the statement made by several research papers based on unconverged simulations. On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- 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 -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- --- Regards, Bipin Singh -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
Acoot Brett wrote: Here I want to talk on the time length of production MD. I have a professor on computational biology. She said for MD only several ps is enough. I have the expereince to run production MD for several ns, and I have got stable conformation. Several ps is insufficient for all but the fastest (and thus smallest) motions in a macromolecule like a protein. But I am sure for some protein system, even a 50 ns MS will not give the stable conformation, thus maybe the results are not reproducible. I am not sure whether my explaination is suitable to you. The time frame necessary depends on what you're hoping to see. Fast motions (like side chain rotation, etc) require short simulations. Domain motions or folding simulations may require hundreds of ns or even more. Some phenomena cannot be modeled efficiently by atomistic MD simulations, though other mesoscale approaches may perform better. -Justin Cheers, Acoot *From:* Matthew Zwier mczw...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, 6 April 2012 4:24 AM *Subject:* Re: [gmx-users] Different results from identical tpr after MD That's an interesting philosophical question. In this case, you'll wind up with a 50 ns trajectory where each configuration is consistent with the thermodynamic ensemble you're approximating. That's as close a definition to realistic as I think is worth worrying about. You'd only need to worry about mdrun not giving you exactly reproducible trajectories to 7 or 8 significant figures of precision in atomic coordinates if, simultaneously, nature behaved completely deterministically, you could observe a molecular system with that degree of precision, and your forcefield was exact; none of those three things are true. That said, 50 ns seems like a very short time to simulate a complex system like protein/DNA/RNA. I'd be very worried about drawing anything other than observations from such a small data set (because you're almost certainly not converged in your sampling, as you allude to in your final question). MZ On Thu, Apr 5, 2012 at 2:08 PM, bipin singh bipinel...@gmail.com mailto:bipinel...@gmail.com wrote: Thanks for the reply. I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. And also how to believe the statement made by several research papers based on unconverged simulations. On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- 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 -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org
Re: [gmx-users] Different results from identical tpr after MD
bipin singh wrote: Thanks for the reply. / /I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. No one can do anything for an infinite amount of time ;) Hence replicate simulations and thorough statistical analysis are required to obtain reliable results and prove that what you've done is to be trusted. The other comments in this thread are quite good so I won't recapitulate other points that have been made. And also how to believe the statement made by several research papers based on unconverged simulations. I wouldn't trust any conclusions drawn from demonstrably unconverged simulations. Not everything that's published has been done correctly. Peer review is an imperfect system, so be careful what you read and apply good scientific judgment. -Justin On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/__Documentation/Terminology/__Reproducibility http://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- --- /Regards,/ Bipin Singh -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: job failed
Hello: thank you very much for kind reply. I tried NVT before I produced NPT MD production. thank you very much -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
Hi Justin, Can you give me your definition of converged MD and unconverged MD? Cheers, Acoot From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 6 April 2012 4:41 AM Subject: Re: [gmx-users] Different results from identical tpr after MD bipin singh wrote: Thanks for the reply. / /I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. No one can do anything for an infinite amount of time ;) Hence replicate simulations and thorough statistical analysis are required to obtain reliable results and prove that what you've done is to be trusted. The other comments in this thread are quite good so I won't recapitulate other points that have been made. And also how to believe the statement made by several research papers based on unconverged simulations. I wouldn't trust any conclusions drawn from demonstrably unconverged simulations. Not everything that's published has been done correctly. Peer review is an imperfect system, so be careful what you read and apply good scientific judgment. -Justin On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/__Documentation/Terminology/__Reproducibility http://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- --- /Regards,/ Bipin Singh -- 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 -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: job failed
On 2012-04-05 08:51:05PM +0200, Albert wrote: Hello: thank you very much for kind reply. I tried NVT before I produced NPT MD production. thank you very much What pressure coupling barostat are you using? (pcoupl) -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: job failed
Peter C. Lai wrote: On 2012-04-05 08:51:05PM +0200, Albert wrote: Hello: thank you very much for kind reply. I tried NVT before I produced NPT MD production. thank you very much What pressure coupling barostat are you using? (pcoupl) A full .mdp file and description of the system being simulated would be even better :) -Justin -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
Acoot Brett wrote: Hi Justin, Can you give me your definition of converged MD and unconverged MD? One could fill many textbook chapters with an answer to this question. Suffice it to say that one would consider a simulation converged if the properties of interest have also converged around stable values, such that extending the simulation longer would not change the result. Knowing when to stop is not something that can be generalized, and depends entirely upon the system at hand, question being asked, and method(s) of analysis. Structural, thermodynamic, or other energetic properties may be of interest, but these are things you should define before you even sit down at your terminal to begin. -Justin Cheers, Acoot *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, 6 April 2012 4:41 AM *Subject:* Re: [gmx-users] Different results from identical tpr after MD bipin singh wrote: Thanks for the reply. / /I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. No one can do anything for an infinite amount of time ;) Hence replicate simulations and thorough statistical analysis are required to obtain reliable results and prove that what you've done is to be trusted. The other comments in this thread are quite good so I won't recapitulate other points that have been made. And also how to believe the statement made by several research papers based on unconverged simulations. I wouldn't trust any conclusions drawn from demonstrably unconverged simulations. Not everything that's published has been done correctly. Peer review is an imperfect system, so be careful what you read and apply good scientific judgment. -Justin On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/__Documentation/Terminology/__Reproducibility http://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin --==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- --- /Regards,/ Bipin Singh -- 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 -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
[gmx-users] Help: Anyone worked with Wall?
Dear all, I'm trying to simulate with pbc=xy and I need two walls. My settings are as follows: pbc = xy nwall = 2 wall_atomtype = C C wall_type = 9-3 wall_r_linpot = -1 -1 wall_density= 20 20 wall_ewald_zfac = 3 The problem is how to define wall_atomtype in my topology file (top/itp)? A want to have this solid carbon wall with 9-3 potential. Where in my top/itp file can I define such atoms? This is my top file: #include ffG53a6.itp #include spc.itp [ system ] Pure Water with walls [ molecules ] SOL216 When I gmxdump the generated tpr file, I saw no C atoms are defined; and it showed: wall_atomtype[0] = 2 wall_atomtype[1] = 2 which corresponds to the hydrogen atom in my top file. And according to my forcefield, the LJ parameters for H is 0,0. So there is basically no wall. When I tried to simulate with this setting, the water molecules went out of the box (in z direction) and moved far away. And according to g_energy, there is no interaction energy between water and wall. So there indeed is no wall. Can you help me with defining wall atom? If you have already finished any tasks with this wall algorithm, can you kindly attach your topology files to me? Soo many thanks! -- Huaichen(Bobby) ZHANG +31 648478172 MSc Sustainable Energy Engineering Royal Institute of Technology (Sweden) Eindhoven University of Technology (Netherland) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Help: Anyone worked with Wall?
For walls, the atoms in the wall are virtual. Remember that 9-3 LJ integratees over the volume behind the wall so you will have to set your atom density appropriately. Setting wall_density to 20/nm^3 for 9-3 wall leads to 20 carbon atoms per nm^3. That's not going to be totally solid, imo. I am using 10-4 2-D walls to effect here: nwall = 2 wall_type = 10-4 wall_density = 5 5 wall_atomtype = CG331 CG331 wall_r_linpot = -1 wall_ewald_zfac = 3 ewald_geometry=3dc pbc=xy (CG331 is just a methyl group carbon specific to my forcefield). On 2012-04-05 10:08:02PM +0200, Huaichen(Bobby) Zhang wrote: Dear all, I'm trying to simulate with pbc=xy and I need two walls. My settings are as follows: pbc = xy nwall = 2 wall_atomtype = C C wall_type = 9-3 wall_r_linpot = -1 -1 wall_density= 20 20 wall_ewald_zfac = 3 The problem is how to define wall_atomtype in my topology file (top/itp)? A want to have this solid carbon wall with 9-3 potential. Where in my top/itp file can I define such atoms? This is my top file: #include ffG53a6.itp #include spc.itp [ system ] Pure Water with walls [ molecules ] SOL216 When I gmxdump the generated tpr file, I saw no C atoms are defined; and it showed: wall_atomtype[0] = 2 wall_atomtype[1] = 2 which corresponds to the hydrogen atom in my top file. And according to my forcefield, the LJ parameters for H is 0,0. So there is basically no wall. When I tried to simulate with this setting, the water molecules went out of the box (in z direction) and moved far away. And according to g_energy, there is no interaction energy between water and wall. So there indeed is no wall. Can you help me with defining wall atom? If you have already finished any tasks with this wall algorithm, can you kindly attach your topology files to me? Soo many thanks! -- Huaichen(Bobby) ZHANG +31 648478172 MSc Sustainable Energy Engineering Royal Institute of Technology (Sweden) Eindhoven University of Technology (Netherland) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: questions about Principal Component Analysis
Hi Thomas, First of all, proteins in solution don't suddenly stop with Brownian motion at some point. It's just the way things move at the microscopic level. Second, the cosine content has nothing to do with randomness. Really. Nothing. On the contrary. The cosine content indicates unidirectional motion. I repeat, the cosine content has NOTHING to do with RANDOM motion! Really really. High cosine content? U-ni-di-rec-tio-nal motion; movement from one point to another point. The trick is realizing that the best reaction coordinate for random motion from point A to point B is the straight line between A and B. Unfortunately, the RMSIP is no help where it comes to convergence. It only tells you whether the directions in conformational space along which most of the motion takes place is similar between two (parts of) simulations. For convergence, you want to check the projections, and the cosine content thereof. The cosine content should indeed be low. Your case, with relatively high cosine content in every window, suggests that there is still motion, c.q. conformational rearrangement, on route to another state of the system. I fear there is no other way of looking at it that will suggest it has converged already. Actually, 20 ns is very little for equilibration, especially if convergence requires rearrangement of protein-protein interactions. Cheers, Tsjerk On Thu, Apr 5, 2012 at 2:38 PM, Thomas Evangelidis teva...@gmail.com wrote: Dear Tserk and the rest of GROMACS users, Last time I measured the cosine content of different time intervals from the PCs of the whole trajectory. This time I did PCA for each time interval and measured the cc which is the right way I suppose. Maisuradze et al., 2009 claim that a CC value below 0.5 indicates that the protein-water system stops behaving as one with Brownian motions. Yet in none of my time intervals the CC dropped below 0.6. Can this happen for an equilibrated system? It is known that RMSIP can be used to measure the overlap between essential subspaces. My question is can RMSIP help me decide at which point to consider a system equilibrated from a thermodynamical point of view, namely the point at which the system stops doing Brownian motion? Does this point necessarily coincide with that where the RMSD is stabilized? Our protein is co-complexed in another one in the crystal structure, which is believed to hold it in an inactive state. However, we simulate the monomer state, hence we expect a large domain motion to occur in the first few nanosecond. Provided that the first 20ns are considered the time for equilibration, does it make sense to do PCA in this time interval? Thanks in advance for your help. Thomas On 12 March 2012 15:44, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Thomas, Whether or not it makes sense to do PCA on the domain only depends on the question you ask. It may well make sense if you aim at characterizing the intra-domain motions. But be aware that you will view those motions within the context of the rest of the protein. It is quite likely that the internal motions depend on the interaction with the surroundings. Concerning the cosine content, there indeed seems to ba a transition. But that is already evident from your RMSD plot. A lot of stuff is still happening in the second half of the simulation. To see if the last part of your simulation is in a (local) equilibrium, you can calculate the average structure from that part, say the alst 10 or 20 ns, and determine the RMSD against the average. The RMSD should then decrease towards the average and level off or oscillate around it to assure you've reached some sort of equilibrium. On the basis of that you could then decide whether it's worthwhile performing PCA on that part only. Cheers, Tsjerk -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
[gmx-users] epsilon_r vs. gb_epsilon_solvent
Hi, all, I have a question regarding epsilon_r value. Do I have to specify the value in .mdp file? What is the default value if I do not specify it? If I use implicit solvent, there is one parameter: gb_epsilon_solvent, which is recommended to be 80 in the manual. What is the difference between gb_epsilon_solvent and epsilon_r? Thank you! Bo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] on the attachment symbol of some e-mail from our GROMACS users
Dear All, Have you paid attention to this fact, for some e-mails from our Discussion list for GROMACS users, although they do not contain attachment files, the attachment file symbols exist. What is the reason? Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] further discussion on the mdrun -append function
Dear All, Frim mdrun -h, I got the following message: -[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation art number to all file names Thus there is the possibility that the series xvg curves can never starts from 0 ns. Do you agree, Cheers, Acoot-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
The following manuscript may be of interest. http://arxiv.org/abs/math/0610124v2 -Robert McGibbon On Apr 5, 2012, at 11:26 AM, Acoot Brett wrote: But we hope finally no matter which trajectory, a stable protein conformation should be got! As for during the production MD, no significant energy change included. I am looking forward to getting more feedback on this topic. Acoot From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 6 April 2012 4:20 AM Subject: Re: [gmx-users] Different results from identical tpr after MD Well you're really supposed to conduct multiple runs anyway. Remember, a single MD run over a period of time only samples 1 possible trajectory out of the ensemble of possible trajectories... On 2012-04-05 11:38:20PM +0530, bipin singh wrote: Thanks for the reply. * *I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. And also how to believe the statement made by several research papers based on unconverged simulations. On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/**Documentation/Terminology/**Reproducibilityhttp://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst| KAUL 752A Genetics, Div. of Research| 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808| == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] further discussion on the mdrun -append function
On 6/04/2012 1:41 PM, Acoot Brett wrote: Dear All, Frim mdrun -h, I got the following message: /-[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation art number to all file names/ Thus there is the possibility that the series xvg curves can never starts from 0 ns. Do you agree, No. If you have your initial trajectory, then I told you about both the available workflows yesterday. I'm going to stop repeating myself. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] further discussion on the mdrun -append function
Sounds like there is a lanugage barrier? Anyway, some cluster filesystems don't support append (e.g. lustre). So I never use append. I will use tpbconv -extend and -o to a *different* tpr file, then run mdrun -deffnm new_extended which generates everything with the new_extended filename prefix. Then I can trjcat or enerconv to concatenate everything together before running the analysis. Detailed Example: md.mdp is configured for 1ns of simulation time grompp -f md.mdp -n index.ndx -p topol.top -c minimized.gro -o md-1ns.tpr mdrun -deffnm md-1ns -deffnm write out all files starting with this parameter: md-1ns.trr, md-1ns.edr, md-1ns.log, etc. Note: do not use a file extension for -deffnm or else it will put that in the resulting filenames. If you use -deffnm md-1ns.tpr it will write out files called md-1ns.tpr.trr md-1ns.tpr.edr etc. ... tpbconv -s md-1ns.tpr -extend 2000 -o md-1ns-to-3ns.tpr mdrun -deffnm md-1ns-to-3ns -cpi md-1ns.cpt If you do not use -cpi here, your simulation will restart from 0, and will be written to files beginning with md-1ns-to-3ns The -cpi makes it continue from md-1ns.cpt but because of *different filenames*, it will not append, and therefore will write new files starting at 1ns. ... trjcat -f md-1ns.trr md-1ns-to-3ns.trr -o md-to-3ns.xtc eneconv -f md-1ns.edr md-1ns-to-3ns.edr -o md-to-3ns.edr g_energy -f md-to-3ns.edr -o total-energy.xvg will give you a continuous .xvg from 0 to 3ns... If you only analysed md-1ns-to-3ns.trr/.edr then your curves will only start from 1ns onwards. Thus the trick is: use different file prefixes all the time and do not use append. It is the least confusing workflow to use. On 2012-04-06 01:56:18PM +1000, Mark Abraham wrote: On 6/04/2012 1:41 PM, Acoot Brett wrote: Dear All, Frim mdrun -h, I got the following message: /-[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation art number to all file names/ Thus there is the possibility that the series xvg curves can never starts from 0 ns. Do you agree, No. If you have your initial trajectory, then I told you about both the available workflows yesterday. I'm going to stop repeating myself. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] further discussion on the mdrun -append function
Thanks for the detailed explaination. Will you please explain the function of -n index.ndx in grompp -f md.mdp -n index.ndx -p topol.top -c minimized.gro -o md-1ns.tpr with some specific examples? Cheers, Acoot From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 6 April 2012 2:24 PM Subject: Re: [gmx-users] further discussion on the mdrun -append function Sounds like there is a lanugage barrier? Anyway, some cluster filesystems don't support append (e.g. lustre). So I never use append. I will use tpbconv -extend and -o to a *different* tpr file, then run mdrun -deffnm new_extended which generates everything with the new_extended filename prefix. Then I can trjcat or enerconv to concatenate everything together before running the analysis. Detailed Example: md.mdp is configured for 1ns of simulation time grompp -f md.mdp -n index.ndx -p topol.top -c minimized.gro -o md-1ns.tpr mdrun -deffnm md-1ns -deffnm write out all files starting with this parameter: md-1ns.trr, md-1ns.edr, md-1ns.log, etc. Note: do not use a file extension for -deffnm or else it will put that in the resulting filenames. If you use -deffnm md-1ns.tpr it will write out files called md-1ns.tpr.trr md-1ns.tpr.edr etc. ... tpbconv -s md-1ns.tpr -extend 2000 -o md-1ns-to-3ns.tpr mdrun -deffnm md-1ns-to-3ns -cpi md-1ns.cpt If you do not use -cpi here, your simulation will restart from 0, and will be written to files beginning with md-1ns-to-3ns The -cpi makes it continue from md-1ns.cpt but because of *different filenames*, it will not append, and therefore will write new files starting at 1ns. ... trjcat -f md-1ns.trr md-1ns-to-3ns.trr -o md-to-3ns.xtc eneconv -f md-1ns.edr md-1ns-to-3ns.edr -o md-to-3ns.edr g_energy -f md-to-3ns.edr -o total-energy.xvg will give you a continuous .xvg from 0 to 3ns... If you only analysed md-1ns-to-3ns.trr/.edr then your curves will only start from 1ns onwards. Thus the trick is: use different file prefixes all the time and do not use append. It is the least confusing workflow to use. On 2012-04-06 01:56:18PM +1000, Mark Abraham wrote: On 6/04/2012 1:41 PM, Acoot Brett wrote: Dear All, Frim mdrun -h, I got the following message: /-[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation art number to all file names/ Thus there is the possibility that the series xvg curves can never starts from 0 ns. Do you agree, No. If you have your initial trajectory, then I told you about both the available workflows yesterday. I'm going to stop repeating myself. Mark -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] further discussion on the mdrun -append function
I sometimes use non-standard index groups in my .mdp. If you only reference the moleculetypes and/or Protein or Non-protein in your .mdp then you don't need a special index.ndx and the -n option becomes optional. Example: I specialize in membrane proteins. In my .mdp I have: tc-grps = Protein POPC Water_and_ions_Ligands Water_and_ions_Ligands is not a standard index group, I have to construct it using make_ndx, so I need to tell grompp where to find the explicit index file. Example (from Justin's tutorial) tc-grps = Protein Non-Protein Then I do not need to use -n in grompp because these standard groups are implicit. You can get a list of implicit standard groups for your system by running make_ndx on your .gro file. Control-C to exit without writing a file. On 2012-04-05 09:51:58PM -0700, Acoot Brett wrote: Thanks for the detailed explaination. Will you please explain the function of -n index.ndx in grompp -f md.mdp -n index.ndx -p topol.top -c minimized.gro -o md-1ns.tpr with some specific examples? Cheers, Acoot From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 6 April 2012 2:24 PM Subject: Re: [gmx-users] further discussion on the mdrun -append function Sounds like there is a lanugage barrier? Anyway, some cluster filesystems don't support append (e.g. lustre). So I never use append. I will use tpbconv -extend and -o to a *different* tpr file, then run mdrun -deffnm new_extended which generates everything with the new_extended filename prefix. Then I can trjcat or enerconv to concatenate everything together before running the analysis. Detailed Example: md.mdp is configured for 1ns of simulation time grompp -f md.mdp -n index.ndx -p topol.top -c minimized.gro -o md-1ns.tpr mdrun -deffnm md-1ns -deffnm write out all files starting with this parameter: md-1ns.trr, md-1ns.edr, md-1ns.log, etc. Note: do not use a file extension for -deffnm or else it will put that in the resulting filenames. If you use -deffnm md-1ns.tpr it will write out files called md-1ns.tpr.trr md-1ns.tpr.edr etc. ... tpbconv -s md-1ns.tpr -extend 2000 -o md-1ns-to-3ns.tpr mdrun -deffnm md-1ns-to-3ns -cpi md-1ns.cpt If you do not use -cpi here, your simulation will restart from 0, and will be written to files beginning with md-1ns-to-3ns The -cpi makes it continue from md-1ns.cpt but because of *different filenames*, it will not append, and therefore will write new files starting at 1ns. ... trjcat -f md-1ns.trr md-1ns-to-3ns.trr -o md-to-3ns.xtc eneconv -f md-1ns.edr md-1ns-to-3ns.edr -o md-to-3ns.edr g_energy -f md-to-3ns.edr -o total-energy.xvg will give you a continuous .xvg from 0 to 3ns... If you only analysed md-1ns-to-3ns.trr/.edr then your curves will only start from 1ns onwards. Thus the trick is: use different file prefixes all the time and do not use append. It is the least confusing workflow to use. On 2012-04-06 01:56:18PM +1000, Mark Abraham wrote: On 6/04/2012 1:41 PM, Acoot Brett wrote: Dear All, Frim mdrun -h, I got the following message: /-[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation art number to all file names/ Thus there is the possibility that the series xvg curves can never starts from 0 ns. Do you agree, No. If you have your initial trajectory, then I told you about both the available workflows yesterday. I'm going to stop repeating myself. Mark -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL
[gmx-users] further discussion on the mdrun -append function
Dear Acoot: You should be able to answer this one yourself. Moreover, you are doing yourself a disservice by relying on the mailing list to do your work for you because you will eventually need to learn how to find answers to these things on your own. Please remember the following: 1. use a title that matches your question, starting a new thread if you have a new question 2. it may sound harsh, but questions like this one in which you have obviously not even tried to find the answer yourself for more than a couple of minutes tend to annoy the very people that you may want help from later on with other issues. 3. whenever you post, please show how you have tried to solve the problem yourself. You may find that in the process of writing such a question you end up solving the problem yourself. 4. read the manual. Chris. -- original message -- Thanks for the detailed explaination. Will you please explain the function of -n index.ndx in grompp -f md.mdp -n index.ndx -p topol.top -c minimized.gro -o md-1ns.tpr with some specific examples? Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Different results from identical tpr after MD
Dear Acoot: The idea of convergence is this: start a large number of simulations from different conformations, analyze some quantity over time in each simulation, and when the deviation of the average value of that quantity from each separate simulation is less than the time-variance within individual simulations, then you can imply that the simulations have converged -- that is, the results of independent simulations which started as different are now similar. There is a huge body of work that uses a single simulations and evaluates its so-called convergence using some assumptions and special methods. That can also be very useful, but I find it informative to think of convergence in its standard non-scientific dictionary definition as the coming together of previously disparate things. For simulations, my working definition is this: a set of simulations has converged the value of some variable when the simulations were initiated from sufficiently distinct conformational basins and then, over time, the ensemble distribution of the time-averages of the specified variable has a variance that is the same as the mean time-averaged variation within independent simulations. The weak point here is the part about sufficiently distinct conformations, but I am not sure that this can be stated less vaguely in the general case. Chris. -- original message -- Hi Justin, Can you give me your definition of converged MD and unconverged MD? Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] further discussion on the mdrun -append function
On Fri, Apr 6, 2012 at 12:24 AM, Peter C. Lai p...@uab.edu wrote: Sounds like there is a lanugage barrier? Anyway, some cluster filesystems don't support append (e.g. lustre). I often use append on lustre. No problem. Why do you think it doesn't work? So I never use append. I will use tpbconv -extend and -o to a *different* tpr file, then run Even if you don't want to use append you don't need to use tpbconv. You can run mdrun -wth -noappend with the total you want for nsteps. mdrun automatically creates files called e.g. traj.part0002.trr. Roland mdrun -deffnm new_extended which generates everything with the new_extended filename prefix. Then I can trjcat or enerconv to concatenate everything together before running the analysis. Detailed Example: md.mdp is configured for 1ns of simulation time grompp -f md.mdp -n index.ndx -p topol.top -c minimized.gro -o md-1ns.tpr mdrun -deffnm md-1ns -deffnm write out all files starting with this parameter: md-1ns.trr, md-1ns.edr, md-1ns.log, etc. Note: do not use a file extension for -deffnm or else it will put that in the resulting filenames. If you use -deffnm md-1ns.tpr it will write out files called md-1ns.tpr.trr md-1ns.tpr.edr etc. ... tpbconv -s md-1ns.tpr -extend 2000 -o md-1ns-to-3ns.tpr mdrun -deffnm md-1ns-to-3ns -cpi md-1ns.cpt If you do not use -cpi here, your simulation will restart from 0, and will be written to files beginning with md-1ns-to-3ns The -cpi makes it continue from md-1ns.cpt but because of *different filenames*, it will not append, and therefore will write new files starting at 1ns. ... trjcat -f md-1ns.trr md-1ns-to-3ns.trr -o md-to-3ns.xtc eneconv -f md-1ns.edr md-1ns-to-3ns.edr -o md-to-3ns.edr g_energy -f md-to-3ns.edr -o total-energy.xvg will give you a continuous .xvg from 0 to 3ns... If you only analysed md-1ns-to-3ns.trr/.edr then your curves will only start from 1ns onwards. Thus the trick is: use different file prefixes all the time and do not use append. It is the least confusing workflow to use. On 2012-04-06 01:56:18PM +1000, Mark Abraham wrote: On 6/04/2012 1:41 PM, Acoot Brett wrote: Dear All, Frim mdrun -h, I got the following message: /-[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation art number to all file names/ Thus there is the possibility that the series xvg curves can never starts from 0 ns. Do you agree, No. If you have your initial trajectory, then I told you about both the available workflows yesterday. I'm going to stop repeating myself. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: job failed
hello: thank you very much for your kind messages. I first did minimization, the NVP with gradually heating the system from 0-310K, and them NPT production: NVT.mpd--- define = -DPOSRES -DPOSRES_LIG constraints= hbonds integrator= md dt= 0.001 ; ps ! nsteps= 300 ; total 3000.0 ps. nstcomm= 10 nstxout= 5000 ; collect data every 1.0 ps nstxtcout= 5000 nstvout= 5000 nstfout= 0 nstlog= 10 nstenergy= 50 nstlist= 10 ns_type= grid rlist= 1.2 coulombtype= PME rcoulomb= 1.2 vdwtype= cut-off rvdw= 1.4 pme_order= 4 ewald_rtol= 1e-5 optimize_fft= yes DispCorr= no ; Berendsen temperature coupling is on Tcoupl= v-rescale tau_t= 0.10.1 tc-grps= protein non-protein ref_t= 310310 ; Pressure coupling is off Pcoupl= no Pcoupltype= isotropic tau_p= 1.0 compressibility= 4.5e-5 ref_p= 1.0 pbc = xyz annealing = singlesingle annealing_npoints = 22 annealing_time = 0 50000 5000 annealing_temp = 0 3100 310 gen_vel = no constraint_algorithm = Lincs ---NPT md.mdp-- constraints= hbonds integrator= md dt= 0.002 ; ps ! nsteps= 500 ; total 10ns. nstcomm= 10 nstxout= 2 ; collect data every nstenergy = 2 nstxtcout = 2 nstvout= 0 nstfout= 0 nstlist= 10 ns_type= grid rlist= 1.2 coulombtype= PME rcoulomb= 1.2 vdwtype= cut-off rvdw= 1.4 pme_order= 4 ewald_rtol= 1e-5 optimize_fft= yes DispCorr= no ; Berendsen temperature coupling is on Tcoupl= v-rescale tau_t= 0.10.1 tc-grps= proteinnon-protein ref_t= 310310 ; Pressure coupling is on Pcoupl= parrinello-rahman Pcoupltype= isotropic tau_p= 1.0 compressibility= 4.5e-5 ref_p= 1.0 ; Generate velocites is on at 310 K. gen_vel= yes gen_temp= 310.0 gen_seed= -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: job failed
On 6/04/2012 3:36 PM, Albert wrote: hello: thank you very much for your kind messages. I first did minimization, the NVP with gradually heating the system from 0-310K, and them NPT production: NVT.mpd--- define = -DPOSRES -DPOSRES_LIG constraints= hbonds integrator= md dt= 0.001 ; ps ! nsteps= 300 ; total 3000.0 ps. nstcomm= 10 nstxout= 5000 ; collect data every 1.0 ps nstxtcout= 5000 nstvout= 5000 nstfout= 0 nstlog= 10 nstenergy= 50 nstlist= 10 ns_type= grid rlist= 1.2 coulombtype= PME rcoulomb= 1.2 vdwtype= cut-off rvdw= 1.4 pme_order= 4 ewald_rtol= 1e-5 optimize_fft= yes DispCorr= no ; Berendsen temperature coupling is on Tcoupl= v-rescale tau_t= 0.10.1 tc-grps= protein non-protein ref_t= 310310 ; Pressure coupling is off Pcoupl= no Pcoupltype= isotropic tau_p= 1.0 compressibility= 4.5e-5 ref_p= 1.0 pbc = xyz annealing = singlesingle annealing_npoints = 22 annealing_time = 0 50000 5000 annealing_temp = 0 3100 310 gen_vel = no constraint_algorithm = Lincs ---NPT md.mdp-- constraints= hbonds integrator= md dt= 0.002 ; ps ! This time step is normally too long for those constraints. See manual 6.5. nsteps= 500 ; total 10ns. nstcomm= 10 nstxout= 2 ; collect data every nstenergy = 2 nstxtcout = 2 nstvout= 0 nstfout= 0 nstlist= 10 ns_type= grid rlist= 1.2 coulombtype= PME rcoulomb= 1.2 vdwtype= cut-off rvdw= 1.4 pme_order= 4 ewald_rtol= 1e-5 optimize_fft= yes DispCorr= no ; Berendsen temperature coupling is on Tcoupl= v-rescale tau_t= 0.10.1 tc-grps= proteinnon-protein ref_t= 310310 ; Pressure coupling is on Pcoupl= parrinello-rahman Don't use algorithms that are known to be unstable for equilibration while you are doing equilibration. See manual. Pcoupltype= isotropic tau_p= 1.0 compressibility= 4.5e-5 ref_p= 1.0 ; Generate velocites is on at 310 K. gen_vel= yes Why bother doing slow heating if you're just going to re-initialize with random velocities again? Mark gen_temp= 310.0 gen_seed= -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Does electric field be screened by the water ?
Dear gmx users: I would like to apply electric field to my simulation box, and I have added these to my input file: ; Format is number of terms (int) and for all terms an amplitude (real) = ; and a phase angle (real) = E_x = 1.0 0.71e-2 0 What I want to know is whether the size of this electric field in my protein inside the box will be screened by the water around the protein? Best wishes! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] further discussion on the mdrun -append function
On 2012-04-06 01:30:20AM -0400, Roland Schulz wrote: On Fri, Apr 6, 2012 at 12:24 AM, Peter C. Lai p...@uab.edu wrote: Sounds like there is a lanugage barrier? Anyway, some cluster filesystems don't support append (e.g. lustre). I often use append on lustre. No problem. Why do you think it doesn't work? On my cluster, lustre it is unable to lock the .log file for append. So it fails. CBA into looking into fixing it (I'd like to stay in recovering sysadmin therapy for just a while longer :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
Yes you are right, that we need to do multiple MD runs before making any conclusion based on single trajectory. But I have not found any single research paper which discuss about conclusions drawn based on ensemble of trajectories. If you have any such research article then please send me the link. On Thu, Apr 5, 2012 at 23:50, Peter C. Lai p...@uab.edu wrote: Well you're really supposed to conduct multiple runs anyway. Remember, a single MD run over a period of time only samples 1 possible trajectory out of the ensemble of possible trajectories... On 2012-04-05 11:38:20PM +0530, bipin singh wrote: Thanks for the reply. * *I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. And also how to believe the statement made by several research papers based on unconverged simulations. On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/**Documentation/Terminology/**Reproducibility http://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- ==**== 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 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- --- *Thanks and Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] something about tpr file
Hi Lina, The xtc/trr files do not contain information about atom names and residues. But surely you have a matching pdb/gro file somewhere? Cheers, Tsjerk On Apr 5, 2012 12:32 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 05/04/12, lina lina.lastn...@gmail.com wrote: Hi, suppose I lost original .tpr file... No Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
Thanks for your valuable suggestions. I am totally agree with your views. On Fri, Apr 6, 2012 at 00:11, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for the reply. / /I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. No one can do anything for an infinite amount of time ;) Hence replicate simulations and thorough statistical analysis are required to obtain reliable results and prove that what you've done is to be trusted. The other comments in this thread are quite good so I won't recapitulate other points that have been made. And also how to believe the statement made by several research papers based on unconverged simulations. I wouldn't trust any conclusions drawn from demonstrably unconverged simulations. Not everything that's published has been done correctly. Peer review is an imperfect system, so be careful what you read and apply good scientific judgment. -Justin On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu mailto: jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/__**Documentation/Terminology/__** Reproducibilityhttp://www.gromacs.org/__Documentation/Terminology/__Reproducibility http://www.gromacs.org/**Documentation/Terminology/**Reproducibilityhttp://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- /Regards,/ Bipin Singh -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- *Regards,* Bipin Singh --
Re: [gmx-users] Different results from identical tpr after MD
On 6/04/2012 3:53 PM, bipin singh wrote: Yes you are right, that we need to do multiple MD runs before making any conclusion based on single trajectory. But I have not found any single research paper which discuss about conclusions drawn based on ensemble of trajectories. If you have any such research article then please send me the link. Doubtless there are others, but Tsjerk's http://dx.doi.org/10.1021/jp068580v is a good start. Mark On Thu, Apr 5, 2012 at 23:50, Peter C. Lai p...@uab.edu mailto:p...@uab.edu wrote: Well you're really supposed to conduct multiple runs anyway. Remember, a single MD run over a period of time only samples 1 possible trajectory out of the ensemble of possible trajectories... On 2012-04-05 11:38:20PM +0530, bipin singh wrote: Thanks for the reply. * *I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. And also how to believe the statement made by several research papers based on unconverged simulations. On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/**Documentation/Terminology/**Reproducibilityhttp://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- *Regards,* Bipin Singh -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu mailto:p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to
