[gmx-users] Analysis of the RMSF of a ligand bound protein structure
Dear all, I am performing MD simulation on a ligand bound dimeric protein structure in Gromacs 5.04. For the calculation of RMSF of this dimeric protein I have used the following command gmx rmsf -s md_0_1.tpr -f md_0_1_traj.xtc -res -o rmsf_res.xvgand selected 'C alpha' group. But the resulting plot shows graph corresponding to the ligand also. Is there any way to plot only the RMSF values of the dimeric protein without the bound ligand in gromacs? Will it be okay if I take the RMSF values of only the protein residues from rmsf_res.xvg and plot in any other graphical interface? Thanks and Regards,Paulami -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with the MDS extended trajectory in Gromacs 5.04
Thank you Justin for the suggestion. I was able to obtain a full trajectory using trjcat. However I would also like to mention that the exact commands I have shown in my previous mails produced the files with 'the names'. Can you please tell me if I want to have the full trajectory from the extension what changes should be made in the command line?Should I use gmx convert-tpr -s md_0_1.tpr -extend 7 -o final_monomer.tpr gmx mdrun -s final_monomer.tpr -v -deffnm md_0_1 -cpi md_0_1.cpt -append Thanks and Regards,Paulami On Friday, 10 July 2015 2:13 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 3:09 PM, PAULAMI CHATTERJEE wrote: I have used the following commands for the initial mdrun gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr gmx mdrun -deffnm md_0_1 Can you please suggest now what went wrong? So you have a trajectory named md_0_1.xtc - that should contain the first part of the run. Then somehow you say you've got traj_comp.xtc (though none of the commands you've shown would produce a file with that name), so if that's the case: gmx trjcat -f md_0_1.xtc traj_comp.xtc -o full.xtc That will have the whole thing. -Justin Paulami On Thursday, 9 July 2015 5:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 4:15 AM, PAULAMI CHATTERJEE wrote: Dear All, I have a 30 ns trajectory which I would like to extend up to 100 ns. For that I gave the following commands gmx convert-tpr -s md_0_1.tpr -extend 7 -o final_monomer.tpr gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append After completion of the extension two new trajectory files were generated- 'traj.trr' and 'traj_comp.xtc' . When I tried to check the length of the trajectory with gmxcheck -f traj_comp.xtc the output is Checking file traj_comp.xtc Reading frame 0 time 3.000 # Atoms 16867 Precision 0.001 (nm) Last frame 35000 time 10.000 This trajectory file contains coordinate values from 30ns to 100ns. I tried to calculate the rmsd with this file (both the trr and xtc file) but the graph abruptly starts from 30ns (instead of 0) and continues upto 100ns.For the calculation I need the total trajectory from time 0 to time 100ns.I think I am missing something. Indeed, you're missing your first trajectory. You specified -append but if you're changing file names then that won't happen and you need to use trjcat afterwards. But since you haven't told us what the initial mdrun command was, there's no way to say what's going on for sure. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Dear All, I have a 30 ns trajectory which I would like to extend up to 100 ns. For that I gave the following commands gmx convert-tpr -s md_0_1.tpr -extend 7 -o final_monomer.tpr gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append After completion of the extension two new trajectory files were generated- 'traj.trr' and 'traj_comp.xtc' . When I tried to check the length of the trajectory with gmxcheck -f traj_comp.xtc the output is Checking file traj_comp.xtc Reading frame 0 time 3.000 # Atoms 16867 Precision 0.001 (nm) Last frame 35000 time 10.000 This trajectory file contains coordinate values from 30ns to 100ns. I tried to calculate the rmsd with this file (both the trr and xtc file) but the graph abruptly starts from 30ns (instead of 0) and continues upto 100ns.For the calculation I need the total trajectory from time 0 to time 100ns.I think I am missing something. Can anyone please suggest anything here? Which one is the total trajectory file then? Thanks in advancePaulami -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem with the MDS extended trajectory in Gromacs 5.04
Dear All, I have a 30 ns trajectory which I would like to extend up to 100 ns. For that I gave the following commands gmx convert-tpr -s md_0_1.tpr -extend 7 -o final_monomer.tpr gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append After completion of the extension two new trajectory files were generated- 'traj.trr' and 'traj_comp.xtc' . When I tried to check the length of the trajectory with gmxcheck -f traj_comp.xtc the output is Checking file traj_comp.xtc Reading frame 0 time 3.000 # Atoms 16867 Precision 0.001 (nm) Last frame 35000 time 10.000 This trajectory file contains coordinate values from 30ns to 100ns. I tried to calculate the rmsd with this file (both the trr and xtc file) but the graph abruptly starts from 30ns (instead of 0) and continues upto 100ns.For the calculation I need the total trajectory from time 0 to time 100ns.I think I am missing something. Can anyone please suggest anything here? Which one is the total trajectory file then? Thanks in advancePaulami -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with the MDS extended trajectory in Gromacs 5.04
I have used the following commands for the initial mdrun gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tprgmx mdrun -deffnm md_0_1 Can you please suggest now what went wrong? Paulami On Thursday, 9 July 2015 5:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 4:15 AM, PAULAMI CHATTERJEE wrote: Dear All, I have a 30 ns trajectory which I would like to extend up to 100 ns. For that I gave the following commands gmx convert-tpr -s md_0_1.tpr -extend 7 -o final_monomer.tpr gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append After completion of the extension two new trajectory files were generated- 'traj.trr' and 'traj_comp.xtc' . When I tried to check the length of the trajectory with gmxcheck -f traj_comp.xtc the output is Checking file traj_comp.xtc Reading frame 0 time 3.000 # Atoms 16867 Precision 0.001 (nm) Last frame 35000 time 10.000 This trajectory file contains coordinate values from 30ns to 100ns. I tried to calculate the rmsd with this file (both the trr and xtc file) but the graph abruptly starts from 30ns (instead of 0) and continues upto 100ns.For the calculation I need the total trajectory from time 0 to time 100ns.I think I am missing something. Indeed, you're missing your first trajectory. You specified -append but if you're changing file names then that won't happen and you need to use trjcat afterwards. But since you haven't told us what the initial mdrun command was, there's no way to say what's going on for sure. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with the MDS extended trajectory in GROMACS 5.0.4
Soumadwip Thank you very much for your response. So you are suggesting that 'gmx mdrun -s final_monomer.tpr -v -deffnm md_0_1 -cpi md_0_1.cpt -append' instead of 'gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append' (which I have used for the extended simulation) can solve my problem. I will surely try this one. Thanks and RegardsPaulami On Thursday, 9 July 2015 6:54 PM, soumadwip ghosh soumadwipgh...@gmail.com wrote: Hi, Say your initial mdrun command for 30 ns were as follow grompp_mpi -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o md_0_1.tpr and mdrun_mpi -deffnm md_0_1 Then you should get the files such as md_0_1.xtc, md_0_1.log, md_0_1.edr, md_0_1.cpt, md_0_1.trr and so on Then you obtain a new tpr file say new_100ns.tpr using tpbconv or gmx convert with appropriate flags. . Now, if you want to extend your simulation by a certain amount of time and want all your previous files appended the exact command should be something like mdrun_mpi -s new_100ns.tpr -v -deffnm md_0_1 -cpi md_0_1.cpt -append I did it once and coordinates were saved from 0ns all the way to 100ns and the same md_0_1.xtc, md_0_1.edr etc files were apeended without any difficulty. I am not quite sure but there's no harm in trying. Cheers, Soumadwip -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Installation problem with Gromacs 5.0.2
Dear all I am trying to install Gromacs 5.0.2 in a GPU machine but coming up with a CMake error. Part of my error looked like this . Downloading: http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz -- [download 0% complete] CMake Error at tests/CMakeLists.txt:58 (message): error: downloading 'http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz' failed status_code: 1 Location: https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz Vary: Accept-Encoding Content-Length: 325 Content-Type: text/html; charset=iso-8859-1 X-Cache: MISS from cb-proxy.boseinst.ernet.in X-Cache-Lookup: MISS from cb-proxy.boseinst.ernet.in:3128 Via: 1.0 cb-proxy.boseinst.ernet.in:3128 (squid/2.6.STABLE6) Connection: close Closing connection #0 Issue another request to this URL: 'https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz' libcurl was built with SSL disabled, https: not supported! unsupported protocol .. Can anyone please suggest anything to troubleshoot this? Thanks in advance. Paulami -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Installation problem with Gromacs 5.0.2
Hello Bikash, Thank you for your prompt response. As you suggested I tried to manually download the 'regressiontests-5.0.2.tar.gz' file from this link https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz But I found This shared file or folder link has been removed.I am sure I am missing something. Can you please suggest any alternative way to download the file? Paulami On Wednesday, 10 December 2014 2:08 PM, Bikash Ranjan Sahoo bikash.bioinformat...@gmail.com wrote: Hi, Don't use the -DREGRESSIONTEST_DOWNLOAD=ON flag in cmake. if u need it then download, configure, install and manually set the path in Cmake configuration. Good luck On Wed, Dec 10, 2014 at 5:10 PM, PAULAMI CHATTERJEE chatterjee_paul...@yahoo.co.in wrote: Dear all I am trying to install Gromacs 5.0.2 in a GPU machine but coming up with a CMake error. Part of my error looked like this . Downloading: http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz -- [download 0% complete] CMake Error at tests/CMakeLists.txt:58 (message): error: downloading 'http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz' failed status_code: 1 Location: https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz Vary: Accept-Encoding Content-Length: 325 Content-Type: text/html; charset=iso-8859-1 X-Cache: MISS from cb-proxy.boseinst.ernet.in X-Cache-Lookup: MISS from cb-proxy.boseinst.ernet.in:3128 Via: 1.0 cb-proxy.boseinst.ernet.in:3128 (squid/2.6.STABLE6) Connection: close Closing connection #0 Issue another request to this URL: 'https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz' libcurl was built with SSL disabled, https: not supported! unsupported protocol .. Can anyone please suggest anything to troubleshoot this? Thanks in advance. Paulami -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
