Re: [gmx-users] about how to create angle.index with specific angles
On 5/2/20 3:12 PM, lazaro monteserin wrote: Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files: I followed the protocol in gromacs website to do dihedral Principal Component Analysis: 1) Created an index file (*dangle.ndx*) with a list of the dihedrals to analyze from my molecule. I wrote this file in a text editor by hand as we discussed before. 2) Then I extracted the sin/cos of the angles in the dangle.ndx from my MD in the file (*dangle.trr*) with the following command: *gmx angle -f md_5ns.xtc -n dangle.ndx -or dangle.trr -type dihedral* (I had 21 angles so it used 14 sin/cos to represent the angles) 3) Then I generated an index file (*covar.ndx*) with a list of numbers from 1 to 14 for trjconv. 4) I runned trjconv to generate the dummy (resized.gro) to use for the covariance analysis: *gmx trjconv -f dangle.trr -s md_5ns.tpr -o resized.gro -n covar.ndx -e 1* 1 was the time in ps for the last frame of the simulation. 5) I runned covar: *gmx covar -f dangle.trr -s resized.gro -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc* 6) Then I got the PMF along one eigenvector and 2D free energy landscape for projections along two eigenvectors: *gmx anaeig -v eigenvec.trr -f dangle.trr -s resized.gro -first 1 -last 2 -2d 2dproj_1_2.xvg* 7) Then I got the projection in 3D of the free energy landscape: *gmx sham -f 2dproj_1_2.xvg -notime -bin bindex-1_2.ndx -lp prob-1_2.xpm -ls gibbs-1_2.xpm -lsh enthalpy-1_2.xpm -g shamlog-1_2 -lss entropy-1_2.xpm* Note: I attached all the files in the dropbox link below https://www.dropbox.com/sh/wez43stnyv4ho31/AABQ3xwgUGf0CuMI_UF7MGsWa?dl=0 I can't access the Dropbox folder because you have given permission for the mailing list email to access it. Please either make it public or upload to a different service. The most relevant files are 2dproj_1_2.xvg and gibbs-1_2.xpm -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] about how to create angle.index with specific angles
Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files: I followed the protocol in gromacs website to do dihedral Principal Component Analysis: 1) Created an index file (*dangle.ndx*) with a list of the dihedrals to analyze from my molecule. I wrote this file in a text editor by hand as we discussed before. 2) Then I extracted the sin/cos of the angles in the dangle.ndx from my MD in the file (*dangle.trr*) with the following command: *gmx angle -f md_5ns.xtc -n dangle.ndx -or dangle.trr -type dihedral* (I had 21 angles so it used 14 sin/cos to represent the angles) 3) Then I generated an index file (*covar.ndx*) with a list of numbers from 1 to 14 for trjconv. 4) I runned trjconv to generate the dummy (resized.gro) to use for the covariance analysis: *gmx trjconv -f dangle.trr -s md_5ns.tpr -o resized.gro -n covar.ndx -e 1* 1 was the time in ps for the last frame of the simulation. 5) I runned covar: *gmx covar -f dangle.trr -s resized.gro -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc* 6) Then I got the PMF along one eigenvector and 2D free energy landscape for projections along two eigenvectors: *gmx anaeig -v eigenvec.trr -f dangle.trr -s resized.gro -first 1 -last 2 -2d 2dproj_1_2.xvg* 7) Then I got the projection in 3D of the free energy landscape: *gmx sham -f 2dproj_1_2.xvg -notime -bin bindex-1_2.ndx -lp prob-1_2.xpm -ls gibbs-1_2.xpm -lsh enthalpy-1_2.xpm -g shamlog-1_2 -lss entropy-1_2.xpm* Note: I attached all the files in the dropbox link below https://www.dropbox.com/sh/wez43stnyv4ho31/AABQ3xwgUGf0CuMI_UF7MGsWa?dl=0 I would appreciate any feedback Thank you in advance Dr. Lemkul Kindly, Lazaro On Sat, May 2, 2020 at 8:47 AM Justin Lemkul wrote: > > > On 4/30/20 2:07 PM, lazaro monteserin wrote: > > Dear Dr. Lemkul I did it. It works. Thank you very much for the advise. > > > > Now I am having issues opening the (.xpm) files generated that contain > for > > example the gibbs energy landscape on the two first eigenvectors of the > > dPCA. > > > > If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o > gibbs-1_2.eps" > > it write this error: "Input error or input inconsistency: > > Invalid XPixMap" > > > > Do you know if I am missing something here? Do I have to install > something > > in my OS to be able to see .xpm images? > > The error is coming from xpm2ps which means there's something wrong with > the .xpm file itself but without seeing how you generated it (exact > command and description of how you prepared the input data file) and > perhaps the .xpm file itself (uploaded somewhere), it's impossible to > comment further. > > -Justin > > > Thanks in advance, > > > > Lazaro > > > > On Wed, Apr 29, 2020 at 8:57 PM Justin Lemkul wrote: > > > >> > >> On 4/29/20 7:11 PM, lazaro monteserin wrote: > >>> Dear Dr. Lemkul it could be possible use that angle.index with the > >> selected > >>> dihedrals written by hand as index file for gmx angle for dihedral > >>> Principal Component Analysis? > >> You can create index groups however you like for whatever analysis you > >> want to perform. > >> > >> -Justin > >> > >>>Kindly, > >>> Lazaro > >>> > >>> On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: > >>> > On 4/29/20 5:01 PM, lazaro monteserin wrote: > > Dear gromacs users, > > > > Is there any way to tell gmx mk_angndx to create the index file with > > dihedral angles from a (.tpr) for specific atom numbers (atom level, > >> e.g > 1, > > 2, 3) from my molecule? > mk_angndx is designed for distributions of similar angles (e.g. > evaluating force field sampling). If you want to compute specific > angles, use make_ndx or simply write the index groups by hand. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >>
Re: [gmx-users] about how to create angle.index with specific angles
On 4/30/20 2:07 PM, lazaro monteserin wrote: Dear Dr. Lemkul I did it. It works. Thank you very much for the advise. Now I am having issues opening the (.xpm) files generated that contain for example the gibbs energy landscape on the two first eigenvectors of the dPCA. If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o gibbs-1_2.eps" it write this error: "Input error or input inconsistency: Invalid XPixMap" Do you know if I am missing something here? Do I have to install something in my OS to be able to see .xpm images? The error is coming from xpm2ps which means there's something wrong with the .xpm file itself but without seeing how you generated it (exact command and description of how you prepared the input data file) and perhaps the .xpm file itself (uploaded somewhere), it's impossible to comment further. -Justin Thanks in advance, Lazaro On Wed, Apr 29, 2020 at 8:57 PM Justin Lemkul wrote: On 4/29/20 7:11 PM, lazaro monteserin wrote: Dear Dr. Lemkul it could be possible use that angle.index with the selected dihedrals written by hand as index file for gmx angle for dihedral Principal Component Analysis? You can create index groups however you like for whatever analysis you want to perform. -Justin Kindly, Lazaro On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: On 4/29/20 5:01 PM, lazaro monteserin wrote: Dear gromacs users, Is there any way to tell gmx mk_angndx to create the index file with dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g 1, 2, 3) from my molecule? mk_angndx is designed for distributions of similar angles (e.g. evaluating force field sampling). If you want to compute specific angles, use make_ndx or simply write the index groups by hand. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] about how to create angle.index with specific angles
Dear Dr. Lemkul I did it. It works. Thank you very much for the advise. Now I am having issues opening the (.xpm) files generated that contain for example the gibbs energy landscape on the two first eigenvectors of the dPCA. If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o gibbs-1_2.eps" it write this error: "Input error or input inconsistency: Invalid XPixMap" Do you know if I am missing something here? Do I have to install something in my OS to be able to see .xpm images? Thanks in advance, Lazaro On Wed, Apr 29, 2020 at 8:57 PM Justin Lemkul wrote: > > > On 4/29/20 7:11 PM, lazaro monteserin wrote: > > Dear Dr. Lemkul it could be possible use that angle.index with the > selected > > dihedrals written by hand as index file for gmx angle for dihedral > > Principal Component Analysis? > > You can create index groups however you like for whatever analysis you > want to perform. > > -Justin > > > Kindly, > > Lazaro > > > > On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: > > > >> > >> On 4/29/20 5:01 PM, lazaro monteserin wrote: > >>> Dear gromacs users, > >>> > >>> Is there any way to tell gmx mk_angndx to create the index file with > >>> dihedral angles from a (.tpr) for specific atom numbers (atom level, > e.g > >> 1, > >>> 2, 3) from my molecule? > >> mk_angndx is designed for distributions of similar angles (e.g. > >> evaluating force field sampling). If you want to compute specific > >> angles, use make_ndx or simply write the index groups by hand. > >> > >> -Justin > >> > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> == > >> > >> -- > >> 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. > >> > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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.
Re: [gmx-users] about how to create angle.index with specific angles
On 4/29/20 7:11 PM, lazaro monteserin wrote: Dear Dr. Lemkul it could be possible use that angle.index with the selected dihedrals written by hand as index file for gmx angle for dihedral Principal Component Analysis? You can create index groups however you like for whatever analysis you want to perform. -Justin Kindly, Lazaro On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: On 4/29/20 5:01 PM, lazaro monteserin wrote: Dear gromacs users, Is there any way to tell gmx mk_angndx to create the index file with dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g 1, 2, 3) from my molecule? mk_angndx is designed for distributions of similar angles (e.g. evaluating force field sampling). If you want to compute specific angles, use make_ndx or simply write the index groups by hand. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] about how to create angle.index with specific angles
Dear Dr. Lemkul it could be possible use that angle.index with the selected dihedrals written by hand as index file for gmx angle for dihedral Principal Component Analysis? Kindly, Lazaro On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: > > > On 4/29/20 5:01 PM, lazaro monteserin wrote: > > Dear gromacs users, > > > > Is there any way to tell gmx mk_angndx to create the index file with > > dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g > 1, > > 2, 3) from my molecule? > > mk_angndx is designed for distributions of similar angles (e.g. > evaluating force field sampling). If you want to compute specific > angles, use make_ndx or simply write the index groups by hand. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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.
Re: [gmx-users] about how to create angle.index with specific angles
On 4/29/20 5:01 PM, lazaro monteserin wrote: Dear gromacs users, Is there any way to tell gmx mk_angndx to create the index file with dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g 1, 2, 3) from my molecule? mk_angndx is designed for distributions of similar angles (e.g. evaluating force field sampling). If you want to compute specific angles, use make_ndx or simply write the index groups by hand. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
