Re: [gmx-users] trjconv
Hi Ram, -fit rot+trans performs an ordinary least-squares fit using the reference structure provided with -s, removing rotational and translational degrees of freedom. Cheers, Tsjerk On Tue, Sep 9, 2008 at 9:47 PM, rams rams [EMAIL PROTECTED] wrote: Dear Users, I have a question about the option -fit in trjconv. The default option with -fit is none. If I use the option as rot+trans, does it mean that the rotational and translational motions are removed from the trajectory ? If not, is there any option in gromacs, to create a translational and rotational free trajectory from the original trajecotry file ? I also want to make sure the usage of the command: trjconv -f original trr -s .tpr -o rot_trans_free.trr -fit rot+trans Thanks in advance. Ram. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: D2O
Hi I would like to simulate the solutes are embeded in D2O solution. Could someone explain the difference of simulating D2O solution and H2O solution? It differs with FF for D instead of H. It's quite primitive for make such exchange in topology. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.
Dear justin, I have made the itp file on a basis of chapter 5 of gromacs. Every things seems fine. my itp file for opls is as follow: ; [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_185 1 DRG HAD 10.02734 1.0080 2 opls_182 1 DRG CAL 10.10638 12.0110 3 opls_185 1 DRG HAE 10.02734 1.0080 4 opls_180 1 DRG OAI 1 -0.36111 15.9994 5 opls_182 1 DRG CAK 10.10638 12.0110 6 opls_185 1 DRG HAB 20.02734 1.0080 7 opls_185 1 DRG HAG 20.02734 1.0080 8 opls_711 1 DRG CAM 20.00235 12.0110 9 opls_777 1 DRG HAF 30.00857 1.0080 10 opls_777 1 DRG HAH 30.00857 1.0080 11 opls_711 1 DRG CAJ 30.00235 12.0110 12 opls_777 1 DRG HAC 30.00857 1.0080 13 opls_777 1 DRG HAA 30.00857 1.0080 [ bonds ] ; ai aj fuc0, c1, ... 1 2 10.109284512.00.109284512.0 ; HAD CAL 2 3 10.109284512.00.109284512.0 ; CAL HAE 2 4 10.141267776.00.141267776.0 ; CAL HAI 2 11 10.152217568.00.152217568.0 ; CAL CAJ 4 5 10.141267776.00.141267776.0 ; OAI CAK 5 6 10.109284512.00.109284512.0 ; CAK HAB 5 7 10.109284512.00.109284512.0 ; CAK HAG 5 8 10.151234304.00.151234304.0 ; CAK CAM 8 9 10.108284512.00.108284512.0 ; CAM HAF 8 10 10.108284512.00.108284512.0 ; CAM HAH 8 11 10.150217568.00.150217568.0 ; CAM CAJ 11 12 10.108284512.00.108284512.0 ; CAJ HAC 11 13 10.108284512.00.108284512.0 ; CAJ HAA [ pairs ] ; ai aj fuc0, c1, ... 1 5 1 ; HAD CAK 1 8 1 ; HAD CAM 1 12 1 ; HAD HAC 1 13 1 ; HAD HAA 2 6 1 ; CAL HAB 2 7 1 ; CAL HAG 2 9 1 ; CAL HAF 2 10 1 ; CAL HAH 3 5 1 ; HAE CAK 3 8 1 ; HAE CAM 3 12 1 ; HAE HAC 3 13 1 ; HAE HAA 4 9 1 ; OAI HAF 4 10 1 ; OAI HAH 4 12 1 ; OAI HAC 4 13 1 ; OAI HAA 5 12 1 ; CAK HAC 5 13 1 ; CAK HAA 6 9 1 ; HAB HAF 6 10 1 ; HAB HAH 6 9 1 ; HAB HAF 6 10 1 ; HAB HAH 6 11 1 ; HAB CAJ 7 9 1 ; HAG HAF 7 10 1 ; HAG HAH 7 11 1 ; HAG CAJ 9 12 1 ; HAF HAC 9 13 1 ; HAF HAA 10 12 1 ; HAH HAC 10 13 1 ; HAH HAA [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 1107.8 276.1107.8 276.1 ; HAD CAL HAE 1 2 4 1109.5 292.8109.5 292.8 ; HAD CAL OAI 1 2 11 1110.7 313.8109.5 397.5 ; HAD CAL CAJ 3 2 4 1109.5 292.8109.5 292.8 ; HAE CAL OAI 3 2 11 1110.7 313.8110.7 313.8 ; HAE CAL CAJ 4 2 11 1109.5 292.8109.5 292.8 ; OAI CAL CAJ 2 4 5 1109.5 502.0109.5 502.0 ; CAL OAI CAK 4 5 6 1109.5 292.8109.5 292.8 ; OAI CAK HAB 4 5 7 1109.5 292.8109.5 292.8 ; OAI CAK HAG 4 5 8 1109.5 292.8109.5 292.8 ; OAI CAK CAM 6 5 7 1107.8 276.1107.8 276.1 ; HAB CAK HAG 6 5 8 1110.7 313.8110.7 313.8
Re: [gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.
Morteza Khabiri wrote: Dear justin, I have made the itp file on a basis of chapter 5 of gromacs. Every things seems fine. my itp file for opls is as follow: Seems fine is your own evaluation, but if grompp is giving you errors about an incorrect topology, then indeed it is not. Did grompp tell you a line number that caused the error? My guess would be yes. If you want free help for solving this, you have to make it easy. What was the line? What is on that line? -Justin ; [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_185 1 DRG HAD 10.02734 1.0080 2 opls_182 1 DRG CAL 10.10638 12.0110 3 opls_185 1 DRG HAE 10.02734 1.0080 4 opls_180 1 DRG OAI 1 -0.36111 15.9994 5 opls_182 1 DRG CAK 10.10638 12.0110 6 opls_185 1 DRG HAB 20.02734 1.0080 7 opls_185 1 DRG HAG 20.02734 1.0080 8 opls_711 1 DRG CAM 20.00235 12.0110 9 opls_777 1 DRG HAF 30.00857 1.0080 10 opls_777 1 DRG HAH 30.00857 1.0080 11 opls_711 1 DRG CAJ 30.00235 12.0110 12 opls_777 1 DRG HAC 30.00857 1.0080 13 opls_777 1 DRG HAA 30.00857 1.0080 [ bonds ] ; ai aj fuc0, c1, ... 1 2 10.109284512.00.109284512.0 ; HAD CAL 2 3 10.109284512.00.109284512.0 ; CAL HAE 2 4 10.141267776.00.141267776.0 ; CAL HAI 2 11 10.152217568.00.152217568.0 ; CAL CAJ 4 5 10.141267776.00.141267776.0 ; OAI CAK 5 6 10.109284512.00.109284512.0 ; CAK HAB 5 7 10.109284512.00.109284512.0 ; CAK HAG 5 8 10.151234304.00.151234304.0 ; CAK CAM 8 9 10.108284512.00.108284512.0 ; CAM HAF 8 10 10.108284512.00.108284512.0 ; CAM HAH 8 11 10.150217568.00.150217568.0 ; CAM CAJ 11 12 10.108284512.00.108284512.0 ; CAJ HAC 11 13 10.108284512.00.108284512.0 ; CAJ HAA [ pairs ] ; ai aj fuc0, c1, ... 1 5 1 ; HAD CAK 1 8 1 ; HAD CAM 1 12 1 ; HAD HAC 1 13 1 ; HAD HAA 2 6 1 ; CAL HAB 2 7 1 ; CAL HAG 2 9 1 ; CAL HAF 2 10 1 ; CAL HAH 3 5 1 ; HAE CAK 3 8 1 ; HAE CAM 3 12 1 ; HAE HAC 3 13 1 ; HAE HAA 4 9 1 ; OAI HAF 4 10 1 ; OAI HAH 4 12 1 ; OAI HAC 4 13 1 ; OAI HAA 5 12 1 ; CAK HAC 5 13 1 ; CAK HAA 6 9 1 ; HAB HAF 6 10 1 ; HAB HAH 6 9 1 ; HAB HAF 6 10 1 ; HAB HAH 6 11 1 ; HAB CAJ 7 9 1 ; HAG HAF 7 10 1 ; HAG HAH 7 11 1 ; HAG CAJ 9 12 1 ; HAF HAC 9 13 1 ; HAF HAA 10 12 1 ; HAH HAC 10 13 1 ; HAH HAA [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 1107.8 276.1107.8 276.1 ; HAD CAL HAE 1 2 4 1109.5 292.8109.5 292.8 ; HAD CAL OAI 1 2 11 1110.7 313.8109.5 397.5 ; HAD CAL CAJ 3 2 4 1109.5 292.8109.5 292.8 ; HAE CAL OAI 3 2 11 1110.7 313.8110.7 313.8 ; HAE CAL CAJ 4 2 11 1109.5 292.8109.5 292.8 ; OAI CAL CAJ 2 4 5 1109.5 502.0109.5 502.0 ; CAL OAI CAK 4 5
[gmx-users] regarding xpm2ps?
I have converted .xpm (which generated from *g_hbond) to .eps by using xpm2ps command, after finished the running of this command showed There are 1 matrices in .xpm Matrix 0 is 37501 x 1 Auto tick spacing failed for X-axis, guessing 2 Auto tick spacing for X-axis: major 2, minor 0.4 Auto tick spacing failed for Y-axis, guessing 0 Auto tick spacing for Y-axis: major 0, minor nan Set the x-size of the box to 0.011 Set the y-size of the box to 0.011 1.is it mean that set the box x and y sizes to 0.111 by using -bx and -by options. 2.How can I execute this .eps for getting map? Could please suggest me Thanks in advance.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] regarding xpm2ps?
minnale wrote: I have converted .xpm (which generated from *g_hbond) to .eps by using xpm2ps command, after finished the running of this command showed There are 1 matrices in .xpm Matrix 0 is 37501 x 1 Auto tick spacing failed for X-axis, guessing 2 Auto tick spacing for X-axis: major 2, minor 0.4 Auto tick spacing failed for Y-axis, guessing 0 Auto tick spacing for Y-axis: major 0, minor nan Set the x-size of the box to 0.011 Set the y-size of the box to 0.011 1.is it mean that set the box x and y sizes to 0.111 by using -bx and -by options. You've got problems somewhere. Did you specify an .m2p file with -di? What was your command line? 2.How can I execute this .eps for getting map? An .eps file can be opened by a number of programs - pretty much anything that can read a PDF (at least, on Linux and Mac), or Gimp. -Justin Could please suggest me Thanks in advance. 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.
Dear Justin, thanks for your help. The last lines of my grompp are: checking input for internal consistency... calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Cleaning up temporary file grompp3eQvh0 --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1180 Fatal error: Incorrect number of parameters - found 4, expected 6 or 12. Thank you very much in advance for your free help. Your sincerely, Morteza ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.
* Justin A. Lemkul [EMAIL PROTECTED] [2008-09-10 05:46:07 -0400]: Morteza Khabiri wrote: Dear justin, I have made the itp file on a basis of chapter 5 of gromacs. Every things seems fine. my itp file for opls is as follow: Seems fine is your own evaluation, but if grompp is giving you errors about an incorrect topology, then indeed it is not. Did grompp tell you a line number that caused the error? My guess would be yes. If you want free help for solving this, you have to make it easy. What was the line? What is on that line? -Justin ; [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_185 1 DRG HAD 10.02734 1.0080 2 opls_182 1 DRG CAL 10.10638 12.0110 3 opls_185 1 DRG HAE 10.02734 1.0080 4 opls_180 1 DRG OAI 1 -0.36111 15.9994 5 opls_182 1 DRG CAK 10.10638 12.0110 6 opls_185 1 DRG HAB 20.02734 1.0080 7 opls_185 1 DRG HAG 20.02734 1.0080 8 opls_711 1 DRG CAM 20.00235 12.0110 9 opls_777 1 DRG HAF 30.00857 1.0080 10 opls_777 1 DRG HAH 30.00857 1.0080 11 opls_711 1 DRG CAJ 30.00235 12.0110 12 opls_777 1 DRG HAC 30.00857 1.0080 13 opls_777 1 DRG HAA 30.00857 1.0080 [ bonds ] ; ai aj fuc0, c1, ... 1 2 10.109284512.00.109284512.0 ; HAD CAL 2 3 10.109284512.00.109284512.0 ; CAL HAE 2 4 10.141267776.00.141267776.0 ; CAL HAI 2 11 10.152217568.00.152217568.0 ; CAL CAJ 4 5 10.141267776.00.141267776.0 ; OAI CAK 5 6 10.109284512.00.109284512.0 ; CAK HAB 5 7 10.109284512.00.109284512.0 ; CAK HAG 5 8 10.151234304.00.151234304.0 ; CAK CAM 8 9 10.108284512.00.108284512.0 ; CAM HAF 8 10 10.108284512.00.108284512.0 ; CAM HAH 8 11 10.150217568.00.150217568.0 ; CAM CAJ 11 12 10.108284512.00.108284512.0 ; CAJ HAC 11 13 10.108284512.00.108284512.0 ; CAJ HAA [ pairs ] ; ai aj fuc0, c1, ... 1 5 1 ; HAD CAK 1 8 1 ; HAD CAM 1 12 1 ; HAD HAC 1 13 1 ; HAD HAA 2 6 1 ; CAL HAB 2 7 1 ; CAL HAG 2 9 1 ; CAL HAF 2 10 1 ; CAL HAH 3 5 1 ; HAE CAK 3 8 1 ; HAE CAM 3 12 1 ; HAE HAC 3 13 1 ; HAE HAA 4 9 1 ; OAI HAF 4 10 1 ; OAI HAH 4 12 1 ; OAI HAC 4 13 1 ; OAI HAA 5 12 1 ; CAK HAC 5 13 1 ; CAK HAA 6 9 1 ; HAB HAF 6 10 1 ; HAB HAH 6 9 1 ; HAB HAF 6 10 1 ; HAB HAH 6 11 1 ; HAB CAJ 7 9 1 ; HAG HAF 7 10 1 ; HAG HAH 7 11 1 ; HAG CAJ 9 12 1 ; HAF HAC 9 13 1 ; HAF HAA 10 12 1 ; HAH HAC 10 13 1 ; HAH HAA [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 1107.8 276.1107.8 276.1 ; HAD CAL HAE 1 2 4 1109.5 292.8109.5 292.8 ; HAD CAL OAI Hello; the bond angles seem to be respondsible. You use function type 1. That means you just have a harmonic potential. To this end gromacs wants an equilibrium angle and a spring constant. You provide 4 numbers. I dont the funtions in mind. However for function 1, it shoudl probably look like : 1 2 11 1
Re: [gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.
Morteza Khabiri wrote: Dear Justin, thanks for your help. The last lines of my grompp are: checking input for internal consistency... calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Cleaning up temporary file grompp3eQvh0 --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1180 Fatal error: Incorrect number of parameters - found 4, expected 6 or 12. The error is probably related to missing dihedral parameters. Was your initial topology constructed by PRODRG? It looks like it. If so, the dihedral parameters will be for use with a GROMOS-type force field, so simply changing type to 3 will not suffice. Have a look in ffoplsaabon.itp for the correct way to define an OPLS-AA dihedral with all the necessary parameters. -Justin Thank you very much in advance for your free help. Your sincerely, Morteza ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] regarding xpm2ps?
I have issued the following command xpm2s -f .xpm -o .eps If I mention option -di with m2p it showed Fatal error: Library file H_hbond.m2p not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Could tell me any suggestion Thanks alot On Wed, 10 Sep 2008 Justin A.Lemkul wrote : minnale wrote: I have converted .xpm (which generated from *g_hbond) to .eps by using xpm2ps command, after finished the running of this command showed There are 1 matrices in .xpm Matrix 0 is 37501 x 1 Auto tick spacing failed for X-axis, guessing 2 Auto tick spacing for X-axis: major 2, minor 0.4 Auto tick spacing failed for Y-axis, guessing 0 Auto tick spacing for Y-axis: major 0, minor nan Set the x-size of the box to 0.011 Set the y-size of the box to 0.011 1.is it mean that set the box x and y sizes to 0.111 by using -bx and -by options. You've got problems somewhere. Did you specify an .m2p file with -di? What was your command line? 2.How can I execute this .eps for getting map? An .eps file can be opened by a number of programs - pretty much anything that can read a PDF (at least, on Linux and Mac), or Gimp. -Justin Could please suggest me Thanks in advance. 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] regarding xpm2ps?
minnale wrote: I have issued the following command xpm2s -f .xpm -o .eps If I mention option -di with m2p it showed Fatal error: Library file H_hbond.m2p not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Could tell me any suggestion Thanks alot If you specify -di you need to give xpm2ps an actual .m2p file, an example of which is online: http://www.gromacs.org/documentation/reference/online/m2p.html -Justin On Wed, 10 Sep 2008 Justin A.Lemkul wrote : minnale wrote: I have converted .xpm (which generated from *g_hbond) to .eps by using xpm2ps command, after finished the running of this command showed There are 1 matrices in .xpm Matrix 0 is 37501 x 1 Auto tick spacing failed for X-axis, guessing 2 Auto tick spacing for X-axis: major 2, minor 0.4 Auto tick spacing failed for Y-axis, guessing 0 Auto tick spacing for Y-axis: major 0, minor nan Set the x-size of the box to 0.011 Set the y-size of the box to 0.011 1.is it mean that set the box x and y sizes to 0.111 by using -bx and -by options. You've got problems somewhere. Did you specify an .m2p file with -di? What was your command line? 2.How can I execute this .eps for getting map? An .eps file can be opened by a number of programs - pretty much anything that can read a PDF (at least, on Linux and Mac), or Gimp. -Justin Could please suggest me Thanks in advance. 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] regarding xpm2ps?
Thanks again Justin for your kind reply I have given command like this xpm2ps -f .xpm -o .eps -di .m2p then it showing the following error Fatal error: Library file H_hbond.m2p not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Could please tell me how can I remedy this problem? Thanks alot On Wed, 10 Sep 2008 Justin A.Lemkul wrote : minnale wrote: I have issued the following command xpm2s -f .xpm -o .eps If I mention option -di with m2p it showed Fatal error: Library file H_hbond.m2p not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) If you specify -di you need to give xpm2ps an actual .m2p file, an example of which is online: http://www.gromacs.org/documentation/reference/online/m2p.html -Justin Could tell me any suggestion Thanks alot On Wed, 10 Sep 2008 Justin A.Lemkul wrote : minnale wrote: I have converted .xpm (which generated from *g_hbond) to .eps by using xpm2ps command, after finished the running of this command showed There are 1 matrices in .xpm Matrix 0 is 37501 x 1 Auto tick spacing failed for X-axis, guessing 2 Auto tick spacing for X-axis: major 2, minor 0.4 Auto tick spacing failed for Y-axis, guessing 0 Auto tick spacing for Y-axis: major 0, minor nan Set the x-size of the box to 0.011 Set the y-size of the box to 0.011 1.is it mean that set the box x and y sizes to 0.111 by using -bx and -by options. You've got problems somewhere. Did you specify an .m2p file with -di? What was your command line? 2.How can I execute this .eps for getting map? An .eps file can be opened by a number of programs - pretty much anything that can read a PDF (at least, on Linux and Mac), or Gimp. -Justin Could please suggest me Thanks in advance. 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] regarding xpm2ps?
minnale wrote: Thanks again Justin for your kind reply I have given command like this xpm2ps -f .xpm -o .eps -di .m2p then it showing the following error Fatal error: Library file H_hbond.m2p not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Could please tell me how can I remedy this problem? The error message is pretty explicit...does such a file exist? -Justin Thanks alot On Wed, 10 Sep 2008 Justin A.Lemkul wrote : minnale wrote: I have issued the following command xpm2s -f .xpm -o .eps If I mention option -di with m2p it showed Fatal error: Library file H_hbond.m2p not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) If you specify -di you need to give xpm2ps an actual .m2p file, an example of which is online: http://www.gromacs.org/documentation/reference/online/m2p.html -Justin Could tell me any suggestion Thanks alot On Wed, 10 Sep 2008 Justin A.Lemkul wrote : minnale wrote: I have converted .xpm (which generated from *g_hbond) to .eps by using xpm2ps command, after finished the running of this command showed There are 1 matrices in .xpm Matrix 0 is 37501 x 1 Auto tick spacing failed for X-axis, guessing 2 Auto tick spacing for X-axis: major 2, minor 0.4 Auto tick spacing failed for Y-axis, guessing 0 Auto tick spacing for Y-axis: major 0, minor nan Set the x-size of the box to 0.011 Set the y-size of the box to 0.011 1.is it mean that set the box x and y sizes to 0.111 by using -bx and -by options. You've got problems somewhere. Did you specify an .m2p file with -di? What was your command line? 2.How can I execute this .eps for getting map? An .eps file can be opened by a number of programs - pretty much anything that can read a PDF (at least, on Linux and Mac), or Gimp. -Justin Could please suggest me Thanks in advance. 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with continuation of md
Hi all, I had used the tpbconv command to give continuation run on a 2ns simulation. I had provided the previois trajectory file, energy file for this. However the continuation run had crashed due to power failure and I again had to give a rerun on it. Everything seems to be working well but surprisingly I find that the coordinates of the atoms at 2ns , as found at the end of the 2ns simulation and the coordinates of the atoms at 2ns at the start of the continuation run are different. This means that the run didn't start from the point at which ended. Can anyone suggest any reason for this? Thanks in advance Sarbani ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with continuation of md
sarbani chattopadhyay wrote: Hi all, I had used the tpbconv command to give continuation run on a 2ns simulation. I had provided the previois trajectory file, energy file for this. However the continuation run had crashed due to power failure and I again had to give a rerun on it. I'm confused. Which part crashed? Start -- 2 ns, or the post-2ns time frame? Please provide the exact commands you gave to tpbconv. Everything seems to be working well but surprisingly I find that the coordinates of the atoms at 2ns , as found at the end of the 2ns simulation and the coordinates of the atoms at 2ns at the start of the continuation run are different. This means that the run didn't start from the point at which ended. How did you make this determination? -Justin Can anyone suggest any reason for this? Thanks in advance Sarbani 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] problem with continuation of md
The post 2ns run had crashed. The commands were tpbconv -f 2ns.trr -e 2ns.edr -s 2ns.tpr -extend 1 When it crashed ,the command given was tpbconv -f ext10ns.trr -s ext10ns.tpr -e ext10ns.edr -o leftrun.tpr On Wed, 10 Sep 2008 Justin A.Lemkul wrote : sarbani chattopadhyay wrote: Hi all, I had used the tpbconv command to give continuation run on a 2ns simulation. I had provided the previois trajectory file, energy file for this. However the continuation run had crashed due to power failure and I again had to give a rerun on it. I'm confused. Which part crashed? Start -- 2 ns, or the post-2ns time frame? Please provide the exact commands you gave to tpbconv. Everything seems to be working well but surprisingly I find that the coordinates of the atoms at 2ns , as found at the end of the 2ns simulation and the coordinates of the atoms at 2ns at the start of the continuation run are different. This means that the run didn't start from the point at which ended. How did you make this determination? -Justin Can anyone suggest any reason for this? Thanks in advance Sarbani 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/ www.rediff.com/signature-default.htm/ [EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with continuation of md
sarbani chattopadhyay wrote: The post 2ns run had crashed. The commands were tpbconv -f 2ns.trr -e 2ns.edr -s 2ns.tpr -extend 1 When it crashed ,the command given was tpbconv -f ext10ns.trr -s ext10ns.tpr -e ext10ns.edr -o leftrun.tpr So what you're saying then is that the coordinates that were the output from the first part (say, 2ns.gro) do not match those you find in ext10ns.tpr? How did you make that determination? Is the trajectory discontinuous? -Justin On Wed, 10 Sep 2008 Justin A.Lemkul wrote : sarbani chattopadhyay wrote: Hi all, I had used the tpbconv command to give continuation run on a 2ns simulation. I had provided the previois trajectory file, energy file for this. However the continuation run had crashed due to power failure and I again had to give a rerun on it. I'm confused. Which part crashed? Start -- 2 ns, or the post-2ns time frame? Please provide the exact commands you gave to tpbconv. Everything seems to be working well but surprisingly I find that the coordinates of the atoms at 2ns , as found at the end of the 2ns simulation and the coordinates of the atoms at 2ns at the start of the continuation run are different. This means that the run didn't start from the point at which ended. How did you make this determination? -Justin Can anyone suggest any reason for this? Thanks in advance Sarbani 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/ www.rediff.com/signature-default.htm/ [EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] regarding xpm2ps?
Am Mittwoch 10 September 2008 13:36:15 schrieb minnale: Thanks Martin yes executing of .eps means read out the file. I am using the following very ugly shell-script to convert to bmp format: #!/bin/bash cat $1 | grep -v ^/\* Generated| grep -v ^/\* This| grep -v ^/\* title| grep -v ^/\* legend| grep -v ^/\* x-label| grep -v ^/\* y-label| grep -v ^/\* type | xpmtoppm | ppmtobmp $2 On the bmp, I apply tools (convert/mogrify) from the imagemagick package to crop convert to png. The png then can then be read in by my python/scipy/numpy scripts as a matrix. Best Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv
Hi Tsjerk, It means the resulting trajectory is free from translational and rotational degrees of freedom which I can use for the studies of internal dynamics i suppose. Ram. On Wed, Sep 10, 2008 at 3:05 AM, Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Hi Ram, -fit rot+trans performs an ordinary least-squares fit using the reference structure provided with -s, removing rotational and translational degrees of freedom. Cheers, Tsjerk On Tue, Sep 9, 2008 at 9:47 PM, rams rams [EMAIL PROTECTED] wrote: Dear Users, I have a question about the option -fit in trjconv. The default option with -fit is none. If I use the option as rot+trans, does it mean that the rotational and translational motions are removed from the trajectory ? If not, is there any option in gromacs, to create a translational and rotational free trajectory from the original trajecotry file ? I also want to make sure the usage of the command: trjconv -f original trr -s .tpr -o rot_trans_free.trr -fit rot+trans Thanks in advance. Ram. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Using gromacs for docking purpose
vivek sharma wrote: Hi Everybody, I am running MD simulation for getting various conformation of a molecule, that can act as better receptor for docking purpose. While doing so, I got a number of doubts. Firstly what should be the range of time step I can keep in .mdp file (right now I am using .002 ps of time step, Can I increase it further ?) That depends largely on your force field and whether or not you're applying constraints. For protein simulations (with constraints), 1-2 fs is pretty standard; some UA lipid simulations use 4-5 fs. My second question is for how long I should run my simulation to get various conformation (or what is the time interval that can be taken as in general after which biomolecule can change their conformation ?) There is no simple answer to this question. Sampling is always an issue in MD. Some conformational changes occur on the nanosecond timescale, others in excess of several hundred ns, or even a few microseconds! Perhaps your system alters its conformation rapidly, such that changes can be observed in a few ns, but that is for you to determine :) How should I pick up various conformation from the mdrun that can make a sense ? Probably the best idea (IMHO) is to run several simulations, each starting from different random velocities. Run each for the same length of time and compare the results. Do all the simulations wind up giving you the same thing? Are there substantial differences in the conformations? As for extracting conformations along a trajectory (using trjconv -dump), this may or may not be relevant. What if a certain conformation occurs once for a single frame in one trajectory, but never again in ten other trajectories? Do you care about that frame? Probably not, based on reasonable sampling. What if a certain conformation occurs a few times over a few trajectories? How do you determine its relevance? Such are the challenges of simulation. You can use g_cluster to do RMSD clustering to determine which conformations are similar along the trajectory. Whether or not any of these make sense is entirely up to you and what you know about your system :) -Justin I know the questions are not strictly related to gromacs. my apologies for putting such questions. If anybody has insight into these questions, please reply. With Thanks, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] problem with continuation of md
It seems that the trajectory is discontinuous. The coordinates in the pdb file generated from the trajectory files show that the model corresponding to 2ns in the 2ns.pdb(at the last ) file is different from the model corresponding to 2ns in the 10ns(extended).pdb( at the first) Sarbani On Wed, 10 Sep 2008 Justin A.Lemkul wrote : sarbani chattopadhyay wrote: The post 2ns run had crashed. The commands were tpbconv -f 2ns.trr -e 2ns.edr -s 2ns.tpr -extend 1 When it crashed ,the command given was tpbconv -f ext10ns.trr -s ext10ns.tpr -e ext10ns.edr -o leftrun.tpr So what you're saying then is that the coordinates that were the output from the first part (say, 2ns.gro) do not match those you find in ext10ns.tpr? How did you make that determination? Is the trajectory discontinuous? -Justin On Wed, 10 Sep 2008 Justin A.Lemkul wrote : sarbani chattopadhyay wrote: Hi all, I had used the tpbconv command to give continuation run on a 2ns simulation. I had provided the previois trajectory file, energy file for this. However the continuation run had crashed due to power failure and I again had to give a rerun on it. I'm confused. Which part crashed? Start -- 2 ns, or the post-2ns time frame? Please provide the exact commands you gave to tpbconv. Everything seems to be working well but surprisingly I find that the coordinates of the atoms at 2ns , as found at the end of the 2ns simulation and the coordinates of the atoms at 2ns at the start of the continuation run are different. This means that the run didn't start from the point at which ended. How did you make this determination? -Justin Can anyone suggest any reason for this? Thanks in advance Sarbani 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/ www.rediff.com/signature-default.htm/ [EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/ www.rediff.com/signature-default.htm/ [EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Using gromacs for docking purpose
Hi Justin, Thank you very much for your quick reply It is really encouraging to get such response For the answer of third question, How can I assign different random velocity ? Is it like assigning the different force-field ? Please elaborate or suggest some reference if you can ? With Thanks, Vivek 2008/9/10 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote: Hi Everybody, I am running MD simulation for getting various conformation of a molecule, that can act as better receptor for docking purpose. While doing so, I got a number of doubts. Firstly what should be the range of time step I can keep in .mdp file (right now I am using .002 ps of time step, Can I increase it further ?) That depends largely on your force field and whether or not you're applying constraints. For protein simulations (with constraints), 1-2 fs is pretty standard; some UA lipid simulations use 4-5 fs. My second question is for how long I should run my simulation to get various conformation (or what is the time interval that can be taken as in general after which biomolecule can change their conformation ?) There is no simple answer to this question. Sampling is always an issue in MD. Some conformational changes occur on the nanosecond timescale, others in excess of several hundred ns, or even a few microseconds! Perhaps your system alters its conformation rapidly, such that changes can be observed in a few ns, but that is for you to determine :) How should I pick up various conformation from the mdrun that can make a sense ? Probably the best idea (IMHO) is to run several simulations, each starting from different random velocities. Run each for the same length of time and compare the results. Do all the simulations wind up giving you the same thing? Are there substantial differences in the conformations? As for extracting conformations along a trajectory (using trjconv -dump), this may or may not be relevant. What if a certain conformation occurs once for a single frame in one trajectory, but never again in ten other trajectories? Do you care about that frame? Probably not, based on reasonable sampling. What if a certain conformation occurs a few times over a few trajectories? How do you determine its relevance? Such are the challenges of simulation. You can use g_cluster to do RMSD clustering to determine which conformations are similar along the trajectory. Whether or not any of these make sense is entirely up to you and what you know about your system :) -Justin I know the questions are not strictly related to gromacs. my apologies for putting such questions. If anybody has insight into these questions, please reply. With Thanks, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CPMD- QM MM simulation
Hi Christian, Thanks for your idea. I'll start writing up a short manual to make it available in the QMMM website in the near future. Meanwhile, it will be great if you and other users can contribute to this manual by writing up small pieces mentioning the difficulties you faced and how you resolved; particular suggestions for any problem with simulations, any particular feature of this code that you would like to highlight/caution to the users, etc. Your contributions will make the manual effective and valuable. cheers, pb. On 9/8/08, Christian Seifert [EMAIL PROTECTED] wrote: Hi. Anyway, it would be nice to have a structured manual for the GMX/CPMD interface. The website http://www.tougaloo.edu/research/qmmm has just a few basic information and further information in this mailing list under http://www.gromacs.org/pipermail/gmx-users/2006-June/022329.html are not that easy to understand. A small guide on how to input new ions into the source code for users how normally do not deal with source code so much for ex. would be nice in such a manual. Or a picture of the MMlayer_radii and qmmmcoul_cutoff with some explanations... It takes a long time to find these things out by try and error and reading the source code. Christian. On Mon, 2008-09-08 at 09:29 +0200, Gerrit Groenhof wrote: Message: 1 Date: Fri, 5 Sep 2008 15:48:12 -0700 From: Chih-Ying Lin [EMAIL PROTECTED] Subject: [gmx-users] CPMD- QM MM simulation To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi I read some papers, which the authors use CPMD - QM MM simulation to reparametrize the force field parameters. But, they did not say the details. Could anyone explain this more here? Why don't you contact the authors? Gerrit -- M. Sc. Christian Seifert Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] which force field for a protein-protein complex?
Short answer, try Amber99SB with Gaff. Alan Message: 1 Date: Fri, 5 Sep 2008 15:06:21 +0200 From: Paula Gonz?lez-Rubio [EMAIL PROTECTED] Subject: [gmx-users] which force field for a protein-protein complex? To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hello there, I would like to do a MD of a protein-protein complex (both with their ligands) so I'm looking for some advise regarding the best force field for simulate my system. For more details, it consists on a ADP-ribosylase (which ligand is the NAD) and a small G protein (GDP binded), we want to see what is the role of a loop in the formation of the complex and on the ADP-ribosilation of the small G protein. Does any one have a good idea of an appropiate force field for this kind of systems ? Do you think gromos 43A1 or ffgmx could be an option? Thanks a lot in advance! Paula -- ! NEW email !! [EMAIL PROTECTED] *** NEW ADDRESS ** Paula GONZALEZ-RUBIO PhD Candidate DSIMB INTS, INSERM UMR-S726 6 rue Alexandre Cabanel 75015 Paris Tel : +33(1) 44 49 30 00 Fax : +33(1) 47 34 74 31 4th Floor. Room 401 Bis Web Site: http://www.dsimb.inserm.fr/ https://paris7.jussieu.fr/Redirect/www.dsimb.inserm.fr/ -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080905/e69b67f9/attachment-0001.html -- -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sdf reference configuration question
I'm getting odd behavior with the reference configuration generated by g_sdf (v. 3.3.3). I am wondering if this is a bug, and if the spatial density profile is similarly affected. My test system has simple, regular geometry: a glycine 15-mer held frozen in a fully extended rod-like configuration, with water solvent. I wish to evaluate, for instance, the spatial distribution of water O around the 15 instances of the glycine O. My understanding is that g_sdf will average the water oxygen SDF around the 15 sites to yield one composite SDF -- is this correct? However, the reference configuration, given by g_sdf -r, seems incorrect when performing the SDF around more than one atom triplet. Based on the documentation, Atom 1 (the GLY O) should be at the origin, and Atom 2 (GLY C) should be offset along the Z-axis only. When there is only one atom triplet (that is, performing sdf around just one GLY O), this is in fact the case. However, when performing an SDF around more than one atom, this is no longer holds, and the offset increases with increasing number of triplets. Below I give the output of three reference .gro files illustrating this. In all cases, Atom 1 is GLY O, Atom 2 is GLY C, Atom 3 is GLY CA; Atom 4 is Water OW. My question is, first, should I expect the GLY O to lie at the origin in all instances? Is this a bug, or user error? And if this is a bug, are the sdf data reliable? Regards, Matt --- Matt Wyczalkowski Doctoral Candidate, Biomedical Engineering Pappu Lab: http://lima.wustl.edu Washington University in St. Louis Reference Configuration .gro files: (constructed with, e.g. g_sdf -f ../traj.xtc -n index-all.ndx -s ../GLY15Frozen.tpr -o OO-all -r OO-all -grid 2 2 2 -b 500 ) For one GLY residue: Protein 7 4 GLYN1 0.187 0.033 -0.090 4 GLYH2 0.041 0.046 -0.090 4 GLY CA3 -0.000 0.193 -0.089 4 GLY HA14 0.086 0.281 -0.088 4 GLY HA25 0.243 0.119 -0.091 4 GLYC6 -0.000 0.000 -0.179 ; OFFSET ALONG Z AXIS 4 GLYO7 0.000 0.000 0.000 ; AT ORIGIN 10.0 10.0 10.0 For two GLY residues: Protein 7 4 GLYN1 0.575 -0.257 -0.087 4 GLYH2 0.430 -0.244 -0.086 4 GLY CA3 0.389 -0.097 -0.088 4 GLY HA14 0.474 -0.009 -0.089 4 GLY HA25 0.632 -0.171 -0.090 4 GLYC6 0.388 -0.291 -0.175 4 GLYO7 0.389 -0.288 0.005 ; NOT AT ORIGIN 10.0 10.0 10.0 For all 15 GLY residues: Protein 7 2 GLYN1 -1.438 1.227 -0.102 2 GLYH2 -1.551 1.280 -0.097 2 GLY CA3 -1.631 1.377 -0.104 2 GLY HA14 -1.595 1.400 -0.112 2 GLY HA25 -1.421 1.256 -0.109 2 GLYC6 -1.572 1.263 -0.123 2 GLYO7 -1.564 1.272 -0.064 ; NOT AT ORIGIN 10.0 10.0 10.0 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Topology of tris-Naphthyl-Benzene
Hi all ! Does anyone have the topology and coordinates of tris-naphthyl-benzene in bulk ? I would be highly grateful if someone can share those with me. Thanks a lot in advance. __ Rohit Malshe 1112, Engineering Hall Tel :001 608 262 3370 Graduate Student1415, Engineering Drive Email: [EMAIL PROTECTED] Chemical and Biological Engineering Madison, WI. University of Wisconsin-Madison USA USA- 53726 __ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] S2 order parameters
Dear users, The S2 order parameters obtained by using g_chi, are they corresponds to the Lipari_Szabo NMR order parameters for characterizing the internal motions? Also it is mentioned in the manual that the obtained S2 parameter corresponds to a dihedral and the generated plot is residue vs S2. Does it mean that the S2 parameters are averaged on each residue ?? Thanks in advance. Ram. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] which force field for a protein-protein complex?
I was working with protein complex, and after tests some FF, I could obtain best results with oplss/aa On Wed, Sep 10, 2008 at 12:07 PM, Alan [EMAIL PROTECTED] wrote: Short answer, try Amber99SB with Gaff. Alan Message: 1 Date: Fri, 5 Sep 2008 15:06:21 +0200 From: Paula Gonz?lez-Rubio [EMAIL PROTECTED] Subject: [gmx-users] which force field for a protein-protein complex? To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hello there, I would like to do a MD of a protein-protein complex (both with their ligands) so I'm looking for some advise regarding the best force field for simulate my system. For more details, it consists on a ADP-ribosylase (which ligand is the NAD) and a small G protein (GDP binded), we want to see what is the role of a loop in the formation of the complex and on the ADP-ribosilation of the small G protein. Does any one have a good idea of an appropiate force field for this kind of systems ? Do you think gromos 43A1 or ffgmx could be an option? Thanks a lot in advance! Paula -- ! NEW email !! [EMAIL PROTECTED] *** NEW ADDRESS ** Paula GONZALEZ-RUBIO PhD Candidate DSIMB INTS, INSERM UMR-S726 6 rue Alexandre Cabanel 75015 Paris Tel : +33(1) 44 49 30 00 Fax : +33(1) 47 34 74 31 4th Floor. Room 401 Bis Web Site: http://www.dsimb.inserm.fr/ https://paris7.jussieu.fr/Redirect/www.dsimb.inserm.fr/ -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080905/e69b67f9/attachment-0001.html -- -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
