Re: [gmx-users] Trjconv error
On 19/06/2012 4:13 PM, Shima Arasteh wrote: Dear gmx users, I want to follow the workflow regarding to http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for the second step I enter the command as below: trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb But I get the error: Index[232] 235 is larger than the number of atoms in the trajectory file (234). There is a mismatch in the contents of your -f, -s and/or -n files I don't have any index file, so what this error is talking about? Then it must mean there's a mismatch in the contents of your -f and -s files... each must refer to the same system. Something about your past management of these two files makes your intended operation a nonsense, but we can't know what. If, for example, you chose xtcgroups in your .mdp file as something other than System, then they do not. Mark How may I solve it? Anybody may suggest me any solution please? I would be so thankful for your suggestions. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Trjconv error
Thanks for your reply. I entered the trjconv as the workflow of http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions And I chose the 'system' as the chosen group. Now, if I want to see the trajectory, am I supposed to load the mdfinal.xtc on the first frame ( 1stframe.pdb ), which I produced earlier? Thanks for your help. Sincerely, Shima From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, June 19, 2012 11:00 AM Subject: Re: [gmx-users] Trjconv error On 19/06/2012 4:13 PM, Shima Arasteh wrote: Dear gmx users, I want to follow the workflow regarding to http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for the second step I enter the command as below: trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb But I get the error: Index[232] 235 is larger than the number of atoms in the trajectory file (234). There is a mismatch in the contents of your -f, -s and/or -n files I don't have any index file, so what this error is talking about? Then it must mean there's a mismatch in the contents of your -f and -s files... each must refer to the same system. Something about your past management of these two files makes your intended operation a nonsense, but we can't know what. If, for example, you chose xtcgroups in your .mdp file as something other than System, then they do not. Mark How may I solve it? Anybody may suggest me any solution please? I would be so thankful for your suggestions. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Trjconv error
On 19/06/2012 5:49 PM, Shima Arasteh wrote: Thanks for your reply. I entered the trjconv as the workflow of http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions And I chose the 'system' as the chosen group. Now, if I want to see the trajectory, am I supposed to load the mdfinal.xtc on the first frame ( 1stframe.pdb ), which I produced earlier? We don't know what you've done. Try it and see... the whole purpose is whether you like the form of what you see, right? Mark Thanks for your help. Sincerely, Shima *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tuesday, June 19, 2012 11:00 AM *Subject:* Re: [gmx-users] Trjconv error On 19/06/2012 4:13 PM, Shima Arasteh wrote: Dear gmx users, I want to follow the workflow regarding to http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for the second step I enter the command as below: trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb But I get the error: Index[232] 235 is larger than the number of atoms in the trajectory file (234). There is a mismatch in the contents of your -f, -s and/or -n files I don't have any index file, so what this error is talking about? Then it must mean there's a mismatch in the contents of your -f and -s files... each must refer to the same system. Something about your past management of these two files makes your intended operation a nonsense, but we can't know what. If, for example, you chose xtcgroups in your .mdp file as something other than System, then they do not. Mark How may I solve it? Anybody may suggest me any solution please? I would be so thankful for your suggestions. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Trjconv error
Actually, I loaded the trajectory of md-run and saw the bonds stretching and behaves strangely . So, as Justin suggested, I decided to do as the work-flow of PBC. So I entered the commands as below: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use |trjconv -|pbc| nojump| after this step. trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc Now I want to know if it is correct to load the final .xtc on the first frame to get a acceptable result? My main propose is to avoid the strange behavior of bonds. I'd like to know if I have done correctly? However I need to say that I saw the final .xtc loaded on the first frame .pdb and got the normal movie. Sincerely, Shima From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, June 19, 2012 12:38 PM Subject: Re: [gmx-users] Trjconv error On 19/06/2012 5:49 PM, Shima Arasteh wrote: Thanks for your reply. I entered the trjconv as the workflow of http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions And I chose the 'system' as the chosen group. Now, if I want to see the trajectory, am I supposed to load the mdfinal.xtc on the first frame ( 1stframe.pdb ), which I produced earlier? We don't know what you've done. Try it and see... the whole purpose is whether you like the form of what you see, right? Mark Thanks for your help. Sincerely, Shima From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, June 19, 2012 11:00 AM Subject: Re: [gmx-users] Trjconv error On 19/06/2012 4:13 PM, Shima Arasteh wrote: Dear gmx users, I want to follow the workflow regarding to http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for the second step I enter the command as below: trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb But I get the error: Index[232] 235 is larger than the number of atoms in the trajectory file (234). There is a mismatch in the contents of your -f, -s and/or -n files I don't have any index file, so what this error is talking about? Then it must mean there's a mismatch in the contents of your -f and -s files... each must refer to the same system. Something about your past management of these two files makes your intended operation a nonsense, but we can't know what. If, for example, you chose xtcgroups in your .mdp file as something other than System, then they do not. Mark How may I solve it? Anybody may suggest me any solution please? I would be so thankful for your suggestions. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv : error
Hello Justin, As you suggest I used tbpconv tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr and I selected group 0 for system group (In system group all atoms are present.) Still I am getting the same error. I have one more question, I am working on solvation glucose in ionic liquids. As I told you I want to show glucose surrounded by cation using iso-surface. After loading grid.cub file in vmd, all atoms are present. How can I do sothat I can get only glucose and plot the iso-surface to show cation position. Can you help me to solve this problem. Thanks Nilesh On Tue, May 11, 2010 5:22 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate spatial distribution function (SDF) for my system. 1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n test.ndx 2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n test.ndx I am getting the following error for step 2. Fatal error: Index[2385] 2410 is larger than the number of atoms in the trajectory file (2409). How can I solve this problem? Duirng my simulation I didn't specify xtc_grps this option in md file. Then it looks like you must have saved only a subset of your system during step 1 or some other post-processing step. Either save the whole system, or use tpbconv to generate a .tpr file that contains only the relevant subset of atoms. -Justin Thanks Nilesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv : error
Nilesh Dhumal wrote: Hello Justin, As you suggest I used tbpconv tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr and I selected group 0 for system group (In system group all atoms are present.) Still I am getting the same error. By selecting System, you are essentially generating the same .tpr file. Using tpbconv to get around this problem is potentially dangerous, since I don't know what groups you're trying to analyze, what's in your trajectory, etc. The better option is to tell us what you've been doing all along, with details of groups selected, etc. The bottom line is you are trying to analyze a trajectory that (somehow) doesn't have all the atoms the .tpr file does, and when you're trying to run analysis on whatever groups you have, the index values are inconsistent. I have one more question, I am working on solvation glucose in ionic liquids. As I told you I want to show glucose surrounded by cation using iso-surface. After loading grid.cub file in vmd, all atoms are present. How can I do sothat I can get only glucose and plot the iso-surface to show cation position. Can you help me to solve this problem. No clue. What are the prompts from g_spatial? What are the groups you are telling it to analyze and/or output? -Justin Thanks Nilesh On Tue, May 11, 2010 5:22 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate spatial distribution function (SDF) for my system. 1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n test.ndx 2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n test.ndx I am getting the following error for step 2. Fatal error: Index[2385] 2410 is larger than the number of atoms in the trajectory file (2409). How can I solve this problem? Duirng my simulation I didn't specify xtc_grps this option in md file. Then it looks like you must have saved only a subset of your system during step 1 or some other post-processing step. Either save the whole system, or use tpbconv to generate a .tpr file that contains only the relevant subset of atoms. -Justin Thanks Nilesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re : [gmx-users] trjconv : error
Hi Nilesh, If you need the whole system you maybe don't need to include the -n flag in the tpbconv command it will still create your new tpr file for continuing your work without errors, I had earlier some similar problem. But as Justin mentioned it is due to some specification in the mpd as for part of your system was selected only.. Gigi -E-mail d'origine- De : Nilesh Dhumal ndhu...@andrew.cmu.edu A : jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Envoyé le : Mercredi, 12 Mai 2010 17:47 Sujet : Re: [gmx-users] trjconv : error Hello Justin, As you suggest I used tbpconv tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr and I selected group 0 for system group (In system group all atoms are present.) Still I am getting the same error. I have one more question, I am working on solvation glucose in ionic liquids. As I told you I want to show glucose surrounded by cation using iso-surface. After loading grid.cub file in vmd, all atoms are present. How can I do sothat I can get only glucose and plot the iso-surface to show cation position. Can you help me to solve this problem. Thanks Nilesh On Tue, May 11, 2010 5:22 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate spatial distribution function (SDF) for my system. 1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n test.ndx 2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n test.ndx I am getting the following error for step 2. Fatal error: Index[2385] 2410 is larger than the number of atoms in the trajectory file (2409). How can I solve this problem? Duirng my simulation I didn't specify xtc_grps this option in md file. Then it looks like you must have saved only a subset of your system during step 1 or some other post-processing step. Either save the whole system, or use tpbconv to generate a .tpr file that contains only the relevant subset of atoms. -Justin Thanks Nilesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re : [gmx-users] trjconv : error
Hello Justin tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr Group 0 ( System) has 2584 elements Group 1 ( Protein) has 2456 elements Group 2 ( Protein-H) has 1036 elements Group 3 ( C-alpha) has 0 elements Group 4 (Backbone) has 128 elements Group 5 ( MainChain) has 129 elements Group 6 (MainChain+Cb) has 129 elements Group 7 ( MainChain+H) has 129 elements Group 8 ( SideChain) has 2327 elements Group 9 ( SideChain-H) has 907 elements Group10 ( Prot-Masses) has 2456 elements Group11 ( Non-Protein) has 128 elements Group12 ( CL) has 128 elements Group13 ( Other) has 128 elements Group14 ( GUL) has24 elements Group15 ( O) has 1 elements -- --- Group39 ( EMI) has 2432 elements Group40 ( C) has 128 elements --- Group57 ( H18) has 128 elements Group58 ( H19) has 128 elements Group59 ( CL) has 128 elements Group60 ( CL) has 128 elements I selected Group 0 After this I followed the steps given in g_spatial -h. I selected residue Group 14 and EMI is Group 39 for trjconv. 1. trjconv -s test.tpr -f 3.xtc -o b.xtc -center -ur compact -pbc none -n glu-emi-cl-128-no.ndx 2. trjconv -s test.tpr -f b.xtc -o c.xtc -fit rot+trans -n glu-emi-cl-128-no.ndx For 2nd step I got the error Fatal error: Index[2385] 2410 is larger than the number of atoms in the trajectory file (2409). As I want to plot how glucose (GLU:Group 14 )is surrounded by cation (EMI:Group 39). Should I select Group 14 in tpbconv ? Sorry for so much details and your help is really appreciated. Thanks Nilesh On Wed, May 12, 2010 10:58 am, gigita...@aol.fr wrote: Hi Nilesh, If you need the whole system you maybe don't need to include the -n flag in the tpbconv command it will still create your new tpr file for continuing your work without errors, I had earlier some similar problem. But as Justin mentioned it is due to some specification in the mpd as for part of your system was selected only.. Gigi -E-mail d'origine- De : Nilesh Dhumal ndhu...@andrew.cmu.edu A : jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Envoyé le : Mercredi, 12 Mai 2010 17:47 Sujet : Re: [gmx-users] trjconv : error Hello Justin, As you suggest I used tbpconv tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr and I selected group 0 for system group (In system group all atoms are present.) Still I am getting the same error. I have one more question, I am working on solvation glucose in ionic liquids. As I told you I want to show glucose surrounded by cation using iso-surface. After loading grid.cub file in vmd, all atoms are present. How can I do sothat I can get only glucose and plot the iso-surface to show cation position. Can you help me to solve this problem. Thanks Nilesh On Tue, May 11, 2010 5:22 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate spatial distribution function (SDF) for my system. 1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n test.ndx 2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n test.ndx I am getting the following error for step 2. Fatal error: Index[2385] 2410 is larger than the number of atoms in the trajectory file (2409). How can I solve this problem? Duirng my simulation I didn't specify xtc_grps this option in md file. Then it looks like you must have saved only a subset of your system during step 1 or some other post-processing step. Either save the whole system, or use tpbconv to generate a .tpr file that contains only the relevant subset of atoms. -Justin Thanks Nilesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users
Re: Re : [gmx-users] trjconv : error
Nilesh Dhumal wrote: Hello Justin tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr Group 0 ( System) has 2584 elements Group 1 ( Protein) has 2456 elements Group 2 ( Protein-H) has 1036 elements Group 3 ( C-alpha) has 0 elements Group 4 (Backbone) has 128 elements Group 5 ( MainChain) has 129 elements Group 6 (MainChain+Cb) has 129 elements Group 7 ( MainChain+H) has 129 elements Group 8 ( SideChain) has 2327 elements Group 9 ( SideChain-H) has 907 elements Group10 ( Prot-Masses) has 2456 elements Group11 ( Non-Protein) has 128 elements Group12 ( CL) has 128 elements Group13 ( Other) has 128 elements Group14 ( GUL) has24 elements Group15 ( O) has 1 elements -- --- Group39 ( EMI) has 2432 elements Group40 ( C) has 128 elements --- Group57 ( H18) has 128 elements Group58 ( H19) has 128 elements Group59 ( CL) has 128 elements Group60 ( CL) has 128 elements I selected Group 0 As I said before, selecting System when running tpbconv to get some subset of atoms is pointless. For now, please abandon the use of tpbconv altogether. I will repeat: I do not think this is the best approach for you to use, and is probably just confusing right now. The output indicates that you have 2584 atoms accounted for in your original .tpr file. How many atoms are in your trajectory (using gmxcheck)? After this I followed the steps given in g_spatial -h. I selected residue Group 14 and EMI is Group 39 for trjconv. So, group 14 (glucose) is for centering, and EMI is your output group? Do you give these same groups for both #1 and #2 below? What if you output the entire system? The only time you should need to use your special index group is for g_spatial itself, as the group to use in the calculation. 1. trjconv -s test.tpr -f 3.xtc -o b.xtc -center -ur compact -pbc none -n glu-emi-cl-128-no.ndx 2. trjconv -s test.tpr -f b.xtc -o c.xtc -fit rot+trans -n glu-emi-cl-128-no.ndx For 2nd step I got the error Fatal error: Index[2385] 2410 is larger than the number of atoms in the trajectory file (2409). This is a consequence of previously outputting some subset of the atoms above. As I want to plot how glucose (GLU:Group 14 )is surrounded by cation (EMI:Group 39). Should I select Group 14 in tpbconv ? No, please discontinue any thought of using tpbconv altogether. Sorry for so much details and your help is really appreciated. More detail is better. The more complete the thread is, the more it helps others and the faster you get a resolution. -Justin Thanks Nilesh On Wed, May 12, 2010 10:58 am, gigita...@aol.fr wrote: Hi Nilesh, If you need the whole system you maybe don't need to include the -n flag in the tpbconv command it will still create your new tpr file for continuing your work without errors, I had earlier some similar problem. But as Justin mentioned it is due to some specification in the mpd as for part of your system was selected only.. Gigi -E-mail d'origine- De : Nilesh Dhumal ndhu...@andrew.cmu.edu A : jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Envoyé le : Mercredi, 12 Mai 2010 17:47 Sujet : Re: [gmx-users] trjconv : error Hello Justin, As you suggest I used tbpconv tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr and I selected group 0 for system group (In system group all atoms are present.) Still I am getting the same error. I have one more question, I am working on solvation glucose in ionic liquids. As I told you I want to show glucose surrounded by cation using iso-surface. After loading grid.cub file in vmd, all atoms are present. How can I do sothat I can get only glucose and plot the iso-surface to show cation position. Can you help me to solve this problem. Thanks Nilesh On Tue, May 11, 2010 5:22 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate spatial distribution function (SDF) for my system. 1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n test.ndx 2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n test.ndx I am getting the following error for step 2. Fatal error: Index[2385] 2410 is larger than the number of atoms in the trajectory file (2409). How can I solve this problem? Duirng my simulation I didn't specify xtc_grps this option in md file. Then it looks like you must have saved only a subset of your system during step 1 or some other post-processing step. Either save the whole system, or use tpbconv to generate a .tpr file that contains only the relevant subset of atoms. -Justin Thanks Nilesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar
Re: Re : [gmx-users] trjconv : error
Ok. Justin. I am centering group 14 (glucose) and EMI is your output group. If I do g_spatial it works well. g_spatial -f 3.xtc -n glu-emi-cl-128-no.ndx -s 3.tpr After loading grid.cube in vmd, I could see whole system. I was expecting that I can see glucose and can plot iso-surface to explain the position of cation. Nilesh Do you give these same groups for both #1 and #2 below? What if you output the entire system? The only time you should need to use your special index group is for g_spatial itself, as the group to use in the calculation. On Wed, May 12, 2010 1:48 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello Justin tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr Group 0 ( System) has 2584 elements Group 1 ( Protein) has 2456 elements Group 2 ( Protein-H) has 1036 elements Group 3 ( C-alpha) has 0 elements Group 4 (Backbone) has 128 elements Group 5 ( MainChain) has 129 elements Group 6 (MainChain+Cb) has 129 elements Group 7 ( MainChain+H) has 129 elements Group 8 ( SideChain) has 2327 elements Group 9 ( SideChain-H) has 907 elements Group10 ( Prot-Masses) has 2456 elements Group11 ( Non-Protein) has 128 elements Group12 ( CL) has 128 elements Group13 ( Other) has 128 elements Group14 ( GUL) has24 elements Group15 ( O) has 1 elements -- --- Group39 ( EMI) has 2432 elements Group40 ( C) has 128 elements --- Group57 ( H18) has 128 elements Group58 ( H19) has 128 elements Group59 ( CL) has 128 elements Group60 ( CL) has 128 elements I selected Group 0 As I said before, selecting System when running tpbconv to get some subset of atoms is pointless. For now, please abandon the use of tpbconv altogether. I will repeat: I do not think this is the best approach for you to use, and is probably just confusing right now. The output indicates that you have 2584 atoms accounted for in your original .tpr file. How many atoms are in your trajectory (using gmxcheck)? After this I followed the steps given in g_spatial -h. I selected residue Group 14 and EMI is Group 39 for trjconv. So, group 14 (glucose) is for centering, and EMI is your output group? Do you give these same groups for both #1 and #2 below? What if you output the entire system? The only time you should need to use your special index group is for g_spatial itself, as the group to use in the calculation. 1. trjconv -s test.tpr -f 3.xtc -o b.xtc -center -ur compact -pbc none -n glu-emi-cl-128-no.ndx 2. trjconv -s test.tpr -f b.xtc -o c.xtc -fit rot+trans -n glu-emi-cl-128-no.ndx For 2nd step I got the error Fatal error: Index[2385] 2410 is larger than the number of atoms in the trajectory file (2409). This is a consequence of previously outputting some subset of the atoms above. As I want to plot how glucose (GLU:Group 14 )is surrounded by cation (EMI:Group 39). Should I select Group 14 in tpbconv ? No, please discontinue any thought of using tpbconv altogether. Sorry for so much details and your help is really appreciated. More detail is better. The more complete the thread is, the more it helps others and the faster you get a resolution. -Justin Thanks Nilesh On Wed, May 12, 2010 10:58 am, gigita...@aol.fr wrote: Hi Nilesh, If you need the whole system you maybe don't need to include the -n flag in the tpbconv command it will still create your new tpr file for continuing your work without errors, I had earlier some similar problem. But as Justin mentioned it is due to some specification in the mpd as for part of your system was selected only.. Gigi -E-mail d'origine- De : Nilesh Dhumal ndhu...@andrew.cmu.edu A : jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Envoyé le : Mercredi, 12 Mai 2010 17:47 Sujet : Re: [gmx-users] trjconv : error Hello Justin, As you suggest I used tbpconv tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr and I selected group 0 for system group (In system group all atoms are present.) Still I am getting the same error. I have one more question, I am working on solvation glucose in ionic liquids. As I told you I want to show glucose surrounded by cation using iso-surface. After loading grid.cub file in vmd, all atoms are present. How can I do sothat I can get only glucose and plot the iso-surface to show cation position. Can you help me to solve this problem. Thanks Nilesh On Tue, May 11, 2010 5:22 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate spatial distribution function (SDF) for my system. 1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n
Re: Re : [gmx-users] trjconv : error
Nilesh Dhumal wrote: Ok. Justin. I am centering group 14 (glucose) and EMI is your output group. If I do g_spatial it works well. g_spatial -f 3.xtc -n glu-emi-cl-128-no.ndx -s 3.tpr After loading grid.cube in vmd, I could see whole system. I was expecting that I can see glucose and can plot iso-surface to explain the position of cation. I don't understand why this is happening. If you do the fitting procedure, then choose EMI for both the calculation and output group for g_spatial, you should get an isosurface of just the position of EMI, it shouldn't overlap with the glucose molecule if the fitting was done properly. Have you loaded the data correctly? If you render the glucose and EMI separately, then load the .cube file into it and display EMI as Isosurface, you should get the visualization you want. -Justin Nilesh Do you give these same groups for both #1 and #2 below? What if you output the entire system? The only time you should need to use your special index group is for g_spatial itself, as the group to use in the calculation. On Wed, May 12, 2010 1:48 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello Justin tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr Group 0 ( System) has 2584 elements Group 1 ( Protein) has 2456 elements Group 2 ( Protein-H) has 1036 elements Group 3 ( C-alpha) has 0 elements Group 4 (Backbone) has 128 elements Group 5 ( MainChain) has 129 elements Group 6 (MainChain+Cb) has 129 elements Group 7 ( MainChain+H) has 129 elements Group 8 ( SideChain) has 2327 elements Group 9 ( SideChain-H) has 907 elements Group10 ( Prot-Masses) has 2456 elements Group11 ( Non-Protein) has 128 elements Group12 ( CL) has 128 elements Group13 ( Other) has 128 elements Group14 ( GUL) has24 elements Group15 ( O) has 1 elements -- --- Group39 ( EMI) has 2432 elements Group40 ( C) has 128 elements --- Group57 ( H18) has 128 elements Group58 ( H19) has 128 elements Group59 ( CL) has 128 elements Group60 ( CL) has 128 elements I selected Group 0 As I said before, selecting System when running tpbconv to get some subset of atoms is pointless. For now, please abandon the use of tpbconv altogether. I will repeat: I do not think this is the best approach for you to use, and is probably just confusing right now. The output indicates that you have 2584 atoms accounted for in your original .tpr file. How many atoms are in your trajectory (using gmxcheck)? After this I followed the steps given in g_spatial -h. I selected residue Group 14 and EMI is Group 39 for trjconv. So, group 14 (glucose) is for centering, and EMI is your output group? Do you give these same groups for both #1 and #2 below? What if you output the entire system? The only time you should need to use your special index group is for g_spatial itself, as the group to use in the calculation. 1. trjconv -s test.tpr -f 3.xtc -o b.xtc -center -ur compact -pbc none -n glu-emi-cl-128-no.ndx 2. trjconv -s test.tpr -f b.xtc -o c.xtc -fit rot+trans -n glu-emi-cl-128-no.ndx For 2nd step I got the error Fatal error: Index[2385] 2410 is larger than the number of atoms in the trajectory file (2409). This is a consequence of previously outputting some subset of the atoms above. As I want to plot how glucose (GLU:Group 14 )is surrounded by cation (EMI:Group 39). Should I select Group 14 in tpbconv ? No, please discontinue any thought of using tpbconv altogether. Sorry for so much details and your help is really appreciated. More detail is better. The more complete the thread is, the more it helps others and the faster you get a resolution. -Justin Thanks Nilesh On Wed, May 12, 2010 10:58 am, gigita...@aol.fr wrote: Hi Nilesh, If you need the whole system you maybe don't need to include the -n flag in the tpbconv command it will still create your new tpr file for continuing your work without errors, I had earlier some similar problem. But as Justin mentioned it is due to some specification in the mpd as for part of your system was selected only.. Gigi -E-mail d'origine- De : Nilesh Dhumal ndhu...@andrew.cmu.edu A : jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Envoyé le : Mercredi, 12 Mai 2010 17:47 Sujet : Re: [gmx-users] trjconv : error Hello Justin, As you suggest I used tbpconv tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr and I selected group 0 for system group (In system group all atoms are present.) Still I am getting the same error. I have one more question, I am working on solvation glucose in ionic liquids. As I told you I want to show glucose surrounded by cation using iso-surface. After loading
Re: [gmx-users] trjconv : error
Hello, I am simulating two carbon nanotubes in water. 1.The two nanotubes are facing each other, end to end, with their end bonded with polymers. 2. I bonded heavy (molecular weight=10) dummy atoms to the carbon atoms of the nanotubes, so that they won't move. Each bond length is initially 0, and spring constant k=2000 kJ/mol. 3. I simulated the two tubes in water and calculated their interaction force through the spring extension. Then I calculated the energy of the mean force. Is the energy free energy or internal energy? Thanks. I am using NVT with PDB. If it is free energy, is it Gibbs or Helmholtz? I am a little puzzled by the entropy. Because I am trying to tabulate this energy vs. distance and use the table as input for another larger scale Monte Carlo simulation. However, if it is the free energy (containing the entropy), then when I applied it to the MC, which automatically include the entropy consideration, will I mis-calculate the free energy during the MC simulation (Seems I may double the entropy effect or neutralize it )? Hope I make myself clear. Thanks, Young -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re : [gmx-users] trjconv : error
. But as Justin mentioned it is due to some specification in the mpd as for part of your system was selected only.. Gigi -E-mail d'origine- De : Nilesh Dhumal ndhu...@andrew.cmu.edu A : jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Envoyé le : Mercredi, 12 Mai 2010 17:47 Sujet : Re: [gmx-users] trjconv : error Hello Justin, As you suggest I used tbpconv tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr and I selected group 0 for system group (In system group all atoms are present.) Still I am getting the same error. I have one more question, I am working on solvation glucose in ionic liquids. As I told you I want to show glucose surrounded by cation using iso-surface. After loading grid.cub file in vmd, all atoms are present. How can I do sothat I can get only glucose and plot the iso-surface to show cation position. Can you help me to solve this problem. Thanks Nilesh On Tue, May 11, 2010 5:22 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate spatial distribution function (SDF) for my system. 1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n test.ndx 2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n test.ndx I am getting the following error for step 2. Fatal error: Index[2385] 2410 is larger than the number of atoms in the trajectory file (2409). How can I solve this problem? Duirng my simulation I didn't specify xtc_grps this option in md file. Then it looks like you must have saved only a subset of your system during step 1 or some other post-processing step. Either save the whole system, or use tpbconv to generate a .tpr file that contains only the relevant subset of atoms. -Justin Thanks Nilesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx
Re: Re : [gmx-users] trjconv : error
others and the faster you get a resolution. -Justin Thanks Nilesh On Wed, May 12, 2010 10:58 am, gigita...@aol.fr wrote: Hi Nilesh, If you need the whole system you maybe don't need to include the -n flag in the tpbconv command it will still create your new tpr file for continuing your work without errors, I had earlier some similar problem. But as Justin mentioned it is due to some specification in the mpd as for part of your system was selected only.. Gigi -E-mail d'origine- De : Nilesh Dhumal ndhu...@andrew.cmu.edu A : jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Envoyé le : Mercredi, 12 Mai 2010 17:47 Sujet : Re: [gmx-users] trjconv : error Hello Justin, As you suggest I used tbpconv tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr and I selected group 0 for system group (In system group all atoms are present.) Still I am getting the same error. I have one more question, I am working on solvation glucose in ionic liquids. As I told you I want to show glucose surrounded by cation using iso-surface. After loading grid.cub file in vmd, all atoms are present. How can I do sothat I can get only glucose and plot the iso-surface to show cation position. Can you help me to solve this problem. Thanks Nilesh On Tue, May 11, 2010 5:22 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate spatial distribution function (SDF) for my system. 1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n test.ndx 2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n test.ndx I am getting the following error for step 2. Fatal error: Index[2385] 2410 is larger than the number of atoms in the trajectory file (2409). How can I solve this problem? Duirng my simulation I didn't specify xtc_grps this option in md file. Then it looks like you must have saved only a subset of your system during step 1 or some other post-processing step. Either save the whole system, or use tpbconv to generate a .tpr file that contains only the relevant subset of atoms. -Justin Thanks Nilesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv : error
Nilesh Dhumal wrote: Hello, I am trying to calculate spatial distribution function (SDF) for my system. 1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n test.ndx 2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n test.ndx I am getting the following error for step 2. Fatal error: Index[2385] 2410 is larger than the number of atoms in the trajectory file (2409). How can I solve this problem? Duirng my simulation I didn't specify xtc_grps this option in md file. Then it looks like you must have saved only a subset of your system during step 1 or some other post-processing step. Either save the whole system, or use tpbconv to generate a .tpr file that contains only the relevant subset of atoms. -Justin Thanks Nilesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv error
Hi Parthiban and Sundar, Did you check the .trr file with gmxcheck? By the way, is this still that same (faulty) trjconv of these sysadmins of yours who compiled it with gcc 4.x? Cheers, Tsjerk On Wed, Aug 27, 2008 at 8:36 AM, [EMAIL PROTECTED] wrote: hi all i can able to get .trr file after running md for 10 hrs but i cannot able to get the .trr to .xtc file which gives out the following error. can anyone guess, what type of error is this, how to resolve it.. Parthiban Sundar --- time3.500 Program trjconv_mpi, VERSION 3.3.1 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file --- ___ 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
Re: [gmx-users] trjconv error
Hi, we have checked it., but of no use it giving some error., for your kind information, this trjconv_mpi command works for a protein with a drug molecule, a protein moleclue, a dimer, etc.. So it's not trjconv_mpi, it's the trajectory that's wrong. Could you give the directory listing? (ls -l) Tsjerk -- 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
Re: [gmx-users] trjconv error
Hi, Thanks for the mail. Well, I am using a old version specifically, even though newer versions are available. It is quite confusing since the same file is being able to be read by other tools like gmxcheck. And it is while running by gmxcheck that I get the Magic number error Raghu --- On Wed, 23/4/08, Mark Abraham [EMAIL PROTECTED] wrote: From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] trjconv error To: Gromacs Users gmx-users@gromacs.org Date: Wednesday, 23 April, 2008, 11:44 AM Ragothaman Yennamalli wrote: Hi, Sorry for not replying immediately. Gromacs ver 3.2.1 OS is Red hat enterprise 4 Initially I had tried reading the file from an external hard disk and now I copied it to another system and tried again. Still the same error. The reason why I was truncating was due to a magic number error I got while reading the trajectory. Fatal error: Magic Number Error in XTC file (read 0, should be 1995) So, I was truncating it at an earlier time from where I didnt see any errors. Dunno. 3.2.1 is a very old version - you should be planning your upgrade to version 4 as soon as it's out, unless you need compatibility for some reason. Otherwise the only reason I can think that gmxdump might succeed where trjconv doesn't is that it isn't actually an XTC file, but some other format with an .xtc extension. Try to replicate your problem with a small simulation. If you can, then you probably have a real issue, but this is very unlikely. If you can't replicate it, then it seems you've probably mangled something and we can't help you. Mark ___ 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 Bring your gang together. Do your thing. Find your favourite Yahoo! group at http://in.promos.yahoo.com/groups/ ___ 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 error
Hi, Sorry for not replying immediately. Gromacs ver 3.2.1 OS is Red hat enterprise 4 Initially I had tried reading the file from an external hard disk and now I copied it to another system and tried again. Still the same error. The reason why I was truncating was due to a magic number error I got while reading the trajectory. Fatal error: Magic Number Error in XTC file (read 0, should be 1995) So, I was truncating it at an earlier time from where I didnt see any errors. Regards, Raghu --- On Fri, 18/4/08, Mark Abraham [EMAIL PROTECTED] wrote: From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] trjconv error To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 18 April, 2008, 8:09 PM Ragothaman Yennamalli wrote: I wanted to truncate a trajectory file and when I use trjconv tool, I get an error: Fatal error: /media/usbdisk1/paul_case4/full_10ns_040408/traj2.xtc is not a trj file, exiting The file is able to read by gmxcheck... What could be the problem? What GROMACS version? What OS? Have you tried copying the file elsewhere and reading from there? Mark ___ 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 Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/ ___ 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 error
Ragothaman Yennamalli wrote: I wanted to truncate a trajectory file and when I use trjconv tool, I get an error: Fatal error: /media/usbdisk1/paul_case4/full_10ns_040408/traj2.xtc is not a trj file, exiting The file is able to read by gmxcheck... What could be the problem? What GROMACS version? What OS? Have you tried copying the file elsewhere and reading from there? Mark ___ 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
