Re: [gmx-users] g_tcaf segmentation fault
I check my .mdp setting and you were right. I haven't been saving the velocities in my .trr file. I change my setting and everything worked fine. Thanks for your help Stelios On 09/27/2012 03:37 PM, Tsjerk Wassenaar wrote: Re: [gmx-users] g_tcaf segmentation fault The .trr file can contain coordinates, velocities, and forces over time, depending on your .mdp settings (nstxout, nstvout, nstfout). For g_tcaf, you need to have velocities. It does say so in the manpage. Run gmxcheck to see what's in your .trr file. A segmentation fault with the analysis tools is usually an indication that there is a mismatch in data, e.g. between trajectory and reference structure, or that some data is missing, like velocities in a trajectory. Of course the developers could try and catch all those things, but they rather spend their time thinking of new things :p Cheers, Tsjerk On Thu, Sep 27, 2012 at 2:18 PM, Stelios Karozis skaro...@ipta.demokritos.gr wrote: Sorry, but i was wrong, the .trr file contains trajectories and the .gro output file contains velocities as it should. Stelios On 09/27/2012 03:03 PM, Stelios Karozis wrote: Hi Tsjerk, I checked my .trr file and it contains the velocities, as it should. Stelios On 09/27/2012 09:12 AM, Tsjerk Wassenaar wrote: Hi Stelios, Does your .trr file contain velocities? Cheers, Tsjerk On Sep 26, 2012 8:24 PM, Stelios Karozis skaro...@ipta.demokritos.gr wrote: Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation fault error. I didn t give it too much thought. Stelios Ο χρήστης Justin Lemkul jalem...@vt.edu έγραψε: On 9/26/12 12:55 PM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the p... The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you wou... -- Justin A. Lemkul, Ph.D. Research Scientist Department ... -- -- Stelios Karozis Research Assistant Environmental Research Lab IN-RAS-TES - NCSR Demokritos - Greece email: skaro...@ipta.demokritos.gr tel : 0030 210 650 3403 -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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 -- -- Stelios Karozis Research Assistant Environmental Research Lab IN-RAS-TES - NCSR Demokritos - Greece email: skaro...@ipta.demokritos.gr tel : 0030 210 650 3403 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
Hi Stelios, Does your .trr file contain velocities? Cheers, Tsjerk On Sep 26, 2012 8:24 PM, Stelios Karozis skaro...@ipta.demokritos.gr wrote: Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation fault error. I didn t give it too much thought. Stelios Ο χρήστης Justin Lemkul jalem...@vt.edu έγραψε: On 9/26/12 12:55 PM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the p... The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you wou... -- Justin A. Lemkul, Ph.D. Research Scientist Department ... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
Hi Tsjerk, I checked my .trr file and it contains the velocities, as it should. Stelios On 09/27/2012 09:12 AM, Tsjerk Wassenaar wrote: Hi Stelios, Does your .trr file contain velocities? Cheers, Tsjerk On Sep 26, 2012 8:24 PM, Stelios Karozis skaro...@ipta.demokritos.gr wrote: Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation fault error. I didn t give it too much thought. Stelios Ο χρήστης Justin Lemkul jalem...@vt.edu έγραψε: On 9/26/12 12:55 PM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the p... The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you wou... -- Justin A. Lemkul, Ph.D. Research Scientist Department ... -- -- Stelios Karozis Research Assistant Environmental Research Lab IN-RAS-TES - NCSR Demokritos - Greece email: skaro...@ipta.demokritos.gr tel : 0030 210 650 3403 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
Sorry, but i was wrong, the .trr file contains trajectories and the .gro output file contains velocities as it should. Stelios On 09/27/2012 03:03 PM, Stelios Karozis wrote: Hi Tsjerk, I checked my .trr file and it contains the velocities, as it should. Stelios On 09/27/2012 09:12 AM, Tsjerk Wassenaar wrote: Hi Stelios, Does your .trr file contain velocities? Cheers, Tsjerk On Sep 26, 2012 8:24 PM, Stelios Karozis skaro...@ipta.demokritos.gr wrote: Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation fault error. I didn t give it too much thought. Stelios Ο χρήστης Justin Lemkul jalem...@vt.edu έγραψε: On 9/26/12 12:55 PM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the p... The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you wou... -- Justin A. Lemkul, Ph.D. Research Scientist Department ... -- -- Stelios Karozis Research Assistant Environmental Research Lab IN-RAS-TES - NCSR Demokritos - Greece email: skaro...@ipta.demokritos.gr tel : 0030 210 650 3403 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
Hi Stelios, But the eigenvec.trr does not. You shouldn't be using that. So what exactly are you doing? How many frames do you have in your .trr file, what do you give for selections, etc? Please paste the exact commands and resulting output. Cheers, Tsjerk On Thu, Sep 27, 2012 at 2:03 PM, Stelios Karozis skaro...@ipta.demokritos.gr wrote: Hi Tsjerk, I checked my .trr file and it contains the velocities, as it should. Stelios On 09/27/2012 09:12 AM, Tsjerk Wassenaar wrote: Hi Stelios, Does your .trr file contain velocities? Cheers, Tsjerk On Sep 26, 2012 8:24 PM, Stelios Karozis skaro...@ipta.demokritos.gr wrote: Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation fault error. I didn t give it too much thought. Stelios Ο χρήστης Justin Lemkul jalem...@vt.edu έγραψε: On 9/26/12 12:55 PM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the p... The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you wou... -- Justin A. Lemkul, Ph.D. Research Scientist Department ... -- -- Stelios Karozis Research Assistant Environmental Research Lab IN-RAS-TES - NCSR Demokritos - Greece email: skaro...@ipta.demokritos.gr tel : 0030 210 650 3403 -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
The .trr file can contain coordinates, velocities, and forces over time, depending on your .mdp settings (nstxout, nstvout, nstfout). For g_tcaf, you need to have velocities. It does say so in the manpage. Run gmxcheck to see what's in your .trr file. A segmentation fault with the analysis tools is usually an indication that there is a mismatch in data, e.g. between trajectory and reference structure, or that some data is missing, like velocities in a trajectory. Of course the developers could try and catch all those things, but they rather spend their time thinking of new things :p Cheers, Tsjerk On Thu, Sep 27, 2012 at 2:18 PM, Stelios Karozis skaro...@ipta.demokritos.gr wrote: Sorry, but i was wrong, the .trr file contains trajectories and the .gro output file contains velocities as it should. Stelios On 09/27/2012 03:03 PM, Stelios Karozis wrote: Hi Tsjerk, I checked my .trr file and it contains the velocities, as it should. Stelios On 09/27/2012 09:12 AM, Tsjerk Wassenaar wrote: Hi Stelios, Does your .trr file contain velocities? Cheers, Tsjerk On Sep 26, 2012 8:24 PM, Stelios Karozis skaro...@ipta.demokritos.gr wrote: Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation fault error. I didn t give it too much thought. Stelios Ο χρήστης Justin Lemkul jalem...@vt.edu έγραψε: On 9/26/12 12:55 PM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the p... The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you wou... -- Justin A. Lemkul, Ph.D. Research Scientist Department ... -- -- Stelios Karozis Research Assistant Environmental Research Lab IN-RAS-TES - NCSR Demokritos - Greece email: skaro...@ipta.demokritos.gr tel : 0030 210 650 3403 -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_tcaf segmentation fault
Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log// //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg/ The result is a Segmentation fault error: /Selected 0: 'System'// //trn version: GMX_trn_file (single precision)// //Last frame -1 time0.000/*/ /**/Segmentation fault/* I use GROMACS 4.5.5 What am I doing wrong? Thanks in advance Stelios -- -- Stelios Karozis Research Assistant Environmental Research Lab IN-RAS-TES - NCSR Demokritos - Greece email: skaro...@ipta.demokritos.gr tel : 0030 210 650 3403 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log// //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg/ -dt 0.001 ? The result is a Segmentation fault error: /Selected 0: 'System'// //trn version: GMX_trn_file (single precision)// //Last frame -1 time0.000/*/ /**/Segmentation fault/* I use GROMACS 4.5.5 What am I doing wrong? Thanks in advance Stelios -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
The -dt flag is the time step between the frames in ps. I tried the command in any combination i could think of. With -dt without, with -b without, and so on. The only way i get a partial result is to use the .trr file from the simulation and not from the g_covar command and even then i get the density of the system and after that segmentation fault Ο χρήστης lina lina.lastn...@gmail.com έγραψε: On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log// //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg/ -dt 0.001 ? The result is a Segmentation fault error: /Selected 0: 'System'// //trn version: GMX_trn_file (single precision)// //Last frame -1 time0.000/*/ /**/Segmentation fault/* I use GROMACS 4.5.5 What am I doing wrong? Thanks in advance Stelios -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: The -dt flag is the time step between the frames in ps. I tried the command in any combination i could think of. With -dt without, with -b without, and so on. The only way i get a partial result is to use the .trr file from the simulation and not from the g_covar command and even then i get the density of the system and after that segmentation fault Segmentation fault involves lots. If I were you, I would try -dt 100 or large to reduce memory requirement. or perhaps try the very short time period. namely -e 200 to see what's going on. Ο χρήστης lina lina.lastn...@gmail.com έγραψε: On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log// //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg/ -dt 0.001 ? The result is a Segmentation fault error: /Selected 0: 'System'// //trn version: GMX_trn_file (single precision)// //Last frame -1 time0.000/*/ /**/Segmentation fault/* I use GROMACS 4.5.5 What am I doing wrong? Thanks in advance Stelios -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
Thanks for the suggestion. I just tried and the problem presists. Just to be clear, the right way is to use the g_covar.trr file, correct? Ο χρήστης lina lina.lastn...@gmail.com έγραψε: On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: The -dt flag is the time step between the frames in ps. I tried the command in any combination i could think of. With -dt without, with -b without, and so on. The only way i get a partial result is to use the .trr file from the simulation and not from the g_covar command and even then i get the density of the system and after that segmentation fault Segmentation fault involves lots. If I were you, I would try -dt 100 or large to reduce memory requirement. or perhaps try the very short time period. namely -e 200 to see what's going on. Ο χρήστης lina lina.lastn...@gmail.com έγραψε: On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log// //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg/ -dt 0.001 ? The result is a Segmentation fault error: /Selected 0: 'System'// //trn version: GMX_trn_file (single precision)// //Last frame -1 time0.000/*/ /**/Segmentation fault/* I use GROMACS 4.5.5 What am I doing wrong? Thanks in advance Stelios -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
On Thursday 27,September,2012 12:55 AM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the problem presists. Just to be clear, the right way is to use the g_covar.trr file, correct? -f traj.trr InputFull precision trajectory: trr trj cpt Here the full precision means double precision? I see you use single precision. I have never tried this one, perhaps someone else may give you some suggestions. Best regards, Ο χρήστης lina lina.lastn...@gmail.com έγραψε: On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: The -dt flag is the time step between the frames in ps. I tried the command in any combination i could think of. With -dt without, with -b without, and so on. The only way i get a partial result is to use the .trr file from the simulation and not from the g_covar command and even then i get the density of the system and after that segmentation fault Segmentation fault involves lots. If I were you, I would try -dt 100 or large to reduce memory requirement. or perhaps try the very short time period. namely -e 200 to see what's going on. Ο χρήστης lina lina.lastn...@gmail.com έγραψε: On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log// //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg/ -dt 0.001 ? The result is a Segmentation fault error: /Selected 0: 'System'// //trn version: GMX_trn_file (single precision)// //Last frame -1 time0.000/*/ /**/Segmentation fault/* I use GROMACS 4.5.5 What am I doing wrong? Thanks in advance Stelios -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
On 9/26/12 12:55 PM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the problem presists. Just to be clear, the right way is to use the g_covar.trr file, correct? The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you would use that here. Use the trajectory from the actual simulation. -Justin Ο χρήστης lina lina.lastn...@gmail.com έγραψε: On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: The -dt flag is the time step between the frames in ps. I tried the command in any combination i could think of. With -dt without, with -b without, and so on. The only way i get a partial result is to use the .trr file from the simulation and not from the g_covar command and even then i get the density of the system and after that segmentation fault Segmentation fault involves lots. If I were you, I would try -dt 100 or large to reduce memory requirement. or perhaps try the very short time period. namely -e 200 to see what's going on. Ο χρήστης lina lina.lastn...@gmail.com έγραψε: On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log// //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg/ -dt 0.001 ? The result is a Segmentation fault error: /Selected 0: 'System'// //trn version: GMX_trn_file (single precision)// //Last frame -1 time0.000/*/ /**/Segmentation fault/* I use GROMACS 4.5.5 What am I doing wrong? Thanks in advance Stelios -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
On 9/26/12 1:12 PM, lina wrote: On Thursday 27,September,2012 12:55 AM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the problem presists. Just to be clear, the right way is to use the g_covar.trr file, correct? -f traj.trr InputFull precision trajectory: trr trj cpt Here the full precision means double precision? I see you use single precision. I have never tried this one, perhaps someone else may give you some suggestions. Full precision and double precision are different, though not completely unrelated in a sense. You can have a single- or double-precision .trr file that is still full precision, all it means is that a different number of decimal points are saved. A .trr has greater precision than an .xtc (independent of a single- or double-precision calculation) simply because it stores more decimal places. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation fault error. I didn t give it too much thought. Stelios Ο χρήστης Justin Lemkul jalem...@vt.edu έγραψε: On 9/26/12 12:55 PM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the problem presists. Just to be clear, the right way is to use the g_covar.trr file, correct? The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you would use that here. Use the trajectory from the actual simulation. -Justin Ο χρήστης lina lina.lastn...@gmail.com έγραψε: On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: The -dt flag is the time step between the frames in ps. I tried the command in any combination i could think of. With -dt without, with -b without, and so on. The only way i get a partial result is to use the .trr file from the simulation and not from the g_covar command and even then i get the density of the system and after that segmentation fault Segmentation fault involves lots. If I were you, I would try -dt 100 or large to reduce memory requirement. or perhaps try the very short time period. namely -e 200 to see what's going on. Ο χρήστης lina lina.lastn...@gmail.com έγραψε: On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log// //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg/ -dt 0.001 ? The result is a Segmentation fault error: /Selected 0: 'System'// //trn version: GMX_trn_file (single precision)// //Last frame -1 time0.000/*/ /**/Segmentation fault/* I use GROMACS 4.5.5 What am I doing wrong? Thanks in advance Stelios -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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
