[gmx-users] no output in g_dist
Hi users, To get the distance between water and protein i did - g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11 from this i should obtain an output file as distance.xvg which i dont get. and my output is printed on the terminal as- t: 1 136 SOL 2336 OW 0.772373 (nm) t: 1 136 SOL 2337 HW1 0.706358 (nm) t: 1 136 SOL 2338 HW2 0.807787 (nm) t: 1 139 SOL 2345 OW 0.821094 (nm) t: 1 139 SOL 2346 HW1 0.810919 (nm) t: 1 139 SOL 2347 HW2 0.771526 (nm) t: 1 7237 SOL 23640 HW1 0.997056 (nm) t: 1 11793 SOL 37307 OW 0.868929 (nm) t: 1 11793 SOL 37308 HW1 0.927205 (nm) t: 1 11793 SOL 37309 HW2 0.776699 (nm) t: 2 125 SOL 2303 OW 0.940527 (nm) In this t: 1 136 SOL 2336 OW 0.772373 (nm) does the 't' states the time frame, 136 SOL states the SOL molecule number and 2336 OW the residue contact from protein and the 0.772373 nm the distance between them. Thanks -- 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] no output in g_dist
aiswarya pawar wrote: Hi users, To get the distance between water and protein i did - g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11 from this i should obtain an output file as distance.xvg which i dont get. Try without specifying -dist simultaneously. Also realize that the distance between the COM of the protein and the COM of water is probably constant (per COM motion removal algorithms) and may actually be zero. and my output is printed on the terminal as- t: 1 136 SOL 2336 OW 0.772373 (nm) t: 1 136 SOL 2337 HW1 0.706358 (nm) t: 1 136 SOL 2338 HW2 0.807787 (nm) t: 1 139 SOL 2345 OW 0.821094 (nm) t: 1 139 SOL 2346 HW1 0.810919 (nm) t: 1 139 SOL 2347 HW2 0.771526 (nm) t: 1 7237 SOL 23640 HW1 0.997056 (nm) t: 1 11793 SOL 37307 OW 0.868929 (nm) t: 1 11793 SOL 37308 HW1 0.927205 (nm) t: 1 11793 SOL 37309 HW2 0.776699 (nm) t: 2 125 SOL 2303 OW 0.940527 (nm) In this t: 1 136 SOL 2336 OW 0.772373 (nm) does the 't' states the time frame, 136 SOL states the SOL molecule number and 2336 OW the residue contact from protein and the 0.772373 nm the distance between them. More or less. OW, HW1, and HW2 are atoms, not residues. But yes, that's what the -dist option does. -Justin -- 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/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] no output in g_dist
On Thu, Sep 8, 2011 at 8:25 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, To get the distance between water and protein i did - g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11 from this i should obtain an output file as distance.xvg which i dont get. The -dist option: Print all atoms in group 2 (water) closer than dist to the center of mass of group 1 (protein in your case). As you have seen, it *print* the result on the screen. To obtain the distance.xvg file, please don't use the -dist option here. and my output is printed on the terminal as- t: 1 136 SOL 2336 OW 0.772373 (nm) t: 1 136 SOL 2337 HW1 0.706358 (nm) t: 1 136 SOL 2338 HW2 0.807787 (nm) t: 1 139 SOL 2345 OW 0.821094 (nm) t: 1 139 SOL 2346 HW1 0.810919 (nm) t: 1 139 SOL 2347 HW2 0.771526 (nm) t: 1 7237 SOL 23640 HW1 0.997056 (nm) t: 1 11793 SOL 37307 OW 0.868929 (nm) t: 1 11793 SOL 37308 HW1 0.927205 (nm) t: 1 11793 SOL 37309 HW2 0.776699 (nm) t: 2 125 SOL 2303 OW 0.940527 (nm) In this t: 1 136 SOL 2336 OW 0.772373 (nm) does the 't' states the time frame, 136 SOL states the SOL molecule number and 2336 OW the residue contact from protein and the 0.772373 nm the distance between them. Thanks -- 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 -- Best Regards, lina -- 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
