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 <[email protected]> A : [email protected]; Discussion list for GROMACS users <[email protected]> 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 list [email protected] > 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 [email protected]. Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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