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 >> Group 10 ( Prot-Masses) has 2456 elements >> Group 11 ( Non-Protein) has 128 elements >> Group 12 ( CL) has 128 elements >> Group 13 ( Other) has 128 elements >> Group 14 ( GUL) has 24 elements >> Group 15 ( O) has 1 elements >> -- >> >> >> >> --- >> Group 39 ( EMI) has 2432 elements >> Group 40 ( C) has 128 elements >> --- >> ---- >> Group 57 ( H18) has 128 elements >> Group 58 ( H19) has 128 elements >> Group 59 ( CL) has 128 elements >> Group 60 ( 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, [email protected] 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 <[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 >>> >>> >>> >>> >>> -- >>> 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 >>> >> >> > > -- > ======================================== > > > 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
