Hello Justin, Using gmxcheck I checked the number of atoms in trajectory. I got the correct no.
I am still stuck with trjconv. 1. trjconv -s test.tpr -f 3.xtc -o b.xtc -center -ur compact -pbc none -n glu-emi-cl-128-no.ndx for above command I selected Group 14 from .ndx file which is glucose molecule I want to centered. 2. trjconv -s 3.tpr -f b.xtc -o c.xtc -fit rot+trans -dt 500 -n test.ndx for this command 1st I selected Group 14 (Glucose)and 2nd is Group 39 (EMI)cation. For this command I got this error. Fatal error:Index[0] 25 is larger than the number of atoms in the trajectory file (24) Nilesh On Wed, May 12, 2010 3:30 pm, Justin A. Lemkul wrote: > > > 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 >>>> 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 >>> >>> >>> >>> >> >> >> > > -- > ======================================== > > > 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
