# Problem in finding MSD for center of mass of a molecule **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools\ **Created:** [April 19, 2023, 7:02am UTC](https://gromacs.bioexcel.eu/t/problem-in-finding-msd-for-center-of-mass-of-a-molecule/6234 "2023-04-19T07:02:33Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![saiqa](https://avatars.discourse-cdn.com/v4/letter/s/b19c9b/32.png) [@saiqa](https://gromacs.bioexcel.eu/u/saiqa)\ **Post date:** [April 19, 2023, 7:02am UTC](https://gromacs.bioexcel.eu/t/problem-in-finding-msd-for-center-of-mass-of-a-molecule/6234/1 "2023-04-19T07:02:33Z")
Hi I am trying **To calculate the Mean Squared Displacement (MSD) of the Center of Mass (COM) of a LI ions molecule in PEO-LiTFSI system (15 peo chains, 15 TFSI molecules and 15 LI ions total 1-9720 atoms) over all points in the trajectory separated by the corresponding time in Gromacs. Here are the steps which i followed:** 1. Generate a trajectory: Run a molecular dynamics simulation of your system and generate a trajectory file (.xtc or .trr) and a topology file (.tpr). 2. Select the TFSI: Create an index file (.ndx) which contains the index of the all atoms of 15 LI (index starting from 9706-9720) that you I want to analyze using the following command gmx make\_ndx -f system.gro -o LI\_index.ndx 1. Calculate COM: Use “gmx traj” command to calculate the center of mass (COM) coordinate of the lithium ion and save it in a .xtc file using command gmx traj -s system.tpr -f system.xtc -n li\_index.ndx -com -nojump -o LI\_com\_output.xtc Now this Li\_com\_ouput.xtc contains only 15 atoms. But after this when i tried to calculate Calculate MSD: Use “gmx msd” command to calculate MSD of the lithium ion COM coordinate by using this command gmx msd -f LI\_com\_output.xtc -s system.tpr -n LI\_index.ndx -mol -trestart 10000 The following errors appears: gmx msd -f LI-com-output.xtc -s md.tpr -n li-index.ndx -mol -trestart 10000 :-) GROMACS - gmx msd, 2022.3 (-: Executable: /home/user/gromacs/bin/gmx Data prefix: /home/user/gromacs Working dir: /media/user/My Book/GROMACS/PEO90-LI-V2/PEOLI-15 Command line: gmx msd -f LI-com-output.xtc -s md.tpr -n li-index.ndx -mol -trestart 10000 Available static index groups: Group 0 “LI” (15 atoms) Specify any number of selections for option ‘sel’ (Selections to compute MSDs for from the reference): (one per line, for status/groups, ‘help’ for help, Ctrl-D to end) > 0 > Selection ‘0’ parsed > Reading file md.tpr, VERSION 2022.3 (single precision) > Reading file md.tpr, VERSION 2022.3 (single precision) > Reading frame 0 time 0.000 * * * Program: gmx msd, version 2022.3 Source file: src/gromacs/pbcutil/mshift.cpp (line 117) Fatal error: Molecule in topology has atom numbers below and above natoms (1). You are probably trying to use a trajectory which does not match the first 1 atoms of the run input file. You can make a matching run input file with gmx convert-tpr. ################# then i used gmx convert-tpr -s md.tpr -n li-index.ndx -o li.tpr to modify topology containing only lithium. and got this result Command line: gmx convert-tpr -s md.tpr -n li-index.ndx -o li.tpr Reading file md.tpr, VERSION 2022.3 (single precision) Group 0 ( LI) has 15 elements There is one group in the index Will write subset LI of original tpx containing 15 atoms Reduced ilist BONDS from 4245 to 0 entries Reduced ilist ANGLES from 17925 to 0 entries Reduced ilist RBDIHS from 20475 to 0 entries Reduced ilist LJ14 from 20475 to 0 entries Reduced ilist CONSTR from 5430 to 0 entries Reduced block excls from 9720 to 15 index-, 105870 to 15 a-entries ####################### after using the modified topology for MSD calculation i got this error. Inconsistency in user input: Invalid index group references encountered Group ‘LI’ cannot be used in selections, because it contains negative atom indices and/or references atoms not present (largest allowed atom index is 15). Now should i modify my LI-index.ndx now? starting randomly 1-15? my original LI-Index.ndx contains lithium index starting from 9706-9720.??? ---
**Author:** ![saiqa](https://avatars.discourse-cdn.com/v4/letter/s/b19c9b/32.png) [@saiqa](https://gromacs.bioexcel.eu/u/saiqa)\ **Post date:** [April 19, 2023, 7:08am UTC](https://gromacs.bioexcel.eu/t/problem-in-finding-msd-for-center-of-mass-of-a-molecule/6234/2 "2023-04-19T07:08:33Z")
Even I also tried to give a random index file starting from 1-15 and running the gmx msd command, i still got this error gmx msd -f LI-com-output.xtc -s li.tpr -n li-index1.ndx -mol -trestart 10000 :-) GROMACS - gmx msd, 2022.3 (-: Available static index groups: Group 0 “LI” (15 atoms) Specify any number of selections for option ‘sel’ (Selections to compute MSDs for from the reference): (one per line, for status/groups, ‘help’ for help, Ctrl-D to end) > 0 > Selection ‘0’ parsed > Reading file li.tpr, VERSION 2022.3 (single precision) > Reading file li.tpr, VERSION 2022.3 (single precision) > Reading frame 0 time 0.000 * * * Program: gmx msd, version 2022.3 Source file: src/gromacs/selection/selectioncollection.cpp (line 901) Function: void gmx::SelectionCollection::evaluate(t\_trxframe\*, t\_pbc\*) Inconsistency in user input: Trajectory has less atoms (1) than what is required for evaluating the provided selections (atoms up to index 15 are required). Now the problem is with trajectory file. How i can match all three trajectory file for COM of LI, topology file for all LI, and index file