Gmx distance using bash for loop

User discussions
1

GROMACS version: 2019
GROMACS modification: No

Dear All,
I want to calculate com distance between two groups using gmx distance, using for loop bash scripting. My script

for (( i=26; i<35; i++ ))
do
gmx distance -s md.tpr -f traj.xtc -n ind1.ndx -oall dist${i}.xvg -tu ns -select ‘com of group “$i” plus com of group 24’
done

This gives the following error Message:

Program: gmx distance, version 2019
Source file: src/gromacs/selection/selectioncollection.cpp (line 666)
Function: void gmx::SelectionCollection::setIndexGroups(gmx_ana_indexgrps_t*)

Inconsistency in user input:
Invalid index group reference(s)
Cannot match ‘group “$i”’, because no such index group can be found.

Simply “i” gives wrong data and I tried several ways for denoting the number in the group section to overcome this, but I failed to solve this issue. I request you, kindly help me to fix this issue. Thanks in advance.

2

Hi,

Try using double quotes around your -select command. With single quotes $i does not evaluate to your variable.

If you need double quotes inside of the command you should escape them, e.g. -select "com of group \"$i\" plus com of group 24". (But you might not need to quote $i inside)

Regards,
Petter

1 Like
3

Thank you so much for your response, Sir.
I used the following command,

gmx distance -s md.tpr -f traj.xtc -n ind1.ndx -oall dist${i}.xvg -tu ns -select “com of group “$i” plus com of group 24”

gave me the required result. Thanks again, Sir.

4

Hello All, I have an index file (attached), having 0-37 groups to calculate the com distance via bash for loop. Using that, first 9 and last one (37th) groups are not considered for the analysis, citing the following reasons

Script

for (( j=2; j<=37; j++ ))
do
gmx distance -s md.tpr -f traj.xtc -n ind1.ndx -oall Dist${j}.xvg -tu ns -select "com of group “$j” plus com of group 0 " -b 99.995 -e 100
done

Error: Multiple groups '2' selected

-------------------------------------------------------
Program:     gmx distance, version 2019
Source file: src/gromacs/selection/selectioncollection.cpp (line 666)
Function:    void gmx::SelectionCollection::setIndexGroups(gmx_ana_indexgrps_t*)

Inconsistency in user input:
Invalid index group reference(s)
  Cannot match 'group "2"', because no such index group can be found.
=================
  gmx distance -s md.tpr -f traj.xtc -n ind1.ndx -oall Dist37.xvg -tu ns -select 'com of group "37" plus com of group 0 ' -b 99.995 -e 100


-------------------------------------------------------
Program:     gmx distance, version 2019
Source file: src/gromacs/selection/selectioncollection.cpp (line 666)
Function:    void gmx::SelectionCollection::setIndexGroups(gmx_ana_indexgrps_t*)

Inconsistency in user input:
Invalid index group reference(s)
  Cannot match 'group "37"', because no such index group can be found.

Index file

Kindly help me to solve this issue. Thanks in advance.

5

Do not enclose the variable $j in double quotes; these are used within selections to choose groups by name (string), e.g. group "Protein" is valid but group "1" is not.

1 Like
6

Thank you so much, Sir. Your advice helped a lot.