Hi dear Ashok Kumar

Visual inspection with a text editor should tell you what's wrong. Either the file is incomplete (i.e. header or box vectors missing) or the coordinates are large(indicating the system became unstable at some point).

Please read this link, can help you:

https://manual.gromacs.org/archive/5.0.3/online/gro.html

Thank you,,

Can you check this attach gro file to see what sort of mistake is there?.

Dear Ashok Kumar

See the documentation

https://manual.gromacs.org/current/reference-manual/file-formats.html#gro

As you can see your gro file has something like 9 positions rather than 5 for the atom number. A quick search and replace will get rid of the problem. Here the updated gro, it works on my GROMACS2021.1.

Dear sir,

Thank you very much for your reply and sending me the same.

How did you prepare this new correct format ?.

How to read the new format trajk_newformat.gro through FORTRAN ?. In gro format first 2 to 10001 lines looks 6 column but after that it looks 5 column . Then how can I read all these in Fortran?.

Dear Ashok Kumar

The problem as I said is in the column of atom numbers. You are using 9 positions, while you should use 5 of them as stated here

https://manual.gromacs.org/current/reference-manual/file-formats.html#gro

Therefore (if _ is a space) you have something like

____1water__OW1________1___1.589___2.807___3.289

while you should have 5 total characters for the column with the atom number, that is not

________1

but

____1

You can get rid of them by searching in your file with a text editor the spaces and change them to nothing to get rid of them, so for example

search: OW1____

substitute with: OW1

If you repeat this for each atom name OW1, HW2, HW3, MW4 you clean up your file. This is not a standard procedure per se but just something I came up with. You should directly generate the files in the correct format, since this search/substitution is error prone and delicate.

About FORTRAN, I don't know, but again read the documentation

https://manual.gromacs.org/current/reference-manual/file-formats.html#gro

There is an example for FORTRAN format. My guess is that reading columns does not work, so you should read the whole line and split it with FORTRAN commands for strings or something like that. If you go line by line you know that the integer of the first 5 characters (once stripped from spaces) is the residue number, then the following five are a string that is the residue name, then again 5 characters that form a string that are atom name, then 5 characters that are an integer and are the atom number etc etc. It is explicit in the page I link, in fortran format as well

Fortran format

(i5,2a5,i5,3f8.3,3f8.4)

Thank you very much for your reply..