GROMACS version:2020
GROMACS modification: Yes/No
Here post your question
number of coordinates in coordinate file (DPPC_with_IL1.gro, 96256)
does not match topology (topol.top, 96281)
I have a membrane system with ionic liquids and while energy minimizing i am getting this error,
things i have already cheaked are , in molecules section of topol.top file the number of each component i have given are correct as by multiplying them with respective number of atoms of each component and totaling i am getting the total as 96256 which is the number of coordinates resent in the gro file. but while gromacs reads the topology file its telling that total coordinates in topol.top is 96281 i.e 25 more than expected.
i also checked the individual itp files to cheak if there are any line gaps or extra or less atoms in itps of lipid ionic liquid or water but no suc things are there as mistakes. so can anyone please help me on this.
I’m afraid I have to advice you to go through the number of molecules in the topology again. If those numbers are correct, you will need to check that the number of atoms in each molecule type is correct. It is usually not that difficult to find a discrepancy of 25 atoms.
If you don’t find it on your own, you will have to post your files here. Otherwise it’s difficult to say where the error is.
dear sir
I reallly have gone through the things you mentioned and found them correct also still the issue is there so I am uploading the files here can you please suggest me something.
as files are not uploadable in gro or itp format I am making them .dat
The problem is that there are [ system ] and [ molecules ] sections at the end of the bondedNO3.itp (adding 4 atoms) and scaled_bondedCHL.itp (adding 21 atoms) files. Removing them makes it work.