[gmx-users] seeking a little help

Subho Chakraborty subho_1997 at yahoo.com
Mon Nov 30 06:04:23 CET 2015

Hi All,
I am a new student of molecular dynamics. I have started using GROMACS since one month. I have a small question to pose to anyone who is happy to help me. 
I have a small box of 8192 molecules each with 3 atoms. I have frozen the last molecule and run the simulation. I even converted the trr file from binary to .gro and checked that the last molecule indeed stayed in the same place. 
However i want the trr file to print the force on each molecule or each atom - in the x, y and z direction. I even set the "nstfout" in the grompp.mdp file to a reasonable non zero number - 5000. 

However the trr file - when converted to .gro - did not show the force. Please can someone tell me what I am doing wrong and how to get GROMACS to save/reveal the force in the trr file.
The second question is this - if I can get it to save the force as part of the snapshot, how can I get it to store the force only on the molecules I specify to be frozen - "the wall" -  (i.e those which have their own .itp file and are specified by the index.ndx file to be held frozen), if this is at all possible - or else I can make do with the forces on all molecules.
Thanks a lot,

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