I am doing the CG mapping of propane using votca (which is given in tutorial section of votca). At first I created the topol.tpr file and the command line is:
gmx grompp -f grompp.mdp -c conf.gro -p topol.top -o topol.tpr
Then, CG structure is obtained using:
csg_map --top topol.tpr --trj conf.gro --cg propane.xml --out conf_cg.gro
Then, to get the itp file of CG propane the command line was:
csg_gmxtopol --top topol.tpr --cg propane.xml --out propane.itp
But, this itp file is lacking proper bon distance, angle values and also non-bonded information and without bonded, nonbonded information it is not possible to do CG-MD simulation using GROMACS. I am not able to resolve the issue.
Any suggestions would be really helpful.
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