Hi all,
Im trying to calculate free volume in a polymer system using “gmx freevolume”.
I have a problem while reading the van der waals radii. I have the radii in .top file and the relation between residue name of .gro and chemical element (united atom model) in .itp file.
From what I understand the command assigns a vdw radius according to the name in .gro file, which is not right for my system.
Do you know how I can assign the radii from my .top file? Or if I could use an index file and in that case how this should be?
Thank you in advance!
Hi,
gmx freevolume should use as standard Bondi radii. These values are stored in the file vdwradii.dat (in $GROMACS_DIR/share/gromacs/top). To check this, you can have a look at the information the tool print out when runs. Tools usually print out where different information are read.
Then if you want to use different vdwradii an option is to copy vdwradii.dat in the working directory and modify the radii values. When the tool runs, it should read first the file in your working directory.
I hope this allow you to assign the radii you want
Best regards
Alessandra
I’m trying to calculate excluded volume for protein in water+Glucose solvent system. so when I -select protein then considering that as the static structure excluded volume wrt all the solvents are being calculated (as per my understanding). and if I want to caculate excluded volume for glucose then, stripping water from trajectory ( such that my system only has protein and glucose) then the excluded volume will be calculated wrt to Glucose, right? and the values I get should be correct? If I’m missing something or I should do it by other way then please comment.