Hi,
I was trying to run heating of a protein keeping all protein heavy atom fixed in its' crystal structure position using GROMACS.I found that gmx genrestr helps to make a .itp file which contain list of atoms to be restrained with certain force constant values but even if I apply high force constant value (e.g 1000 kcal/mol/A^2) to the heavy protein atoms rmsd calculation on obtained trajectory shows that protein havy atoms fluctuate.How can I completely cease protein heavy atom motion in constrained MD simulation in GROMACS ?
Did you include .itp file heavy metals to topol.top (topology) file. Then heavy atoms should not show.much fluctuation.
Yes I included and I get little fluctuation but I want no motion of protein heavy atoms.
Then you can apply strong position restrain of 10000 or 100000 kcal/mol/A^2. Please see if it works.
1. Create a group of atoms in index.ndx file that you want to keep frozen
2. use freezegrps in your mdp file.
That should help. Positions of the atoms from this group will be frozen during simulation.
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