Dear all,
I have performed MD simulation of protein in water and in osmolytes. Now, I want to calculate the SDF of water and osmolyte molecules around particular loops of the protein using gromacs command. For that I have made the index of particular loops and calculated the SDF using the following commands
gmx make_ndx -f md_0_1.gro -o indexp.ndx (12=water)
gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_S.xtc -boxcenter tric -ur compact -pbc none (0=system)
gmx trjconv -s md_0_1.tpr -f md_0_1_S.xtc -o protein_fit.xtc -fit rot+trans (4=backbone of protein , 0=system)
gmx_mpi spatial -s md_0_1.tpr -f protein_fit.xtc -n indexp.ndx -nab 300 -bin 0.1 (12=water, 1=protein)
Grid.cube file was obtained as an output. After visualising the results in vmd, it is found to be similar in all the cases. I am also attaching the output file obtained from VMD below.
Any help regarding this will be highly appreciated.
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