My system consists of protein and lipids and I want to calculate energy of some residues. I made index file for these residues and build a tpr file again with that index and used g_energy..but in that list it did not show the groups of those residue?
What can I do? Should I do simulation again by determining energy grps in mdp file? Is there another way without running again?
I'm afraid you will need to do so called rerun. http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
If you provide a trajectory to mdrun -rerun, the energies will be calculated for all of the frames.
You're right with the energygrps keyword. G_energy will find the groups then and allow you to select them. Check also energygrps-excl, it may speed-up the rerun considerably...
Thanks dear Michal,
Am I right?..should I 1-edit mdp file by adding desired groups for energygrp and 2-then with new tpr file and old trr 3-do this mdrun -s new.tpr -rerun old.trr?
yes, you're right.
adding energygrps-excl = SOL SOL may speed up the rerun too.
Note that PME energy cannot be decomposed into interactions between specific parts of your system.
Michal H. Kolář , Where should you add energygrps-excl = SOL SOL?
In the mdp file I guess?
Hello Erik Marklund
I made the index for water milecule 1(r_130), added "energygrps= r_130" in .mdp file, and extracted potential energy of this water molecule. However, the columbic part is curious. Term Coul-SR:r_130-r_130 is not 0. Is this correct? By the way, I used PME method in the rerun process. Do you have any idea about this problem?
@ s0 legend "Coul-SR:r_130-r_130" @ s1 legend "Coul-14:r_130-r_130" @ s2 legend "Coul-SR:r_130-rest" @ s3 legend "Coul-14:r_130-rest" @ s4 legend "Coul-SR:rest-rest" @ s5 legend "Coul-14:rest-rest" 0.000000 -4.046188 0.000000 -79.345924 0.000000 -633651.750000 7718.288574
Hi Erik Marklund and Michal H. Kolář ,
I wanted to characterize pairwise interaction between two residues in my protein (LJ-14). How should I edit my energygrps in *.mdp?
Currently my selection is Protein Sol and I want to indicate residue x and residue y.
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