How about temperature replica exchange with de novo folding, then convert the
probabilities of the folded and unfolded states into a free energy difference?
You'll obviously need to be really careful about cutting off a sufficient
amount of initial simulation time as equilibration, but you might
You can get the coordinates of all P and N atoms with g_traj and then write an
awk script to process the output (determine the angles and make the histogram).
But if g_angle in gromacs 5 can do it, then why not just use that? Many
analysis programs will take a .gro file for the -s option, and if
Hi all,
I know there are some methods for calculating free energy of* binding*
between a ligand and a receptor.
1.Are there any methods for calculating free energy of *unfolding *proteins?
4_helix bundle protein makes my system,
2.Is scientifically reasonable for my system to calculate free ene
Dears,
I simulated a DMPC lipid bilayer. I want to calculate the distribution of angle
between phosphorus - nitrogen vector (P-N vector) and Z axis. Is there any
command to calculate angle distribution between a vector and an axis? My
Gromacs version is 4.5.4.
I searched and found gangle co
Dear Bahare:
this is not necessarily a problem. If what you are saying is that in two
separate runs of the same system from the same coordinates you got different
trajectories then this is expected under most conditions:
http://www.gromacs.org/Documentation/Terminology/Reproducibility
However,
Thanks chris for your answer. I'm using Gromacs 4.6.3 with AMBER03 force field.
i had a 20ns run with this command:mdrun -s .tpr -v -deffnm but after some
days and passing less than 4 ns of run, power turned out and the run was
crashed. i used this command to restart the run:mdrun -s .tpr
Dear Bahare:
what data does not match what other thing? What type of crash did you
encounter? What version of gromacs? etc... Please provide as much detail as you
can. As your question stands, we could as easily answer the question "how deep
is water?"
Chris.
_
