[gmx-users] Free energy calculation

[nazli kashani javid]

Dear all

I'm trying to calculate free energy of solvation according to Justin's
tutorial for my protein in water.

Is it true to follow that tutorial for my protein? any special changes in
MDP file is necessary ?

If there is no differences for systems to calculate free energy of
solvation according to Justin's tutorial. I have set all my residue's
charges to zero. and there is no ions into my solvent.

I received this error several times during minimization (em_steep). Even
when I change  some parameters in .mdp file such as pme_order or rvdw or
vdw-type  and ...., the error didn't change.


Fatal error:
There is no domain decomposition for 10 nodes that is compatible with the
given box and a minimum cell size of 4.2267 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I checked the website but I didn't get any helpful hint for my system.

any help is appreciated.