[gmx-users] free energy calculation for methane

[elham tazikeh]

Dear Justin
thanks for your reply

i trying to follow your tutorial but when i want to produce neccesary files
per lambdas by this command:
Perl write_mdp.pl em_steep.mdp
i received 20 files as i expected but they are empty,
for this reason i try to change some important parameters in your mdp file
(we have mdp files for lambda=0) in other lambdas.for instance
*init_lambda_state=0.05
or 0.1 or 0.15 , ...*
but i dont know what value is instead of *delta_lambda?*

*mdp file for lambda=0*
; Free energy control stuff
free_energy              = yes

**init_lambda_state        = 0**delta_lambda             = 0**
calc_lambda_neighbors    = 1        ; only immediate neighboring windows
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for
each simulation
; init_lambda_state        0    1    2    3    4    5    6    7    8
9    10   11   12   13   14   15   16   17   18   19   20
vdw_lambdas              = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00

also, you mentioned about *foreign_lambda* in your tutorial, but i didnot
see it in mdp files.

at the end, i want to know about the differences between *write_mdp.pl
<http://write_mdp.pl>* and *write_sh.pl <http://write_sh.pl>* and* job.sh*?

regards
elham