[gmx-users] free energy calculation for methane

[Justin Lemkul]

On 10/16/14 9:33 AM, elham tazikeh wrote:
> 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,

No idea.  Works perfectly for me.

> 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 , ...*

The value of init_lambda_state is an integer index, specifying which lambda 
vector is being used.  See the comment line in, e.g., em_steep.mdp for the 
labeling (which is also printed in the tutorial in step 3).

> but i dont know what value is instead of *delta_lambda?*
>

It is not used.  See step 3 of the tutorial where this is explained.

> *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.
>

Some of the wording in step 7 was an artifact of the old tutorial.  That has 
been fixed for the most part now, but I still probably need to do a bit of 
revising.  The concept of "native" and "foreign" lambda still applies in 
understanding BAR, for which you will have to read the actual Bennett paper.

> 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*?
>

One writes the .mdp files, the other writes bash scripts that execute the runs.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================