[gmx-users] Doubt about -linfix, -linacc, -radfix, -radacc, -radcon

[Bert de Groot]

-- Anirban Ghosh wrote:
> Hi All,
> I want to perform ED sampling along first principle
> component in GROMACS. For that I am using the make_edi
> command to generate the required .edi file to be
> subsequently used in mdrun. But I cannot understand
> the meaning of the algorithms -linfix, -linacc,
> -radfix, -radacc and -radcon. What does fixed step
> linear expansion and fixed step radius expansion
> specify here? 

as make_edi -h says:

-linfix: perform fixed-step linear expansion along selected eigenvectors.

-linacc: perform acceptance linear expansion along selected eigenvectors.
(steps in the desired directions will be accepted, others will be rejected).

-radfix: perform fixed-step radius expansion along selected eigenvectors.

-radacc: perform acceptance radius expansion along selected eigenvectors.
(steps in the desired direction will be accepted, others will be rejected).
Note: by default the starting MD structure will be taken as origin of the
first expansion cycle for radius expansion. If -ori is specified, you will be
able to read in a structure file that defines an external origin.

-radcon: perform acceptance radius contraction along selected eigenvectors
towards a target structure specified with -tar.NOTE: each eigenvector can be
selected only once.




If you only want to constrain the position along the first eigenvector, linfix
and linacc are probably the most meaningful options. With -linfix, you impose a
predefined fixed stepsize per MD step (specified with -linstep). In that case,
you could use something like:

make_edi -f -s -n -linfix "1" -linstep "-0.0001"

Using -linacc, you don't specify a fixed stepsize, but let the MD decide the
stepsize. The only constraint that is applied in that case that (if you choose
the forward direction as target) that backward steps are prohibited. In that
case, use something like:

make_edi -f -s -n -linfix "1" -accdir "1.0"

(here the positive sign of the "accdir" argument specifies the direction).


> How should I give the string options for
> these algorithms

see example above

> and which one should I use? 

that we cannot answer for you. It all depends on the question you're trying to
address with these simulations.



Bert

______________________________________
Bert de Groot, PhD

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302
http://www.mpibpc.mpg.de/groups/de_groot