-- 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
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