Sanku M wrote:
Hi,
I am running a simulation where I have 100 chains of molecule in a box
. I am trying to calculate the distance between two particular atoms (
present in each molecule) averaged over all the chains of molecule. i.e
If I have atom C1 and C2 in each of the molecule-chain, I want to
calculate the distance between C1 and C2 atom in each chain and average
over them.
I was trying to use gromacs 4.0.7 g_dist tool . For that, I first
created two index-groups of all C1 and C2 . But. I realized that
g_dist will give me actually the distance between center of mass of all
C1 and center of mass of all C2 which is NOT certainly I was looking for.
So, I was wondering whether there is any other tool which can split the
entire index group by deviding it by total number of chains and then
calculate each individual distances for each chain and then do an
average over them.
You can split the group within make_ndx. There are various splitting keywords
(like 'splitat' or 'splitres') that can divide up your index groups. Then
script the 100 calls to g_dist.
-Justin
An analogous tool exists for g_gyrate where where one can use -nmol
option to split the entire index accordingly and calculate the radius of
gyration averaged over all the molecules. I was looking for something
for calculating distances between two atoms for many chain molecules.
I looked at the mailing list but I could not find any solutions for
these. Any help will be appreciated.
Sanku
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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