On 30/08/2012 10:02 PM, mohan maruthi sena wrote:
Hi,
I am going through it , i will understand it and try to build
the topology.
Fundamentally, harmonic bonds do not serve your purpose, since you need
an interaction that is harmonic in the change in distance, not harmonic
in the distance. Hence your problems with collapsing systems. As such,
you want to look at using distance restraints, rather than [bonds].
Mark
Thank you,
Mohan
On Thu, Aug 30, 2012 at 5:12 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
Hi Mohan,
You need to check chapter 5 of the gromacs manual to understand the
topology format to write. You probably need only to define one atom
type and the C6/C12 parameters could probably even be set to zero. You
need to write an [ atoms ] section, and a [ bonds ] section, according
to the specifications in the manual.
Cheers,
Tsjerk
On Thu, Aug 30, 2012 at 1:32 PM, mohan maruthi sena
<maruthi.s...@gmail.com> wrote:
Hi,
Thanks for a quick reply. In these models we use a distance
cut-off method. Around a particular atom we take a cut-off distance
and connect to all those atoms which fall in the cut-off. I do not
understand, how to connect this atoms with the other atoms falling in
cut-off distance. I have written a script to know the atom numbers
falling with in cut-off distance. I replace bonds section in topology
with these atom connectivity information that i got from script. Is
this method correct or else please suggest me a way.Can you elaborate
on "write a script to generate .top"
Thank you very much,
Mohan
On Thu, Aug 30, 2012 at 3:18 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
Hi Mohan,
Elastic network modeling consists of building a Hessian matrix based
on the distances. That matrix is then diagonalized and the modes are
further investigated. You could write a script to generate a .top file
with a [ bonds ] section, capturing the elastic bonds, and then use
Gromacs to generate the Hessian using the nm integrator. But that
seems more trouble than it's worth. If you think of building such a
model and then simulate it using an md integrator, be warned that
these models are very incomplete and are intended to only capture the
tangents around the starting structure.
Hope it helps,
Tsjerk
On Thu, Aug 30, 2012 at 9:22 AM, mohan maruthi sena
<maruthi.s...@gmail.com> wrote:
Hi all,
Can any one suggest me how to build elastic network model
in gromacs.
Thanks,
Mohan
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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