ram bio wrote:
Thanks for the comments and info, but is there any way to take a
particular frame for eg. the last frame of CG simulation and extend
the run into all-atom simulation further ...
There are tools out there to reconstruct an atomistic representation of a CG
system (see link below, and poke around Google for a few minutes). If you want
to start a whole new simulation, that is certainly possible after (of course)
regenerating your system topology to match the new system.
-Justin
On Tue, May 25, 2010 at 5:32 PM, Jared James Thompson
<thomp...@purdue.edu> wrote:
I agree with Justin on this one. Simulations run using CG that is not optimized
for reconstruction may not actually reflect the type of interactions you are
looking for. The current result of this simulation may not directly correspond
to a full atomistic result, so even if a reconstruction were performed you would
most likely NOT be able to draw conclusions from it.
Otherwise, everyone would run really fast simulations in CG, then reconstruct
their systems afterward. :)
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
ram bio wrote:
thanks,
but i am using gromacs version 4.0.07
I think the general consensus thus far is you won't be able to do what you
want
without significant effort to reconstruct your system, and perhaps then you
should question whether any tools that seek to build optimal hydrogens from
CG
structures are going to bias the result. Would those hydrogen bonds have
actually formed in an AA simulation? Hard to tell. If you want to analyze
hydrogen bonds, CG approximations are not probably sufficient.
This is a good exercise in planning your analysis before conducting your
simulation. You can probably estimate some sort of polar contacts from your
CG
representation, but not hydrogen bonds.
-Justin
On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi
<egv...@gmail.com> wrote:
Hi,
To change between representations (atomistic <--> coarse grained), if you
are using the MARTINI FF, you can use the modified version of Gromacs
3.3,
check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt
If you don't want to switch to full-atomistic representation, check which
CG
atom types are able to form hydrogen bonds and look for interactions
between
them. Obviously, this will be an approximation.
Esteban G. Vega-Hissi
UNSL
San Luis
Argentina
--
On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson
<thomp...@purdue.edu>
wrote:
There are programs around for reconstruction of full-atomistic
representations
from coarse-grained representations, however. I don't know if there are
any
available for the GROMACS architecture.
Quoting Nuno Azoia <naz...@det.uminho.pt>:
Hi there!
I never worked with coarse grain simulations, but if you used a coarse
grain methodology you didn't include all the atoms, so you didn't
included hydrogens. So now you can not see them, of course. They are
not
there.
If you need to "know the hydrogen bond interactions" you need to do
some
"all atoms" simulation, not coarse grain.
Nuno Azoia
On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote:
Dear Gromacs Users,
I have done coarse grain simulation for 2 peptides in bilayer for
1000ns, and now i would like to know the hydrogen bond interactions
between these two peptides. Please let me know how to do this, i can
visualize the trajectory in VMD, but unable to calculate the hydrogen
bonding distance and the hydrogen bonds existing..
Thanks
Ram
--
Nuno Gonçalo Azoia Lopes
Laboratório de Investigação em Acabamento
Departamento de Engenharia Têxtil
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Portugal
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========================================
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
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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
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