Monisha Hajra wrote:
Hi Justin,
I am trying to follow the protocol only.
More than the Gromacs own website, I find
http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production link is
more useful.
Clearly. This is one of many tutorials linked from the site I posted before.
However, I am stuck at one step which is mentioned :
http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html
I am not able to understand how to create traj.trr, traj.xtc and
ener.edr file. Remaining all is self explained in the previous link.
These files are output by mdrun, i.e. actually running a simulation.
-Justin
Really appreciate any help.
Regards
Monisha
On Fri, Apr 15, 2011 at 8:06 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Monisha Hajra wrote:
Hi User,
I have a protein which I have modeled by Homology modelling. The
modeled protein has no water molecules in its surrounding
environment.
How should I add water molecule so that I can start the
simulation process?
Please refer to the abundant tutorial material on the website:
http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
-Justin
Regards
Monisha
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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