Indeed :-)
2011/4/16 João Henriques <[email protected]> > With all due respect, this is clearly a RT*M moment. > > * = F > > Joao Henriques > > On Fri, Apr 15, 2011 at 1:03 PM, Justin A. Lemkul <[email protected]> wrote: > >> >> >> 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 >>> >>> ======================================== >>> -- gmx-users mailing list [email protected] >>> <mailto:[email protected]> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to [email protected] >>> <mailto:[email protected]>. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >> -- >> ======================================== >> >> 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 >> >> ======================================== >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: [email protected] [email protected] website: https://sites.google.com/site/thomasevangelidishomepage/
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