Thank you a lot justin for offering me help. I am interested to use g_sham ..( And if the other command give me my output, I am also interested to know the other way )
I was confuse with the input that I have to give with g_sham. I proceed the following command g_energy is used to get potential ( pot.xvg ) g_rmsdist is used to get rmsdist.xvg What sis next ???????? My confusion start with the input to give the g_sas ... As you mention The input file is simple. It can be one of two forms: time x y or simply: x y But what is flag for command input and out put. I also read g_sham -h and manual. Please accept my apology. I will be grateful to you for help ... With best regards, Rama david. On Thu, Apr 4, 2013 at 6:24 PM, Justin Lemkul <[email protected]> wrote: > > > On 4/4/13 5:50 AM, rama david wrote: > >> Thank you justin, >> >> I read the articles, archive and also g_sham -h, >> >> As I mentioned in previous mail, I simulated four random coil peptide , >> they started to form >> Beta sheet structure after 20 ns ..( simulation time 100ns ) >> >> My interest is how to draw the Free energy diagram for Potential energy >> and >> Structures...(eg. RMSD, Gyrate, different cluster , >> with different structure at particular time ) . >> >> >> Would you please tell me how to do it in gromacs with command line and >> needed input. >> >> > The command issued depends on what you're doing. If you want help in that > respect, post the command that you're using and seek specific assistance. > There are too many permutations of possibly "correct" ways of doing > something for me to offer you a guess. > > The input file is simple. It can be one of two forms: > > time x y > > or simply: > > x y > > In the latter case, use the -notime option of g_sham. > > Choose your favorite parsing language to extract values from the output of > g_energy, g_rms, etc to create the combined file. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
