Dear all,
I would like to calculate how three dihedrals in my protein are evolving during the simulation time, but I don't understand which is the correct command to do. In particular, I would like to know: - what is the value of a specified dihedral (in degrees) - if this value changes during the time of simulation - what is the probability distribution of this angle. In order to answer to these questions, first, I created an index file with make_ndx, in which I set the three dihedrals of my interest by selecting the atoms of the dihedrals. Then I used the command G_ANGLE -F PROT.XTC -N PROT.NDX -TYPE DIHEDRAL -OD PROT_DIHDIST.XVG -OV PROT_DIHAVER.XVG -OT PROT_DIHTRANS4.XVG -OH PROT_TRHISTO.XVG -OC PROT_DIHCORR.XVG Then, I had a look at the results, but I really don't understand them...in any case, they are not what I was expected to find. I was expecting to find somewhere a graph in which on the X axis I have the time, and on the Y axis the oscillation of the angle around an average value, expressed in degrees. Moreover, I was expecting to create a graph with a Gaussian-like shape, indicating what is the most frequent value assumed by this dihedral during my simulation. None of the resulting graphs appear like that. Finally, I used g_sgangle in order to understand if, during the simulation, the distance and the angle between two aromatic residues varies during the time. In the case of the angle variation, the values on the Y axis of the resulting graph vary in all cases between -1 and 1. On the Y axis the legend states "Angle(degrees)" but it seems very strange to me that all my dihedrals are set on this very narrow range of values. Could you please help me? Many thanks and best regards Anna -- ______________________________________________ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni Paolo II, 132 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 Web page: http://www.unisa.it/docenti/annamarabotti/index "Indifference is the eighth deadly sin" (don Andrea Gallo) -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
