Ok Justin, So which gmx tool i can use to obtain the angle between two vectors defined by two atom pairs ?
SA sa wrote: > > Hi all > > > > This message is related with my previous message (see below) about the > > calculation of the order value for the DPC alkyl chain in a micelle. So > > if I understand well the previous angel's message, I need to compute the > > theta angle between the 2 vectors defined by the (i-1,i+1) and (i, i+2). > > So for carbon atom C14, I have created an index file with two groups > > defined as following > > > > aC14 | aC16 and aC14 | aC16 with make_ndx_mpi > > > > and used the command g_sgangle_mpi -s run_1.tpr -f *.xtc -b 100000 -e > > 101000 -n index.ndx and choose the C13_C15 and C14_C16 groups. > > Unfortunately i obtain the following error > > > > Group C13_C15 contains the following atoms: > > Atomname 0: C13 > > Atomname 1: C15 > > Atomname 2: C13 > > Atomname 3: C15 > > Atomname 4: C13 > > Atomname 5: C15 > > Atomname 6: C13 > > Atomname 7: C15 > > Atomname 8: C13 > > Atomname 9: C1 > > ... > > > > Group C14_C16 contains the following atoms: > > Atomname 0: C14 > > Atomname 1: C16 > > Atomname 2: C14 > > Atomname 3: C16 > > Atomname 4: C14 > > > > ... > > Atomname 105: C16 > > Atomname 106: C14 > > Atomname 107: C16 > > > > Careful: distance only makes sense in some situations. > > > > Reading frame 0 time 100000.000 > > Back Off! I just backed up sg_angle.xvg to ./#sg_angle.xvg.2# > > > > ------------------------------------------------------- > > Program g_sgangle_mpi, VERSION 4.5.3 > > Source code file: gmx_sgangle.c, line: 127 > > > > Fatal error: > > Something wrong with contents of index file. > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > > > Did I make a error, what is the correct approach. to obtain the angle > > between 2 vectors ? > > > > Per the description in g_sgangle -h, groups can only be two or three atoms > in > size. It seems as if this tool would be very inefficient for any more than > a > few calculations. > > -Justin > > > Thank you in advance > > > > SA > > > > > > > > ------------------------------ > > > > Message: 3 > > Date: Wed, 16 Mar 2011 10:06:44 +0100 > > From: ?ngel Pi?eiro <angel.pine...@usc.es <mailto: > angel.pine...@usc.es>> > > Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 106 > > To: Discussion list for GROMACS users <gmx-users@gromacs.org > > <mailto:gmx-users@gromacs.org>> > > Message-ID: <1300266404.6843.29.camel@arginine> > > Content-Type: text/plain; charset="utf-8" > > > > Then, please, let us know how it works for your systems. The results > for > > my systems were exactly as expected. This allows to evaluate the > order > > of the C-chains regardless their orientation... but I do not know if > > there is a better method to do this. I would be happy to know the > > opinion of anyone else who want to try this or to propose an > alternative > > method. > > > > Cheers, > > > > Ã ngel. > > > > > > > > On Wed, 2011-03-16 at 09:42 +0100, sa wrote: > > > > > Thank you Angel, I will try your suggestion. > > > > > > Cheers > > > > > > SA > > > > > > > > > > > > > > > Hi > > > very recently I faced the same problem with a system that > > > gives micelles > > > of different geometries and, as far as I saw, g_order > > don't do > > > that. > > > Then I decided to compute a kind of local order parameters > > > defined as: > > > > > > S_i=(3 cos(\theta)-1)/2 > > > > > > where theta is the angle between the segments joining the > > > carbon atoms > > > (i-1,i+1) and (i, i+2) in a linear C-chain. Perhaps you > find > > > this > > > reasonable for your analysis... > > > > > > Cheers, > > > > > > Ã ngel. > > > > > > > > > > > > -- > ======================================== > > 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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