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 ? Thank you in advance SA > ------------------------------ > > Message: 3 > Date: Wed, 16 Mar 2011 10:06:44 +0100 > From: ?ngel Pi?eiro <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> > 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. > > > > >
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