Dear SA To be honest I am not sure this can be done by using g_angle, I used my own code for this calculation. I could send it to you if you send me a message off the list... but I would prefer to talk with a non-anonymous.
Cheers, Ángel. On Wed, 2011-03-16 at 15:58 +0100, 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 ? > > Thank you in advance > > SA > > > > > ------------------------------ > > Message: 3 > Date: Wed, 16 Mar 2011 10:06:44 +0100 > From: ?ngel Pi?eiro <[email protected]> > Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue > 106 > To: Discussion list for GROMACS users <[email protected]> > 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. > > > > > > > > -- > 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
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