# [gmx-users] harmonic angle potential

David spoel at xray.bmc.uu.se
Mon Sep 20 19:43:53 CEST 2004

```On Mon, 2004-09-20 at 18:47, Grace Brannigan wrote:
> >In calculating the potential, gromacs takes the difference betwen the
> >actual angle and the reference angle value in radians,  not in degrees.
> >Maybe there is the difference.
>
> >Marcos.
>
> Yes, that occurred to me too (is it spelled out in the manual?) but that's
> not the problem. I'm working in radians.
>
> This is just sort of mystifying. Again, my program and g_angle agree on
> the average angle (~166degrees).
> If you plug that angle into
> V = K/2 * (166 - 180)^2, where
> K = 5 * (6 angles) * (pi rad/ 180 deg)^2

do you really want angles of 180? The force has a singularity at 180,
which means its direction is undefined.
>
> you get V = 0.9
> but Gromacs tells me Vbond = 1.1
>
> (reduced units)
> Could it have anything to do with my constraints on the bond length?
>
> Here are my .top and .gro files:
>
> /*******************************************************************/
> conf.gro:
>
> Two Chains
>    10
>     1LIPG    PG    1   0.085   2.523   3.385 -2.6878  7.6361  9.8849
>     1LIPG    SG    2   0.786   3.236   3.395  4.5329  8.0346 -1.3729
>     1LIPG     G    3   1.351   4.046   3.258 -2.6881 -4.2935  7.4651
>     1LIPG     G    4   2.181   4.593   3.152 13.5878  3.3816  3.9792
>     1LIPG     G    5   3.006   5.130   2.963  4.6537 -3.6607  4.5302
>     2LIPG    PG    6   3.619   6.709   3.556 -8.2967  4.0282 -0.0105
>     2LIPG    SG    7   2.873   6.049   3.548  0.6960 -8.3603  2.5179
>     2LIPG     G    8   2.155   5.375   3.707  6.6096  5.3158 -1.0018
>     2LIPG     G    9   1.260   4.941   3.600 -2.3264  6.9400  1.5371
>     2LIPG     G   10   0.472   4.361   3.387 -4.9276 -6.0048  0.1470
>   20.00000  20.00000  20.00000
>
> /********************************************************/
> topol.top
>
> ;
> ;	File 'topol.top' was generated
> ;	By user: grace (508)
> ;	On host: centaur
> ;	At date: Fri Sep 17 13:47:11 2004
> ;
> ;	This is your topology file
> ;	Two Chains
> ;
> ; Include forcefield parameters
> #include "ffgmx.itp"
>
> [ moleculetype ]
> ; Name            nrexcl
> Protein              5
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
>    chargeB      massB
>      1         PG      1   LIPG     PG      1          0     	1   ; qtot 0
>      2         SG      1   LIPG     SG      1          0     	1   ; qtot 0
>      3          G      1   LIPG      G      1          0     	1   ; qtot 0
>      4          G      1   LIPG      G      1          0        1   ; qtot 0
>      5          G      1   LIPG      G      1          0        1   ; qtot 0
>      6         PG      2   LIPG     PG      1          0     	1   ; qtot 0
>      7         SG      2   LIPG     SG      1          0     	1   ; qtot 0
>      8          G      2   LIPG      G      1          0     	1   ; qtot 0
>      9          G      2   LIPG      G      1          0        1   ; qtot 0
>     10          G      2   LIPG      G      1          0        1   ; qtot 0
>
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     1    1	100000
>     2     3     1    1	100000
>     3     4     1    1  100000
>     4     5     1    1  100000
>     6     7     1    1  100000
>     7     8     1    1  100000
>     8     9     1    1  100000
>     9    10     1    1  100000
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2
>   c3
>     1     2     3     1    180	5
>     2     3     4     1    180  5
>     3     4     5     1    180	5
>     6     7     8     1    180  5
>     7     8     9     1    180  5
>     8     9    10     1    180  5
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> Monte Carlo Simulation of Lipids
>
> [ molecules ]
> ; Compound        #mols
> Protein             1
>
> On Monday, September 20, 2004, at 09:23 AM, gmx-users-request at gromacs.org
> wrote:
>
> Message: 1
> Date: Mon, 20 Sep 2004 08:38:23 -0300
> From: Marcos Villarreal <arloa at dqb.fcq.unc.edu.ar>
> Subject: Re: [gmx-users] harmonic angle potential
> To: <gmx-users at gromacs.org>
> Message-ID: <200409200838.23216.arloa at dqb.fcq.unc.edu.ar>
> Content-Type: text/plain;  charset="iso-8859-1"
>
> On Sunday 19 September 2004 17:56, Grace Brannigan wrote:
> Hi,
>
> I'm trying to use Gromacs for simulations of short Lennard-Jones type
> chains. I already have home-made MC code. When I compare Gromacs'
> assesment of the potential energy with that of my own code, for one
> configuration of two 5mers, the values of the bond angle potential
> disagree.
>
> I was looking through the Gromacs source code to make sure I had
> consistent potentials, and I noticed that in the function "angles", the
> sum goes over the number of bonds. I guess this makes sense for the
> forces, but it seems weird for the potential; it seems like it should go
> over the number of angles (i.e., num_bonds - 1). Is it possible that one
> angle is being counted twice? Maybe I'm misunderstanding how this function
> works...
>
> Has anybody else had this problem? I'm hoping there's a simple thing I'm
> doing wrong but I haven't found it in my own code.
>
> -Grace
>
> In calculating the potential, gromacs takes the difference betwen the actual
> angle and the reference angle value in radians,  not in degrees. Maybe there
> is the difference.
>
> Marcos.
>
>
>
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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