[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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