[gmx-users] [ angle_restraints_z ]

[Terry Nelson]

Dear Berk,

Thanks for the reply.

Yes. In fact I made the choice of multiplicity=1 based on  the explanation
in eq. 4.68:

"A multiplicity (n) of 2 is useful when you do not want to distinguish
between parallel and anti-parallel vectors."

Since my molecule is slightly polar and it may matter whether it is at 0 or
180 orientation, I decided to use multiplicity of 1.

Please correct me if I am missing something.

If multiplicity 1 is OK do you still think that the force constant 1000
kJ/mo is too large in my system?


On Mon, May 19, 2008 at 5:34 PM, Berk Hess <gmx3 at hotmail.com> wrote:

>
>
>
>
> ------------------------------
> Date: Sat, 17 May 2008 08:48:28 +0330
> From: terry.b.nelson at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] [ angle_restraints_z ]
>
>
> Hi all,
>
> There are atoms (a1 and a2) in my small molecule coordinate file  that have
> the same z component:
> a1: atom#22 (x1,y1,60.231)
> a2: atom#45 (x2,y2,60.231)If I use these lines only
>
> Therefore the vector a1-a2 makes theta=90o with the z-axis.  in my previous
> MD runs the a1-a2 were flexible (theta was observed in the range of 30-120
> degrees).
> To restrain a1-a2 at this orientation throughout my MD calculations I
> included these lines to my starting topology:
>
> ; Restrain the molecules wrt z-axis...
> [ angle_restraints_z ]
> ; #1 #2  type    theta0(degrees)  k_c(kJ mpl^(-1))  multiplicity
> 22  45     1       90     1000    1
>
> Would someone comment on:
> - Is this is all I need to do to restrain a1-12 wrt z-axis?
> - Are the above parameters (theta/K/multiplicity) reasonable/correct?
> - with this I should expect a1 and a2 stay in xy-plane (with their z
> component equal at each frame) during minimization, equilibration and
> production?
>
> Thanks.
>
> --
> Cheers,
> Terry
>
>
> Did you look at formula 4.68 in the manual?
> What you want is a minimum at 90 and maxima at 0 and 180.
> So you need to use a multiplicity of 2.
> 1000 as a force constant seems too large to me, this means that
> the 0/180 degrees is penalized by 2000 kJ/mol.
>
> Berk.
>
>
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-- 
Cheers,
Terry
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