[gmx-users] [ angle_restraints_z ]

[Berk Hess]

Hi,

I think you do not want to distinguish between parallel and anti-parallel.
But in your case using multiplicity 1 or 2 does not matter much.
1000 kJ/mol makes the orientation extremely rigid, but I don't know
how rigid you want to have it.
100 kJ/mol is probably a more reasonable order of magnitude.

Berk


Date: Tue, 20 May 2008 16:39:22 +0430
From: terry.b.nelson at gmail.com
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] [ angle_restraints_z ]

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.



Express yourself instantly with MSN Messenger! MSN Messenger

_______________________________________________

gmx-users mailing list    gmx-users at gromacs.org

http://www.gromacs.org/mailman/listinfo/gmx-users

Please search the archive at http://www.gromacs.org/search before posting!

Please don't post (un)subscribe requests to the list. Use the

www interface or send it to gmx-users-request at gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
Cheers,
Terry

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080520/f2e576b4/attachment.html>