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: [EMAIL PROTECTED]
To: gmx-users@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 <[EMAIL PROTECTED]> wrote:
Date: Sat, 17 May 2008 08:48:28 +0330
From: [EMAIL PROTECTED]
To: gmx-users@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@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 [EMAIL PROTECTED]
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/
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
