On 7/5/15 12:56 AM, Christopher Neale wrote:
Dear Justin:
Thank you for your help. I am glad to see that I was not way out to lunch in my
interpretation of multiplicity and proper dihedral angles.
First, the out-of-plane motions are not minor. Even just in EM, the dihedral
angles along the
Dear Justin:
here is a topology followed by initial coordinates (in which the rings of both
Phe are planar, straight out of molefacture/pdb2gmx). Run this in EM or MD and
the SC ring of Phe #1 will distort. However, replace 0 15.1669998 2 by 180
15.1669998 2 and everything is groovy.
On 7/5/15 9:10 AM, Christopher Neale wrote:
Dear Justin:
here is a topology followed by initial coordinates (in which the rings of both Phe are planar,
straight out of molefacture/pdb2gmx). Run this in EM or MD and the SC ring of Phe #1 will distort.
However, replace 0 15.1669998 2 by 180
I see, thank you Justin. I guess that even though I did read the equation,
which is:
K(1 + cos(n*phi - phi_s)
I was actually thinking:
K(1 + cos(n* [ phi - phi_s ] )
so everything is as it should be.
Thanks for all your help,
Chris.
From:
Dear Gromacs users:
I have been working on creating a topology for an exotic molecule. It contains
aromatic rings and my parameters always seemed to allow the rings to buckle and
become non-planer, much like a glucose ring would (though a little less
extensively). However, I have managed to
Verified same behaviour in gromacs 4.6.7 and 5.0.5 for the Phe-Phe system.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Christopher
Neale chris.ne...@alum.utoronto.ca
Sent: 05 July
Dear Justin:
Thank you for your help. I am glad to see that I was not way out to lunch in my
interpretation of multiplicity and proper dihedral angles.
First, the out-of-plane motions are not minor. Even just in EM, the dihedral
angles along the main ring convert from near 0 deg to about 50
On 7/4/15 3:32 AM, Christopher Neale wrote:
Dear Gromacs users:
I have been working on creating a topology for an exotic molecule. It
contains aromatic rings and my parameters always seemed to allow the rings to
buckle and become non-planer, much like a glucose ring would (though a little
