R: Re: [gmx-users] Rotation Constraints - PMF - external potential

battistia at libero.it battistia at libero.it
Wed Jul 24 17:53:40 CEST 2013

Dear Carsten

could you give me more information about your suggestions?
I tried but probably I did not understand well what you meant.

In order to avoid the rotation of the structure A and of the structure B,  I 
have defined into the index file a group A_B that contains A+B and  I have 
setted in the mdp file the following parameters:

; Orientation restraints: No or Yes
orire                    = yes
; Orientation restraints force constant and tau for time averaging
orire-fc                 = 500
orire-tau                = 100
orire-fitgrp             = A_B
; Output frequency for trace(SD) and S to energy file
nstorireout              = 100

As I have synthetically described in the first post , the structures A and B 
(characterized by a cylindrical shape) are defined by a number of 32  unit-
structures that I call s.

Into the itp is defined the topology for the s structure, and so in order to 
put an orientation restraints between atoms that are not included into the same 
itp file,
 I cannot put into the topology a section like that described into the manual 
4.6.2 pag. 92 namely,  [ orientation_restraints ],  could I ?

Could you tell me How I can fix the orientation of the systems A and B?

I don't understand the manual's explanation about the   orire-fitgrp:
(fit group for orientation restraining. This group of atoms is used to 
determine the rotation
R of the system with respect to the reference orientation. The reference 
orientation is the
starting conformation of the first subsystem. For a protein, backbone is a 
reasonable choice)

How one have to give the group? using an index file or defining the group in 
the topology?

Thank you very much!


>----Messaggio originale----
>Da: ckutzne at gwdg.de
>Data: 23/07/2013 13.09
>A: "battistia at libero.it"<battistia at libero.it>, "Discussion list for GROMACS 
users"<gmx-users at gromacs.org>
>Ogg: Re: [gmx-users] Rotation Constraints - PMF
>Hi Anna,
>please have a look at the Enforced Rotation Section in the Gromacs 4.6 
>You can restrain the angle of rotation about an axis by setting the rotation 
>to zero. There is also a 4.5 add-on available with rotational restraints in
>the Gromacs git repository (branch "rotation"). For more info you may want to
>look at this page:
>  Carsten
>On Jul 23, 2013, at 12:18 PM, battistia at libero.it wrote:
>> Dear user and expert,
>> I'd like ask you a suggestion about a problem that I will try present you 
>> I have got a structure "s" and I have generated the topolgy file itp for it.
A number of separate "s" in turn generate a complex structure A, that is 
characterized by a cylindrical shape.
>> Now, I constructed a system with two cylindrical structures, A and B (in 
total made by 64 "s" structures), and I'd like make an Umbrella Sampling 
calculation in order to study the PMF varying the distance between A and B.
>> My problem is that I'd like fix the orientation of the axis of each 
structure A and B long the z axis, during the dynamics.
>> So I need to put a force into the system or a constrain, such that when the 
axis of A or B rotates respect to z axis, the force puts back the axis of the 
structure in the z direction.
>> It this possible?  If it is so, could you tell me how to do that?
>> Than you very much,
>> Anna
>> -- 
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>Dr. Carsten Kutzner
>Max Planck Institute for Biophysical Chemistry
>Theoretical and Computational Biophysics
>Am Fassberg 11, 37077 Goettingen, Germany
>Tel. +49-551-2012313, Fax: +49-551-2012302

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