R: Re: [gmx-users] Rotation Constraints - PMF + rerun

battistia at libero.it battistia at libero.it
Wed Jul 24 12:30:59 CEST 2013

Dear Carsten,

Thank you very much for your very useful help!
I'm making some tries to test the orire options that probably will solve my 

In order to do not waste resource, I thought using the rerun option of mdrun I 
can use the trajectories generated before, where my mistake was to allow the 
rotation of my structure. 
So I generated a new topol.tpr file changing the orire options in the mdp and 
I made:

1. mdrun -rerun ../traj.xtc -s topol.tpr -o trj.trr
2. trjcat -f traj.trr -o trajout.xtc

but in the trajout.xtc there is only one point as I can check for example 
3. g_gyrate -f trajout.xtc -s topol.tpr -n index.ndx

Could you confirm me that it is not possible follow this idea?
In fact I suppose that this method it is not applicable;  but  it is necessary 
to generate a new trajectory, because the angular restraints modify completely 
the trajectory.

Or, just to be sure,  did I not made the things in the right way? 

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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