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

battistia at libero.it battistia at libero.it
Fri Jul 26 11:17:24 CEST 2013

Dear Carsten,

thank you very much for your support!

At the beginning I did not follow your indications correctly but now, using 
the orientation restraints and the indication in the paper

Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic 
Simulations with GROMACS
Kutzner C, Czub J, and Grubmüller H
J. Chem Theory and Comp. 7: 1381-1393 (2011)

I believe I made it.  

Just few questions to be sure, if I can:
how the vector v ( namely the axis rotation defined in the paper) is defined?
giving a (large) number of atoms as rotation group, I suppose that the vector 
u identify the center of mass of the group, and in this point the v vector 
defines the direction that one gives with the  rot_vec entry in mdp file. Is it 

I suppose that in order to just keep the direction of the v axis during the 
dynamics, my choise have to be rote_rate=0, is it correct?

Thanks again,


>----Messaggio originale----
>Da: ckutzne at gwdg.de
>Data: 25/07/2013 11.12
>A: "battistia at libero.it"<battistia at libero.it>
>Cc: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
>Ogg: Re: [gmx-users] Rotation Constraints - PMF - external potential
>On Jul 24, 2013, at 5:53 PM, battistia at libero.it wrote:
>> Dear Carsten
>> could you give me more information about your suggestions?
>> I tried but probably I did not understand well what you meant.
>Hi Anna,
>I suggested to use the enforced rotation module of Gromacs 4.6
>to restrain the orientation of your molecule(s). If you want to
>use the orientation restraints module instead, I am afraid I
>can not help you much with that, maybe someone else on this list? 
>> In order to avoid the rotation of the structure A and of the structure B,  
>> 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 
>> (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 
>> put an orientation restraints between atoms that are not included into the 
>> itp file,
>> I cannot put into the topology a section like that described into the 
>> 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?
>Using the enforced rotation module you would choose an index group and an 
>for each group that you want to fix the orientation, set the rotation angle 
>zero and choose an appropriate force constant. Appropriate potential 
>would be the pivot-free ones if I understand your setting correctly.
>> 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 
>> the topology?
>This is the "orire-fitgrp = A_B" mdp file setting that you made.
>  Carsten
>>> ----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 
>> 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 
>> manual.
>>> You can restrain the angle of rotation about an axis by setting the 
>> rate
>>> to zero. There is also a 4.5 add-on available with rotational restraints 
>>> the Gromacs git repository (branch "rotation"). For more info you may want 
>>> look at this page:
>>> http://www.mpibpc.mpg.de/grubmueller/rotation
>>> Best,
>>> 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 
>> schematically.
>>>> I have got a structure "s" and I have generated the topolgy file itp for 
>> 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 
>> axis of A or B rotates respect to z axis, the force puts back the axis of 
>> 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
>>> http://www.mpibpc.mpg.de/grubmueller/kutzner
>>> http://www.mpibpc.mpg.de/grubmueller/sppexa
>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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