[gmx-users] Rotation Constraints - PMF - external potential

[Carsten Kutzner]

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,  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?
Using the enforced rotation module you would choose an index group and an axis 
for each group that you want to fix the orientation, set the rotation angle to 
zero and choose an appropriate force constant. Appropriate potential functions
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 in 
> the topology?
This is the "orire-fitgrp = A_B" mdp file setting that you made.

Best,
  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 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 
> manual.
>> You can restrain the angle of rotation about an axis by setting the rotation 
> rate
>> 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:
>> 
>> 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 you 
> schematically.
>>> 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
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at http://www.gromacs.
> org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the 
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> 
>> --
>> 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
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa