[gmx-users] Rotation Constraints - PMF + rerun

[Carsten Kutzner]

On Jul 24, 2013, at 12:30 PM, battistia at libero.it wrote:

> 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 
> problem.
> 
> 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 
Hm, I am not sure, maybe you need to use -x trj.xtc instead of -o trj.trr
to trigger output of all .xtc frames. How many frames are in ../traj.xtc?

Carsten

> with: 
> 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!
> 
> Anna
> 
> 
>> ----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
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
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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
>> 
>> 
> 
> 
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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