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

[battistia at libero.it]

in my traj.xtc file there are 1 frame every 10 ps  from 0 ps  to 10000 ps,  
therefore in total 1001 frames.

I tried -x trj.xtc instead -o trj.trr, but mdrun has generated a file trj.xtc.
trr

Many thanks!

Anna


>----Messaggio originale----
>Da: ckutzne at gwdg.de
>Data: 24/07/2013 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  + rerun
>
>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
>
>