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<p><a name="stopSpelling"></a>
<br></p>
<p>Hi Berk, </p>
<p><br></p>
<p>BH> I think this would require complete rewriting of all the (required) analysis tools.</p>
<p>BH> Currently all tools assume that you have a static, fixed length list of atoms.</p>
<p>BH> You can not "simply" make this list dynamic.</p>
<p>BH> It would be very useful to have such a functionality, but one would like to</p>
<p>BH> have this implemented at a higher level.</p>
<p><br></p>
<p>You are absolutely true here. It is more convenient to firstly treat a trajectory and then apply analysis tools.</p>
<p><br></p>
<p>Does GROMACS team plan to add such functionality in the nearest future? No matter in what way it will be implemented.</p>
<p><br></p>
<p><br></p>
<p>BH> There is currently a (limited) similar functionality via trjorder.</p>
<p>BH> trjorder can order atoms based on distance. </p>
<p>BH> This effectively makes</p>
<p>BH> you index group dynamic, but the size is fixed.</p>
<p>BH> (although not for g_velacc, which needs time correlation, but there</p>
<p>BH> it becomes difficult to define what you want to calculate exactly</p>
<p>BH> with dynamic groups)</p>
<p><br></p>
<p>Why not? One can want to calculate a diffusion constant in the solvation shell of an ion,</p>
<p>inside and outside any confinements, like zeolites, nanotubes, etc. To do this, we need molecules which are</p>
<p>currently located there. If the molecule goes out, it should be simply removed to no longer take</p>
<p>part in the calculation. When the other molecule comes to the area of interest the calculation (for example, VACF)</p>
<p>should just start for it from the beginning.</p>
<p><br></p>
<p>The 'trjorder' as I understand can only resort the trajectory file to have the needed particles at the beginning. The problem</p>
<p>is that when one particle replaces another in the area of interest the analysis tool "thinks" it is the same molecule. I don't know </p>
<p>if it can lead to significant inaccuracy. Maybe not.</p>
<p><br></p>
<p><br></p>
<p>Best,</p>
<p>Vitaly</p>
<p><br></p>
<p><br></p>
<p><br></p>
<p>>> Date: Wed, 25 Jun 2008 15:35:46 +0300</p>
<p>>> To: gmx-users@gromacs.org</p>
<p>>> From: vvchaban@gmail.com</p>
<p>>> Subject: [gmx-users] Dynamical atom groups in 'index.ndx'</p>
<p>>> </p>
<p>>> Dear Colleagues,</p>
<p>>> </p>
<p>>> Did not anybody try to implement a possibility to use a changeable</p>
<p>>> 'index.ndx' when analyzing a trajectory (g_rdf, g_velacc, etc)?</p>
<p>>> I mean that the atoms numbers in 'index.ndx' could change,</p>
<p>>> being different for different frames.</p>
<p>>> </p>
<p>>> This trick can be used for evaluating properties of molecules located</p>
<p>>> in the definite area at the current moment. Now we can control the</p>
<p>>> particles but how can we check if these particles are still located</p>
<p>>> in the same area where they were before they started to move?</p>
<p>>> </p>
<p>>> Of course, one is able to do it by visualizing trajectory and then</p>
<p>>> edit the particles number by hand but it is quite unlucky solution, as</p>
<p>>> for me.</p>
<p>>> </p>
<p>>> Probably I'll try to make something like it if time permits.</p>
<p>>> If somebody has got any considerations on this topic, please let me know.</p>
<p><br></p>
<p><span class=rvts9><br></span></p>
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