[gmx-users] Re: Groups based on distance criteria

[Vitaly V. Chaban]

Hi Vasya,

Glad to hear from you here! I did not work with -rerun yet - it's a useful
option I see now.

On Mon, Jul 20, 2009 at 5:39 PM, Vasilii Artyukhov <darth.vasya at gmail.com>wrote:

>
>
> 2009/7/20 Vitaly V. Chaban <vvchaban at gmail.com>
>
>> Hi Matteus,
>>
>> Yeah, dynamic groups would be a powerfull tool. But such mechanism is
>> still under development if I am not out-of-time.
>>
>> The possible way to proceed with such kind of research (as Berk advised me
>> here long ago) is to sort the trajectory (trjorder) based on the distance
>> criteria. Then you can make an index file with N first numbers (which are
>> close to the protein) and use g_energy with this group and protein group. It
>> seems for your task this way is a perfect solution.
>>
>
> Or better yet, use mdrun -rerun on your reordered trajectory and _then_ use
> g_energy? This way you would be free of any problems with molecules going in
> and out of your solvation shell, if I am getting things right.
>



-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua,vvchaban at gmail.com
skype: vvchaban, mob.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===================================
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