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

Vitaly V. Chaban vvchaban at gmail.com
Mon Jul 20 17:15:43 CEST 2009

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.

Please also search the list archive for the details (about a year ago, maybe
a bit more).

~ Vitaly

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
!!! Looking for a postdoctoral position !!!

> I would like to extract the interaction energy between a protein and the
> solvent within a certain distance from the protein.
> Is it possible to define a group based on a distance criteria from the
> protein? I have not found any such feature unfortunately. Any other way of
> accomplish this?
> Thank you!
> Matteus Lindgren
> ---------------------------------------------------------
> Matteus Lindgren, graduate student
> Department of Chemistry, Umeå University
> SE-901 87 Umeå, Sweden
> Phone:  +46 (0)90-7865368
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