[gmx-users] com motion

Mustafa Toprakçý denn22 at excite.com
Tue Apr 15 11:30:01 CEST 2003

Thanks Anton and everybody for all.


 --- On Mon 04/14, Anton Feenstra < feenstra at chem.vu.nl > wrote:
From: Anton Feenstra [mailto: feenstra at chem.vu.nl]
To: gmx-users at gromacs.org
Date: Mon, 14 Apr 2003 08:38:37 +0200
Subject: Re: [gmx-users] com motion

Mustafa Toprakçý wrote:<br>> Hi Anton,<br>> I almost understood the situation. As you say the binding cavity in my<br>> complex is very narrow. So it needs longer time first. Then I have to<br>> tether the protein not freeze. Increasing the temperature is not much<br>> affective bacause it goes to internal motion. Because there is no <br>> temperature coupling for comm group option in the code. <br>>  And I sould define protein as comm_group, this way ligand comm motion<br>> will be free.<br><br>That sounds about right. Still, even with the protein 'tethered' (ie,<br>with position restraints) and not frozen, your ligand might be very<br>tightly bound and have only very little mobility. You could consider to<br>use the 'pull' option to pull your ligand out of the binding cavity,<br>if you want to get an idea of the barriers and/or path involved.<br><br><br>-- <br>Groetjes,<br><br>Anton<br>  _____________ _______________________________________________________<br>|             
 |                                                       |<br>|  _   _  ___,| K. Anton Feenstra                                     |<br>| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |<br>|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |<br>| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |<br>|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |<br>|             | "If You See Me Getting High, Knock Me Down"           |<br>|             | (Red Hot Chili Peppers)                               |<br>|_____________|_______________________________________________________|<br><br><br>_______________________________________________<br>gmx-users mailing list<br>gmx-users at gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request at gromacs.org.<br>

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