[gmx-users] com motion

Mustafa Toprakçý denn22 at excite.com
Thu Apr 10 12:37:01 CEST 2003

Hi Anton,
I almost understood the situation. As you say the binding cavity in my
complex is very narrow. So it needs longer time first. Then I have to
tether the protein not freeze. Increasing the temperature is not much
affective bacause it goes to internal motion. Because there is no 
temperature coupling for comm group option in the code. 
 And I sould define protein as comm_group, this way ligand comm motion
will be free.


 --- On Tue 04/08, Anton Feenstra < feenstra at chem.vu.nl > wrote:
From: Anton Feenstra [mailto: feenstra at chem.vu.nl]
To: gmx-users at gromacs.org
Date: Tue, 08 Apr 2003 18:13:56 +0200
Subject: Re: [gmx-users] com motion

Mustafa Toprakçý wrote:<br>> Hi David,<br>> Yes, this is a complex. In the topology file I have given it as one <br>> molecule under [molecules] header. I have manually placed the ligand<br>> and miniöized it using steep. I made two groups, proteýn and ligand<br>> then heated the temp of the ligand to 1000K while keeping the protein<br>> at 300K. After this I made 400ps. simulation. Here is my mdp file:<br><br>If you freeze the protein, the ligand simply may only have very little<br>space to move in. 400 ps, after all, isn't that long.<br><br>I did simulations of octane in a Cytochrome P450 enzyme, where the<br>binding cavity is many times larger than octane. Still, the mobility<br>of the octane is relatively low. It 'sticks' to certain places for<br>long times (~1n is no exception). My simulations were 10 ns, the<br>protein is ~450 residues.<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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