Re: How to fix the Center of mass of protein when performing SMD?

From: 张勇 (
Date: Wed Dec 17 2008 - 22:06:14 CST

Hello, Mr. Harish:
     Thanks a lot for your response!
     In fact, I want to pull a ligand from a protein in order to observe the
conformational change of the protein. So, I don't think I can fix some atoms
because I am not sure that which group of atoms do not change their positions
largely druing ligand unbinding.
     Futhermore, I find that there is translation and roration for the protein
sometimes when I carry out the MD simulation for a protein system in the water
box. can I avoid them by setting some parameters?


>From: "harish vashisth" <>
>To: "张勇" <>
>Subject: Re: namd-l: How to fix the Center of mass of protein when performing
>Date:Tue, 16 Dec 2008 00:21:28 -0500
>Generally in SMD, some atom is already fixed and you are pulling on some
>other atom or group of atoms.....for example, people try to unfold some
>protein by pulling. On the other hand, if you are trying to pull something
>that is non-covalently bound inside the protein like certain hydrophobic
>ligand--then SMD can induce angular velocity as well as translation of
>protein if pulling force or velocity is too large--------in such situation,
>you should try to fix say some terminal alpha-carbons or once in my case, i
>fixed metallic ions like Zn/Cu around which individual subunits of my
>protein were assembled...if you clarify what you are trying to do then i
>might suggest something more appropriate?
>On Mon, Dec 15, 2008 at 10:54 PM, 张勇 <> wrote:
>> Dear all,
>> I have a question when I perform the SMD simulation. It is found that
>> there are
>> the translation and rotation happened to the protein in the water box. so,
>> how to
>> avoid this problem.
>> anyone can help me ?
>> Cheers
>> Clark

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