[gmx-users] Re: RE:Com Pulling

[lloyd riggs]

Dear Chris Neale,

I wanted to generate directed initial velocities for two seperate multiprotein complexes, but just so they start to move through the void towards each other.  The only way I found to do this was to use the COM pulling, but then it is a "biasing" force applied across the entire MD sim.  Basically I want to minimize the bias, if possible, but was asking if there is a way to apply an initial directional (instead of the random)velocity/force without a constant applied force like the COM pulling.  If it is the only way, I can do the calculations with COM pulling and correct for my applied force, but was hopeing there was another way I did not find which would be more simple, or just something I missed.

In Solvent, the complexes move (albeit random), and one only need to let it run long enough, or apply walls, but in vacuo if there is no applied force, the atoms within the complexes move around, but not the molecules as a whole, they just sit waving at each other across a void.

As they are in a void however, an initial force would not dissapate until the two larger molecules connected, so I am woundering if there would even be a difference between what I wanted, and general COM pulling.

reguardless,thanks for any reply.

Sincerely,

Stephan Watkins

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Message: 4
Date: Wed, 15 Dec 2010 11:04:12 -0500
From: chris.neale at utoronto.ca
Subject: [gmx-users] Com Pulling
To: gmx-users at gromacs.org
Message-ID: <20101215110412.imqto29twk8ksk80 at webmail.utoronto.ca>
Content-Type: text/plain;    charset=ISO-8859-1;    DelSp="Yes";
    format="flowed"

If I understand correctly, you want to apply a biasing force and you  
also want to have an "unbiased" simulation. These two things are not  
possible in combination. There are a variety of techniques available  
that will give you particular information. For example, you can  
extract the unbiased PMF from umbrella sampling (but not the unbiased  
dynamics); you can also study some things with reaction path sampling  
or slow AFM pulling, but for us to help you you will need to describe  
what you want to do.

Chris.

-- original message --

Dear All,

I was setting up things to use COM pulling for a multiprotein complex.  
  My question after going through the gromacs documentation(online) is:

Is there a way to limit either the time or distance two groups are  
pulled towards each other(reguarding only the applied force), as I  
could not find anything.  Basically, if I run something in vacuo, the  
groups (proteins) do not move globally even when constraints, etc are  
set to none.  To measure any Gibbs , delta H etc...I need the groups  
too move towards each other and form the interactions I am measuring,  
but do not want the pull force to interfear with overall calculations.

My thoughts were to do a very short run, and then either remove the  
pull force, etc from the .mdp file, and use a checkpoint to re-start  
it, but do not know if this would work or would maintain the movement  
however arbitrary in the general correct direction.

that or use such a small (.2 kcal/mol nm2) that it does not matter very much.

Sincerely,

Stephan Watkins
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