[gmx-users] Com Pulling

[chris.neale at utoronto.ca]

I understand your intention now. It might be possible to do this with  
gromacs 3.3.3 (short pull code simulation, then restart without the  
pull code but using the .trr from the previous run) but I'm not sure  
if you can do that with 4.x. Note that a thermostat is going to remove  
this directed velocity over time.

You can put velocities into a .gro file .. I presume that these are  
used if you set gen_vel=no, but I'm not sure about that. Test that by  
loading in a .gro with velocities and set gen_vel=no and nstep=0 and  
see if you have an instantaneous temperature near 300K or near 0K. If  
it works, then you can write a script or program to set your own  
initial velocities this way.

Chris.

-- original message --

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

------------------------------

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
-- 
Sicherer, schneller und einfacher. Die aktuellen Internet-Browser -
jetzt kostenlos herunterladen! http://portal.gmx.net/de/go/chbrowser
-- 
Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief!
Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail