[gmx-users] simulation with position constraint by a harmonic potential

[Justin A. Lemkul]

Liu, Liang wrote:
> Thanks for the information.
> 
> It looks the pdb2gmx can generate the posre.itp file and what I use 
> is "pdb2gmx -ignh -ff amber03 -f *.pdb -o *.gro -p *.top -water spce".
> The file shows:
> ; In this topology include file, you will find position restraint
> ; entries for all the heavy atoms in your original pdb file.
> ; This means that all the protons which were added by pdb2gmx are
> ; not restrained."
> [ position_restraints ]
> ; atom  type      fx      fy      fz
>      1     1  1000  1000  1000

<snip>

It is unnecessary to paste this information.

> 
> So how to adjust the force constraint to the harmonic poteitial E = 
> k(r-r0)^2, with different values of k?
> 

The file format is discussed in the manual, Chapter 4.  You can alter the force 
constants in x, y, and z dimensions independently.  The force constants are 
listed in the fx, fy, and fz columns.

> I am totally a new user of Gromacs, even MD simulation. Please help, 

I would suggest you familiarize yourself with Gromacs capabilities, file 
formats, and workflows by working through any of the multitude of tutorials 
linked on the Gromacs website.

-Justin

> Thanks a lot.
> 
> On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Liu, Liang wrote:
> 
>         Firstly I want to thank for your reply, yes, it should be
>         position restraint.
> 
>         I don't know how to reply in the thread, actually that was my
>         first post. Therefore I have to ask you here, hope it also work
>         to you.
> 
> 
>     Simply reply to the message.  The discussion needs to stay on the
>     list.  The members are not private tutors.
> 
>         My question is how to perform a position restraint simulation
>         with the heavy atom constrained to its initial position by a
>         harmonic potential E=k(r-r0)^2,
>         which changes with k equal to 0, 10, 20, ..., 90, 100, and so on?
> 
> 
>     You can adjust the force constant in the posre.itp file.  There is
>     no automated way of decreasing or increasing a restraint;
>     independent simulations must be run on the different topologies.
> 
>     -Justin
> 
>         Thanks, and any helps will be highly appreciated.
> 
>         -- 
>         Best,
>         Liang Liu
> 
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
> 
> 
> 
> 
> -- 
> Best,
> Liang Liu
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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