[gmx-users] bonds section in the topology file

[Justin A. Lemkul]

Amir Marcovitz wrote:
> Thank you Justin,
>  
> actually, i have two parallel rigid plates that are free to move towards 
> each other on the Y-axis (i used position restrain on Y and Z axes)
> later on i will umbrella sampling to obtain the plate-plate PMF at 
> various distances from each other (thanks a lot for the helpful tutorial!)
>  
> so i will try bond type 6 as you suggested.
>  
> up until now i observed , especially during the the NPT run ,that the 
> atoms are fluctuating , and if the time step was 0.002psec or even 0.001 
> psec the system was very un-robust and the simulation explodes. (that is 
> my main concern and the reason for my previous post)
>  
> do you think bond type 6 will settle this?
>  

Not likely.  If your system is blowing up that means there is something 
physically unrealistic about it (insufficient EM or equilibration, inappropriate 
parameters or .mdp settings, etc).  There's tons of useful information on the 
Gromacs site and in the list archive to help you.  Otherwise you'll have to 
provide substantially more information regarding all the points I raised above 
to get any useful advice.

-Justin

> anyway, thanks a lot for the quick reply!
> Amir
> 
> On Thu, Feb 4, 2010 at 7:32 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Amir Marcovitz wrote:
> 
>         Hi,
>          i'm simulating a surface in water and ions which is composed of
>         6X6 Carbon atoms arranged on a 2-d lattice. (using ffamber99)
>         i want to keep the spacing between C-C neighbouring atoms at
>         0.34 Angstrom (or some other spacing of choice..), and to
>         maintain the surface rigid and planar
>          for that i added to the [  bonds ] section at the topology file
>         c0 values and force constants as following:
>          [ bonds ]
>         ;  ai    aj funct            c0            c1            c2    
>                c3
>            1     2     1  3.400000e-01 3.744680e+05
>            1     7     1  3.400000e-01 3.744680e+05
>            2     3     1  3.400000e-01 3.744680e+05
>         ..
>         and so on..
>          and similarly  added 90 and 180 degrees bond angle constrains
>         between triads of atoms in the surface according to their location.
>          the thing is , i'm affraid my constraint of c0 of 3.4 Angst. is
>         in some conflict with the definition of C-C bond length which is
>         defined somewhere in the amber files (if i'm turning the
>         constraint on co off the atoms approach each other and the
>         spacing is lost)
>          my questions are:
>         a) do you think i should define a new dummy atom? and in which
>         files should it be done? - i'm asking because i didn't find a
>         clear answer in the manual
>         b) is there any other bond function  (what number?) which may
>         ignore the definition of the C-C length and treat only the c0
>         constraint?
> 
> 
>     Two options I can think of:
> 
>     1. Why not position restrain your carbon lattices to parallel planes?
>     2. Use bond type 6 to define a harmonic potential between the atoms
>     you want to restrain.  If the two lattices are part of the same
>     molecultype definition (unclear from your post), then you can use
>     distance restraints.  If they are separate molecules, however, you
>     can't, and hence why bond type 6 is a viable option.
> 
>     -Justin
> 
> 
>          if someone can answer or guide me to relevant sections in the
>         manual i'll be most thankful!
>         amir
>           
> 
> 
>     -- 
>     ========================================
> 
>     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
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

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

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

========================================