[gmx-users] bonds section in the topology file

Amir Marcovitz amarcovitz at gmail.com
Thu Feb 4 23:03:57 CET 2010

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?

anyway, thanks a lot for the quick reply!

On Thu, Feb 4, 2010 at 7:32 PM, Justin A. Lemkul <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
> 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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