[gmx-users] Re: Dimer Dissociation Problem

[Justin Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing the list and ask that further comments and 
questions will be posted there.

On 2/25/13 7:42 AM, mrdayer at gmail.com wrote:
> Dear Justin
> Greetings
> I simulate HIV-1 Protease with its substrate for 20ns in cubic box filled with SPC water using the following parameters:
> title               =  n.pdb
> cpp                 =  /lib/cpp
> constraints         =  none
> integrator          =  md
> dt                  =  0.001
> nsteps              =  20000000
> nstcomm             =  1
> comm_mode           =  Linear
> comm_grps           =
> nstxout             =  250
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  100
> nstenergy           =  100
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.2
> coulombtype         =  PME
> rcoulomb            =  1.2
> rvdw                =  1.4
> fourierspacing      =  0.12
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order           =  4
> ewald_rtol          =  1e-5
> optimize_fft        =  yes
>
> ; Berendsen temperature coupling is on in three groups
> Tcoupl              =  berendsen
> tau_t               =  0.1
> tc-grps		    =  system
> ref_t               =  310
> ; Pressure coupling is  on
> Pcoupl              =  berendsen
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 310 K.
> gen_vel             =  yes
> gen_temp            =  310.0
> gen_seed            =  173529
> Unfortunately the dimer is dissociate to its monomers. what is the problem causing this unwanted event?
> thank you very much for your considerations

I doubt it's actually dissociating.  What you're seeing is probably a simple 
result of periodic boundary conditions.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

If a trajectory that has been properly post-processed by trjconv shows a 
dissociation event, then you should be able to easily observe why it happens by 
watching the trajectory in your favorite visualization software.

-Justin

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

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

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