[gmx-users] General Question

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 24 13:36:29 CEST 2010

pawan raghav wrote:
> Dear GROMACS team members,
> I have a general question about the GROMACS, actually I have used 
> GROMACS for the simulation of 59 amino acids domain part of the protein 
> containing within it. This domain lies in the position from 34-92 out of 
> 239 residues, this loop having only 12 residues similarity whose does 
> not found any similarity in this region. I have an objective to predict 
> the behaviour of such a large loop flexibility. So my question is that 
> at what level of accuracy, the loop optimization and prediction would be 
> correct. Is it possible to predict the loop structure on the basis of 
> simulation or can predict the structure of unstructure loop of a 
> protein? Please comment on this because some people criticising MD 

The ability to predict loop conformations (and protein conformations in general) 
is a function of both the force field and the conditions applied.  Different 
force fields (unfortunately) have different "preferences" for certain 
configurations.  Such is the limitation of what we do.  You may have to either 
conduct your simulations with different force fields to eliminate such a bias. 
At the very least, you need well-converged data.  That means either numerous 
simulations of sufficiently long trajectories, or apply techniques like REMD.

> simulations prediction. Can we predict the folded loop of a protein by 
> using simulation? if yes then tell me about the analysis methods in 
> gromacs for loop particularly. One more question is about the "dt" that 

The type of analysis depends on what you know about your system.  Different 
structural analyses are certainly possible, but what might be more significant 
is the identification of known interactions within your structure (amino acid 
contacts, etc).

> it can be possible to change the value of dt in .mdp file instead of 
> 0.002 ps to 0.003 if yes then what is the significance of this and what 
> is the efeect of this on simulation?

Anything is possible.  You still have to demonstrate that your simulation is 
stable, energy is conserved, etc.  Pretty rare to see a 3 fs timestep.  If 
you're just trying to speed up your simulations, use virtual sites in 
conjunction with constraints and go straight for a 4-5 fs timestep.


> -- 
> Pawan


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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