[gmx-users] Re: gmx-users Digest, Vol 78, Issue 123

Gerrit Groenhof ggroenh at gwdg.de
Mon Oct 18 10:19:02 CEST 2010

>     3. Simulation parameter problem about protein unfolding (Chen)

You write it yourself: In paper you mention, they have used a 0.8 nm 
cutoff range for both electrostatics and cutoff. You are doing something 
different by using PME for the electrostatics. Also you are using a much 
longer cutoff for the VDW interactions.

If you want to reproduce their results, you need to stick to to the 
parameters mentioned in that paper and use cut-offs as well.

BTW I do not believe this to be a good idea though.


Hi All,

I met a problem when I try to unfold a protein using Gromacs, It seemed the protein cannot be totally unfolded!

The simulated system has one Engrailed Homeodomain (En) protein (a three helix bundle protein with 54 residues, 629 atoms), total 4848 spce waters, and 7 Cl- used to neutralize the system in a 5.752(nm)3  water BOX. I use the NTP ensemble with T=498K and P=26atm. The system has 1nm thick water in each side of the En protein, and the density of the system has been adjusted to0.829 g/cm3.

The simulation lasted 24ns. The helixes disappeared at about 4ns. And after that some beta sheet formed in the N terminal of the protein. However, the protein kept in a compact state during the 24ns simulation. The radius of gyration of the protein fluctuated around 1.1nm during the simulation.

I've also noticed similar simulation done by others. For example, David Becka and Valerie Daggett reviewed their En protein unfolding in paper "Methods for molecular dynamics simulations of protein folding/unfolding in solution. Methods 34 (2004) 112¨C120". The simulations were performed with ENCAD and ilmm, and used an 0.8nm cutoff range. And the ensemble they used is NVE as I know. A stretched unfolding state occurred at about 5ns in their 60ns simulation in 498K, with little helix structure.

I was wondering whether the difference is caused by using different MD software and force field, or by some wrong parameters in my .mdp file. I've also conducted another 18ns simulation, and the result is almost the same. I list he mdp file below. Any comment is appreciated!

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