Question: Disrupted protein structure after 5 nanoseconds of GROMACS molecular dynamics
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gravatar for Nestor Wendt
3.6 years ago by
Nestor Wendt100
Brazil
Nestor Wendt100 wrote:

Hello, I have been trying perform a molecular dynamics using GROMACS. The idea is to simulate a system with the Human FABP2 and palmitic acid. My simulation is based on this tutorial. After about 5 nanoseconds my structure starts to show a strange behavior, as shows the figure.

Start of molecular dynamics: Human FABP2 with palmitic acid.Middle of molecular dynamics: Human FABP2 with palmitic acid.

Starting structure (left). Structure after 5 nanoseconds of simulation (right).

 

Does anyone know what causes this problem? I basically followed the tutorial, using the GROMOS96 force field. I suspect that this kind of behavior is called 'blowing up', although I am not sure and want to hear the opinion from more experienced bioinformaticians.

Thank you.

molecular dynamics gromacs • 1.5k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Nestor Wendt100

Did you use the same parameters as tutorial, or did you adapt them to you simulation? I personally use Amber package, and I have never observed this king of 'blowing up'. 

What are your parameters? (Time step, pressure, Temperature, cut-off?) Thanks to provide details. ;)

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by glihm590

I used the same parameters. The only change was in the ions, as my structure had a different net charge if compared to the protein used in the tutorial. I did not see this behavior in the equilibration steps, only in the final dynamics. A few parameters:

Time step = 2 fs

Pressure = 1 bar

Temperature = 300 K for all groups

I am not sure if that's the cut-off parameters you are looking for, but the cut-off scheme was Verlet.

If I run the simulation without the ligand, using another force field, this disruption does not happen. I have been trying to find a tool to generate the ligand topology for another force field, but I could not find a working one.

ADD REPLYlink written 3.6 years ago by Nestor Wendt100
0
gravatar for Nestor Wendt
3.6 years ago by
Nestor Wendt100
Brazil
Nestor Wendt100 wrote:

For those who encounter this problem in the future. After converting the trajectory file (.trr) to (.xtc) using 'gmx trjconv' with the following parameter '-pbc nojump', these jumps stop appearing. This tutorial called this jumps 'pdc artifacts', and there, before visual analysis they were removed. Here's the gmx trjconv help page.

Thanks.

ADD COMMENTlink written 3.6 years ago by Nestor Wendt100
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