[gmx-users] system explode when running in MD production

[Justin Lemkul]

On 4/21/13 8:09 PM, Nur Syafiqah Abdul Ghani wrote:
> HI guys,
>
> I got this problem when I running my protein and metal in mix solvent.
> First of all,my question is can we use the original file of pdb and
> dock it with metal and run it by simulation?
>

Maybe.  Dealing with metals is tricky and not all force fields are well suited 
to simulating them.

http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

> Second question, after the equilibration part where the pressure and
> temperature is on.The pressure that I need is should be 1 bar but the
> result that i had first is in negative value but after extend the time
> steps the average of the pressure become positive with the value was
> 1.6 bar. Therefore I continue to MD production by using the equili.gro
> file.
>

Instantaneous values of pressure mean very little.

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

Assessing whether or not your system has stabilized to the desired value (not 
just the pressure value in a given frame) is what is important.

> Not so long after that the system said that my protein in this
> simulation was explode and results shows it produce a lot of pdb file
> at the certain step.Can you tell me why it is happened?
>

Without a complete description of what you're doing (the points that I posted in 
the last message), there is no way to know.

-Justin

-- 
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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

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