[gmx-users] system explode when running in MD production
jalemkul at vt.edu
Mon Apr 22 02:12:48 CEST 2013
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.
> 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
Instantaneous values of pressure mean very little.
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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