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
--
========================================
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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