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

[Nur Syafiqah Abdul Ghani]

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?

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.

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?

I have no idea with this situation.

--
Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
alternative email : syafiqahabdulghani at gmail.com