From: Pablo Campomanes (pablo.campomanes_at_epfl.ch)
Date: Fri Mar 05 2010 - 22:50:53 CST
Hi,
If you are running a simulation in the NVT ensemble, you are not allowing your simulation box to change by definition.
I am afraid that you will not get so much help if you do not provide the appropriate files to investigate what is going wrong.
Regards,
Pablo.
_____________________________________________
Pablo Campomanes
Laboratory of Computational Chemistry and Biochemistry
BCH 4118 EPF Lausanne
On Mar 6, 2010, at 4:59 AM, Aditya Ranganathan wrote:
> Hi Everyone,
> I`m trying to simulate a system of 2 ACTH and 2 Beta Endorphin peptides and intend to study the interaction between them. I first minimized the peptides before solvating it (and added Na and Cl ions to neutralize the box) and then minimized the solvated system again. I then heated the system slowly for 300ps with an increment of 0.001K per step and then equilibrated the system at 300K for another 300ps.
> I then started the final production run and intend to run it for a minimum of 10 ns to study any interaction or aggregation tendency between the peptides. However, what started as a Cubical waterbox initially has now become an almost cylindrical shaped water `box`. The configuration I`ve used is of an NVT simulation. However, even in the cylindrical system, the peptides are fully surrounded by water and not exposed out of the solvent. The simulation has now run for almost 4ns and still continues to run without any crashes or errors.
> However my question is whether the change in shape of the water box is a sign of an inappropriate simulation or an undesirable change.
>
> Thanks,
> Srivastav Ranganathan (Aditya)
> Junior Research Assistant
> Department of Biosciences and Bioengineering,
> IIT Bombay,
> Mumbai-400076
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