[gmx-users] Simulations in extreme conditions

CipPruteanu C.Pruteanu at ed.ac.uk
Sat Feb 15 12:54:55 CET 2014

Justin Lemkul wrote
> I'm assuming that NPT and the data collection period are effectively the
> same, 
> since you likely don't have anything worth restraining to distinguish any
> sort 
> of distinct equilibration period.  The main question is: do your systems 
> equilibrate at the desired conditions?  25 kbar is a bit crazy for the 
> biomolecular force fields in Gromacs, and given the inherent fluctuations
> in 
> pressure coupling, I would be a bit surprised if you actually achieved
> such 
> pressures in that amount of time.

Dear Justin,

Thank you very much for the prompt reply. I am aware that it is very unusual
to try to use GROMACS for extreme conditions simulations (such as inside
planets and satellites, which is where this system is found in reality).

Far as I can tell (and also people who do this for biological systems on a
daily basis, at our university) the system equilibrates properly. It reaches
the desired pressure and temperature. The fluctuations are large but
bearable on the scale of the system (less than 0.5 kbars for 25 kbars and
less than 1 kbar for 150 kbars, from my trials so far). There doesn't seem
to be a problem with excessive pressure scaling (only once GROMACS gave the
warning that the pressure scaled too much during a NPT equilibration, and it
turned out it was my fault since I forgot to do the NVT equilibration before
the NPT one). 

Justin Lemkul wrote
> The biggest culprit, in my mind, is the force field.  OPLS and other 
> biomolecular force fields weren't designed for extreme conditions like
> this, and 
> interactions with water under ambient, biological conditions, will be
> wildly 
> different from what you're trying to do.  That's not to say it can't be
> done, of 
> course, but the "standard" parameters may no longer apply.
> -Justin

I am completely aware of this, but the simulations raise some interesting
problems even in this situation. They do successfully show some physical
trends and even something resembling what we are expecting from experiment,
to a certain degree. Some people seem to find it very interesting like this,
and are quite keen to push things just to see what happens and maybe this
would point to some specific shortcomings of the forcefield. 

Thank you again for your reply!


PhD Student
Centre for Science at Extreme Conditions
University of Edinburgh, UK
View this message in context: http://gromacs.5086.x6.nabble.com/Simulations-in-extreme-conditions-tp5014553p5014569.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list