[gmx-users] Strange jumps in box dimensions

[Justin Lemkul]

On 3/12/18 10:27 AM, Igor Ariz wrote:
> Hi all,
>
> I am simulating a small membrane protein system:
>
> Protein  1 (256 aminoacids)
> DPPC    104
> SOL    4377
> CL    7
> NA    1
>
> using CHARMM36m force-field, short cut-offs (0.9 nm) and 
> semi-isotropic Berendsen p-coupling.
>

Short cutoffs can lead to bad lipid properties. There is extensive 
literature on proper cutoff and switching distances for CHARMM lipids.

> I am experiencing sudden jumps in box dimensions from [6.52 6.52 6.96] 
> to [5.05 5.05 7.72]
> in tens of nanoseconds, which take hundreds of nanoseconds to go back 
> to the previous box size.
>

This suggests you have some instability in the system, perhaps void 
space that compresses down.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================