[gmx-users] Strange jumps in box dimensions
jalemkul at vt.edu
Mon Mar 12 15:39:59 CET 2018
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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