A new fat node has been added to the cluster. This is based on an Intel Core i7-13700KF (1700/3.4 GHz/30 MB), an NVIDIA MSI RTX 4070 Ti VENTUS 3X 12Gb OC 3, 8GB DDR4@3200 MHz, and two 2TB disks in a RAID1 array.

Initial tests confirmed that this is our new fastest machine, delivering with gromacs and HMR ~3930 ns/day on the FipWW 8,000 atom/5fs system. As with the other machines, with smaller systems the performance flattens at approximately ~4.1 μs/day (again with gromacs & HMR).

Martini & Gromacs & VMD & Bendix (and ROP)

 Have been playing with the Martini force field for some time now. Still digging. Here is a short movie of a ROP mutant using Martini & Gromacs, and visualized with VMD & Bendix.

Just came out ...

«A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations.»

https://doi.org/10.1371/journal.pone.0243429

OpenDX rendering of folding landscapes

Folding landscape (from dPCA) of the M2TM peptide in TFE, rendered with OpenDX. Too much red probably.

New fat box arrived

A new fat node has been added to the cluster. This is based on an Intel i9-9900K, a GTX-1080, 8GB DDR4@3000 MHz, and a two-disk RAID 0 @ 4TB.

Initial tests confirmed that this is indeed our new fastest machine, delivering ~560 ns/day on the standard 10,000 atom benchmark (second best is this one with 460 ns/day). With smaller systems, however, the performance flattens (giving with the CLN025 system 570 ns/day@2fs, ~730 ns/day@2.5fs).

Molecular simulation of peptides review

Just came out : "Molecular simulation of peptides coming of age: Accurate prediction of folding, dynamics and structures"

http://doi.org/10.1016/j.abb.2019.01.033

αLa : add 15SB to the family

The same image as before, after adding results from the 15SB force field :

A definite improvement over both 12SB and 14SB.

gp41 paper

Just came out : "Folding Molecular Dynamics Simulation of a gp41-Derived Peptide Reconcile Divergent Structure Determinations", ACS Omega, 3, 14746-14754 :

http://doi.org/10.1021/acsomega.8b01579

Just came out :

«Folding Simulations of a Nuclear Receptor Box-Containing Peptide Demonstrate the Structural Persistence of the LxxLL Motif Even in the Absence of Its Cognate Receptor»

http://dx.doi.org/10.1021/acs.jpcb.7b10292

Amber 14SB vs 99SB-STAR-ILDN [2]

Have been looking for a mostly disordered peptide (with NMR data available) for which the two force fields would demonstrate detectably different secondary structure preferences. I think I found one :

The upper graph is from 99SB-STAR-ILDN, the lower from 14SB. The two simulations were 24 μs each, both using adaptive tempering (280K-380K). Comparison between observed and calculated  NOEs plus chemical shifts should suffice. Given that this is a mostly disordered peptide ,we should probably also compare the computationally expected vs experimentally observed number of NOEs.

Amber 14SB vs 99SB-STAR-ILDN : αLa peptide

Weblogo representations of secondary structure preferences for human α-Lactalbumin 101-111 peptide with the AMBER ff14SB plus a whole lot of other AMBER force fields. The 14SB simulation was 3 μs, all other 2 μs.

On the way from 12SB to 14SB the α-helical preference was significantly reduced, but the mainly 3₁₀-helical nature of this peptide can not be faithfully reproduced. At least for the time, AMBER99SB-STAR-ILDN still looks like the best force field for this peptide.

New paper from the group just came-out :

Force-field dependent secondary structure preferences

Weblogo representations of the per-residue secondary structure preferences (as produced by STRIDE) for folding simulations of the α-Lactalbumin-derived peptide studied in this paper. Results from seven force fields are shown. The experimental NMR results indicate a mostly 310-helical N-terminal part (residues 3-6) with an occupancy of ~50%, and a completely disordered C-terminus. The symbols in the weblogo diagrams are G => 310 helix, H => α helix, T => turn, C => random coil, E => extended. The force fields are CHARMM22, OPLSaa, AMBER ff12SB, AMBER ff99SB, and three variants of AMBER ff99SB (99SB-ILDN-NMR, 99SB-ILDN, 99SB-STAR-ILDN). It does look like a clear take-home message is present in these diagrams...

Adaptive tempering & folding simulations

Playing with adaptive tempering using a very short (200 ns) folding simulation of the CLN025 decapeptide. Interesting diagrams, see this Norma page ...

Folding landscapes

Page added (in the form of a norma tutorial) for the calculation of 'folding landscapes' using native contacts and selected principal components from, say, dihedral PCA. The image below depicts one such matrix rendered with OpenDX.

Folding to atomistic detail with molecular dynamics simulations

Comparison between the experimental (X-ray) structure of a 14-mer peptide (upper panel), and the structure derived from a folding simulation (lower panel) using the AMBER99SB-ILDN force field and starting from the fully extended (unfolded) structure. This is impressive ... :-)

... and a direct comparison using anaglyph stereo (red-cyan glasses required) :

Homepage update

Publications and abstracts updated to include latest J. Phys. Chem. B paper