Saturday, March 23, 2019

OpenDX rendering of folding landscapes

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

Saturday, February 16, 2019

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).

Friday, February 8, 2019

Monday, January 14, 2019

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.

Wednesday, December 26, 2018

Love fish

This is it. Forget tcsh and bash. Love fish :

ps. There are problems however : both CCP4 and PHENIX provide setup scripts for only bash and csh/tcsh ⇨Ignore, this is fixable through bass.

Saturday, November 3, 2018

gp41 paper

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

Thursday, October 18, 2018

Running dropbox on old linux machines

Dropbox recently changed the linux system requirements. This may be a meaningful choice from the company's perspective, but I am not prepared to give-up on some of my old machines which have software that I find it hard to move to newer hardware. So, I was looking for a software solution that could work with ubuntu 10.04, ubuntu 11.04 and a relatively new centos machine which uses xfs instead of ext4. First I will describe the technical steps for the procedure I'm currently using, then I will discuss the shortcomings.

Technical steps (based on rclone and inotifywait)

[1] Install rclone as described in . Surpisingly, this may be the hardest part of the procedure due to old versions of curl not being compatible with the server-side ssl. On both of my machines I had to install openssl from source and then install curl again from source (using the newest ssl libraries). Expect suffering at this stage.

[2] Configure rclone as described in . This is easy.

[3] Do a dry run to confirm that rclone is working as expected (change 'mydropbox' and 'user'):

rclone --dry-run sync -u mydropbox: /home/user/Dropbox

[4] Install inotify-tools if you don't have them already.

[5] If you reached this stage, you are practically done :

(a) Prepare a hidden file in your home directory (for example /home/user/ containing the following bash script :

while true; do

inotifywait -e modify,create -r /home/user/Dropbox && \
 pgrep rclone > /dev/null || rclone copy -u /home/user/Dropbox mydropbox:


Make this file executable (with chmod 755 /home/user/

(b) Edit your crontab and insert the following two lines :

@reboot      /home/user/ >& /dev/null
*/30 * * * * pgrep rclone > /dev/null || rclone sync -u mydropbox: /home/user/Dropbox

(c) Add the following to your .bashrc :

alias dropboxfetch='pgrep rclone > /dev/null || rclone copy -u mydropbox: /home/user/Dropbox'

(d) Reboot the machine and confirm that is running.

What you get from all that

(a) When you add a file to the dropbox directory of the local (old) machine, it will be immediately transferred to the dropbox servers (and, thus, to all of your other machines).

(b) When you modify the dropbox directory from other (non-old) machines, the changes in the old machines will appear at the time interval defined in the crontab (every 30 minutes in the example above). If you want to immediately fetch new files from dropbox to the local (old) machines use the dropboxfetch alias.

(c) You can not push file deletions from the old machines to dropbox. Dropbox files can only be deleted from newer machines that run the real dropbox daemon. The deletions will appear at the crontab specified interval. Think what you may, but this is a great precaution (and do note that at no point do we do a sync from the old machine to dropbox, which is the definition of better-safe-than-sorry).

Things can definitely go wrong. Notice for example these pgrep's ? These are to avoid some obvious race conditions that arise if you end-up having two rclone jobs running simultaneously. But I bet (especially with dropboxfetch) you can still get artifacts. The thing is that in the absence of a sync from the old machine to dropbox, the worst case scenario is that some files you thought you deleted, may end-up being well and alive. (famous last words I hear you say).