VMD/NMAD on AWS

From: Strenic Computations (strenicamazon_at_gmail.com)
Date: Sat Mar 17 2018 - 18:50:17 CDT

Hello all,

I was trying to play with VMD/NAMD image which is provided by TCBG on
Amazon Cloud. I used the recommenced g2.2xlage instance.
With a few hiccups I was able to run some protein MD using helper QwikMD
configuration file generator as swell as namd directly in multi- and
single-thread modes but only for implicit water cases.

Wherever I am trying to run an MD ( multi- or single-thread, CPU or GPU)
with explicit water at the very first step of MD am getting the error
nfo) Using multithreaded IMD implementation.
------------- Processor 6 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Periodic cell has become too small for original patch
grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

for every thread where the simulations are running.

I tried to increase margin and lay with langevin dynamics settings which
did not changed simulation behavior.
I tried to use the latest nightly build of NAMD with the same results.

I downloaded the set of files of ubiqutin MD in a water box with periodic
boundary conditions from NAMD tutorials.
http://www.ks.uiuc.edu/Training/Tutorials/namd/archive/2010-12-06/namd-tutorial-files-bak/

and tried to run it directly with NAND with the same results.

So, I would be really thankful for anybody with the experience of running
protein MD on AWS, who could help me sending a working configuration script
for any protein MD with explicit water in periodic boundary conditions
which worked on AWS.

Thank you very much in advance for your help!

Yaroslav Ryabov

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