From: Strenic Computations (strenicamazon_at_gmail.com)
Date: Sat Mar 17 2018 - 18:50:17 CDT
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
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.
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!
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:19:46 CST