From: Ritu Arora (ritu.arora_at_mail.concordia.ca)
Date: Tue Sep 15 2020 - 13:26:11 CDT
Hi Hemanth,
Thanks for sharing your experience. The given output was just a portion of the log file, I start getting 'nan' energy values right after 2 ns of simulation time. There is no issue with the xsc file; I believe that something is wrong with my input in the configuration file. I am not sure if I am applying the proper boost or if something is wrong with the way I am using dual boost. I calculated accelMDE and accelMDalpha as reported in the tutorials, and considering the first 50 ns conventional MD simulations.
#aMD
accelMD on;
accelMDdihe on;
accelMDE 8581; #followed NAMD tutorial to calculate accelMDE and accelMDalpha
accelMDalpha 533;
accelMDOutFreq 5000;
Any further help from NAMD users or developers will be appreciated.
Thanks and regards,
Ritu
________________________________
From: HEMANTH H <hemanth.h_at_iitgn.ac.in>
Sent: Tuesday, September 15, 2020 1:55 AM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>; Ritu Arora <ritu.arora_at_mail.concordia.ca>
Subject: Re: namd-l: NAN in output of aMD
Ms. Arora,
1. I assume that your simulation had worked fine till the step 18050000. In that case, the best way would be to visually check your trajectory to see what is happening there. I had run into something similar before, but my issue was related to the xsc file being not parsed properly. Check your last checkpoint file and you should be able to figure it out.
Regards
Hemanth
On Mon, Sep 14, 2020 at 8:06 PM Ritu Arora <ritu.arora_at_mail.concordia.ca<mailto:ritu.arora_at_mail.concordia.ca>> wrote:
Hello All,
I am trying accelerated MD simulations on my protein system. To do so I added the following commands in the configuration file of production run:
#aMD
accelMD on;
accelMDdihe on;
accelMDE 8581; #followed NAMD tutorial to calculate accelMDE and accelMDalpha
accelMDalpha 533;
accelMDOutFreq 5000;
Unfortunately, my output file contains nan:
TIMING: 18050000 CPU: 253081, 0.0139727/step Wall: 259046, 0.0141721/step, 27.36 hours remaining, 1189.199219 MB of memory in use.
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 18050000 nan nan -nan -nan nan nan 0.0000 0.0000 nan nan nan nan nan nan nan nan nan nan nan
I am not sure how-to solve this problem; can anyone help me with this regard? I am sorry if I have re-posted this message.
Thank you.
Best,
Ritu
-- Hemanth H 18310019 Research Scholar IIT Gandhinagar
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