From: HEMANTH H (hemanth.h_at_iitgn.ac.in)
Date: Tue Sep 15 2020 - 00:55:59 CDT
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>
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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