From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Sep 16 2020 - 16:25:36 CDT
Hello Ritu, Hemanth's advice is a common and quite sensible one. Check the
trajectory or the latest checkpoint (i.e. restart) file prior to the
instability occurring to see what is going on.
You also mention using parameters from the AMD tutorial, but have you
checked what do they mean in the user's guide?
https://www.ks.uiuc.edu/Research/namd/2.14/ug/node69.html
These numbers were probably appropriate for the system shown in the
tutorial, but are they for *your* system?
Giacomo
On Tue, Sep 15, 2020 at 2:28 PM Ritu Arora <ritu.arora_at_mail.concordia.ca>
wrote:
> 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>
> 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
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Research collaborator, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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