[AMBER] NaN and asterisks error in md.out, and mdinfo files

From: Hoshin Kim <85hskim.gmail.com>
Date: Mon, 4 Aug 2014 15:04:34 -0400

Dear all,

I am doing MD simulations of DNA grafted on Au surface. For simulations,
Amber GPU computing system are being used (Exxact, GTX 780)

Now I am having a hard time performing MD simulations because of following

When I do MD simulation (I've tried both NVT, and NPT conditions), all
information in md.restrt and some terms in mdinfo (md.out) suddenly turned
into NaN, and NaN with asterisks, respectively, at random time step.
To figure this problem, I took a restrt file right before error occurred,
and reran MD. It worked fine first time, but identical error occurred again
at random time step.

Here is an example of mdinfo file
 NSTEP = 49999500 TIME(PS) = 100039.000 TEMP(K) = NaN PRESS =
 Etot = NaN EKtot = NaN EPtot =
 BOND = 0.0000 ANGLE = 70230.8688 DIHED =
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
 EELEC = ************** EHBOND = 0.0000 RESTRAINT =

Interestingly, no errors were observed when I did same MD simulations using
CPU, instead of GPU. Plus, For more simple conditions (e.g. just DNA in
water) using same input parameters for minimization, heating, and
production run, I had no problems using GPU.


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Received on Mon Aug 04 2014 - 12:30:02 PDT
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