Hi David,
Thanks for the reply.
I have run heating step using the CPU version (pmemd) and CPU-MPI (pmemd.MPI). The job stopped and failed at step of "NAN" appeared.
> &wt
> type='TEMP0',
> istep1 = 0, istep2 = 8000,
> value1 = 50.0, value2 = 298.0
> /
Then, I removed the above and re-run heating step. I got the exact same result.
Jianxiong DIAO
________________________________
·¢¼þÈË: David A Case <david.case.rutgers.edu>
·¢ËÍʱ¼ä: 2016Äê9ÔÂ28ÈÕ 6:04
ÊÕ¼þÈË: AMBER Mailing List
Ö÷Ìâ: Re: [AMBER] Amber NaN error
On Tue, Sep 27, 2016, DIAO Jianxiong wrote:
>
> I'm setting up a MD simulation of a solvated ligand with pmemd.cuda in
> Amber v16. I used "SolvateOct ligand TIP3PBOX 20.0 0.75" to add the
> water box and I thought the box was large enough (box size 55.7437501
> 55.7437501 55.7437501; cut=8.0, skinnb=2.0).
This is indeed plenty big enough. It's not clear what is causing your
problem. Certainly, the first thing to do is to try a short heating run
using the CPU version (pmemd rather than pmemd.cuda).
> &wt
> type='TEMP0',
> istep1 = 0, istep2 = 8000,
> value1 = 50.0, value2 = 298.0
> /
Second, even with pmemd.cuda, try removing the above, and just heating in the
more conventional way. It's possible that there is some problem
(CUDA-specific?) with having a variable TEMP0 specification.
...good luck...dac
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Received on Wed Sep 28 2016 - 14:30:03 PDT
