What a nice expression: NaNdyland.. :)
I used pmemd.sander or cuda (single GPU) for the simulation, all of
them blew up. I will reparameterize the molecule and see what happens.
If it still goes wrong, I will let you know!
Kind regards
Niels
Citeren Jason Swails <jason.swails.gmail.com>:
> On Thu, Jul 17, 2014 at 11:02 PM, Niels Geudens <Niels.Geudens.ugent.be>
> wrote:
>
>> Hi all,
>>
>> I would like to see the cis-trans isomerisation of a proline dipeptide
>> (with non-proteinic caps). For this I am trying to use scaled MD in
>> Amber14. I first ran a simulation without the scaledMD flag in the
>> input file:
>>
>> &cntrl
>> iwrap = 1
>> imin = 0, irest = 1, ntx = 7,
>> ntb = 2, pres0 = 1.0, ntp = 1,
>> taup = 2.0,
>> cut = 10.0, ntr = 0,
>> ntc = 2, ntf = 2,
>> tempi = 300.0, temp0 = 300.0,
>> ntt = 3, gamma_ln = 1.0,
>> nstlim = 5000000, dt = 0.002,
>> ntpr = 100, ntwx = 500, ntwr = 1000
>> ioutfm = 1
>> /
>>
>> This simulation ran without any errors, but no isomerisation is
>> present. Next, I added the scaledMD (with lamba = 0.7). At first, this
>> simulation also runs without any problems. However, after a variable
>> number of frames (I retried a few times), the molecule seems to
>> "disappear" when viewed with vmd. The last meaningfull entry in the
>> scaledMD.log file is:
>>
>> 500 354500 -9646.920713734136 0.700000000000
>> -6752.844499613895 2894.076214120241
>> 500 355000 NaN 0.700000000000
>> NaN NaN
>>
>
> Your simulation went off to NaNdyland (i.e., it blew up). There are many
> things that could cause this. Since scaled MD is quite new, it's entirely
> possible that there is a bug. It could also be atoms collapsing onto each
> other as a consequence of either the input parameters or force field
> parameters you used.
>
> However, there are currently 3 different implementations of Scaled MD in
> Amber 14 -- the one in sander, the one in pmemd (CPU), and the one in
> pmemd.cuda (GPU). Which one are you using? Can you try one of the others
> and see if you get similar behavior? (If the problem lies with your
> system, the CPU may take longer to blow up than the GPU version given its
> higher tolerance for large numbers).
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Jul 18 2014 - 01:00:02 PDT
