Re: [AMBER] NVE GPU question

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 23 Jan 2015 06:04:59 -0800

Hi Joe,

Yes you should have nscm=0 here. You should also devise a list of simulations that tests things in a systematic fashion. I would start by trying the CPU code and also DPFP - this will show you the effect of the precision model. As Jason pointed out the dynamic range of the individual forces may be much larger for an ionic liquid due to the high charges. It would help to establish what the dynamic range is compared with a typical protein in water simulation. If the dynamic range is too large then it may be inappropriate for the SPFP precision - at least to the point that you may be losing precision - especially if you have lots of forces of opposite sign that ultimately sum to zero.

All the best
Ross

> On Jan 22, 2015, at 4:58 PM, Hector A. Baldoni <hbaldoni.unsl.edu.ar> wrote:
>
> Hi Joe,
>
> If you don't mind you would try the input in the previous post:
>
> http://archive.ambermd.org/201410/0198.html
>
> May be, the steps in the Etot vs time curves could be due nscm <> 0.
>
>
> Greeting,
> Hector.
>
>
>> Here is a plot with different values of dsum_tol, with a 1 fs timestep, 8
>> A
>> cutoff. The drifts are from a linear fit to the entire data set (not
>> great,
>> obviously, but gives the trends). The black curve is shorter just because
>> I
>> ran it less steps (forgot to change nstlim to a smaller number in the
>> other
>> three simulations). Y-axis units are the units of Etot in the Amber
>> output,
>> and x-axis is picoseconds.
>>
>> Black curve (dsum_tol = default)
>> drift = 7.4 x 10^-4 kT/ns/dof
>>
>> Red curve (dsum_tol = 1 x 10^-6)
>> drift = 4.6 x 10^-4 kT/ns/dof
>>
>> Green curve (dsum_tol = 1 x 10^-7)
>> drift = 3.2 x 10^-4 kT/ns/dof
>>
>> Blue curve (dsum_tol = 1 x 10^-8)
>> drift = -1.1 x 10^-4 kT/ns/dof
>>
>> So, dsum_tol does appear to have an influence on the energy conservation.
>> Is it still not as good as one would like at dsum_tol = 1 x 10^-8? Also,
>> is
>> it strange that there are "steps" in the Etot vs time curves?
>>
>> Thanks,
>> Joe
>>
>>
>> On Thu, Jan 22, 2015 at 6:24 PM, Joseph Baker <bakerj.tcnj.edu> wrote:
>>
>>> Hi all,
>>>
>>> Jason, I did have a dt=0.0001 test and there the drift was 1.8 x 10^-4
>>> kT/ns/dof (compared to 2.9 x 10^-4 and 3.6 x 10^-4 for dt=0.005 and
>>> dt=0.001, respectively). So better, but not by leaps and bounds.
>>>
>>> I am trying dsum_tol tests now, and will see how that goes. I have not
>>> tried the PME order because I have been using pmemd.cuda, as you
>>> mention.
>>>
>>> I haven't tried ntwf to check the forces yet, and I don't have CPU data
>>> for this system. I will check that to see if the drift is better on the
>>> CPU.
>>>
>>> Gerald, I've been computing the drift by using the regression tool in
>>> xmgrace to fit a line to the Etot vs time data from the amber output
>>> file.
>>> That slope I then I convert to kT/ns/dof by taking
>>> slope/0.593*1000/(3*number of atoms) (the factor of 1000 is to convert
>>> to
>>> ns since the time unit in the Etot vs time file is ps)
>>>
>>> Thomas, thanks for the additional input on the grid size.
>>>
>>> Joe
>>>
>>>
>>>
>>> On Thu, Jan 22, 2015 at 5:58 PM, Thomas Cheatham <tec3.utah.edu> wrote:
>>>
>>>>
>>>>> €‹Ah, ew_type=1 means pure Ewald (no PME). So rsum_tol doesn't do
>>>> what I
>>>>> thought it did... I guess dsum_tol is the setting to play with,
>>>> although
>>>>> it's not clear to me that that will improve overall accuracy.
>>>>>
>>>>> You could also try to set the PME order to 5 or so (I don't think
>>>> that
>>>> will
>>>>> work with pmemd.cuda, but it should work with pmemd, and hopefully
>>>> give
>>>>> better accuracy in the reciprocal forces).
>>>>
>>>> ...and increase FFT grid size (in addition to order) for the
>>>> reciprocal...
>>>>
>>>> --tec3
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>>>>
>>>
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>
>
> --------------------------------------
> Dr. Hector A. Baldoni
> Area de Quimica General e Inorganica
> Universidad Nacional de San Luis
> Chacabuco 917 (D5700BWS)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.:+54-(0)266-4520300 ext. 6157
> --------------------------------------
>
>
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Received on Fri Jan 23 2015 - 06:30:03 PST
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