Is he using shake on the gold atoms in any way? If so, that's borked for
more than 4 hydrogens...
On Aug 6, 2014 11:40 AM, "Ross Walker" <ross.rosswalker.co.uk> wrote:
> Hi Hoshin,
>
> I can confirm that I can repro this with AMBER 14. It happens with an
> without iwrap. The bonding in your gold surface is way beyond what we've
> tested previously so the problem may lie in there - looks like you have
> something like 8 bonds to every gold atom in some huge lattice. I thought
> initially the problem might be the code trying to image your entire gold
> surface but setting iwrap=0 the problem still occurs. I still think it
> might be some kind of imagining issue though.
>
> I'll file a bug on it and we'll try and investigate some more. In the
> meantime if you could run a sufficiently long CPU run for me to confirm
> that this never happens with the CPU code that would be helpful.
>
> Thanks.
>
> All the best
> Ross
>
>
> On 8/5/14, 11:08 AM, "Hoshin Kim" <85hskim.gmail.com> wrote:
>
> >Dear Dr. Walker,
> >
> >Since size of prmtop file is huge (55mb), I can't send it through an
> >e-mail. I would appreciate it a lot if you let me know the proper way to
> >send these files to you.
> >
> >Also, thanks in advance for sparing your precious time for me.
> >
> >Regards,
> >
> >Hoshin
> >
> >
> >On Tue, Aug 5, 2014 at 1:55 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
> >
> >> Ok - thanks.
> >>
> >> Please send me your prmtop, inpcrd file and mdin file and I will see if
> >>I
> >> can replicate this.
> >>
> >> All the best
> >> Ross
> >>
> >>
> >> On 8/5/14, 10:49 AM, "Hoshin Kim" <85hskim.gmail.com> wrote:
> >>
> >> >Firstly, please confirm that you are using AMBER 14 with all the latest
> >> >patches. Look in your mdout file for the section that begins:
> >> >--------------------- INFORMATION ----------------------
> >> >| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> >> >And paste in the reported version and date here.
> >> >Unfortunately, we are still using AMBER 12 with the latest bug fixes.
> >> > Version 12.3.1
> >> > 08/07/2013
> >> >
> >> >Next try running your heating and initial equilibration on the CPU and
> >> >then switch to the GPU and see if that helps.
> >> >I got same error when I tried to do MD simulations using minimization
> >>and
> >> >equilibratiion steps performed by CPUs.
> >> >
> >> >Finally confirm that if you use the exact same input with the exact
> >>same
> >> >random seed (set ig explicitly) that the situation yields NANs at
> >>exactly
> >> >the same point. This is critical and will establish that it is a bug in
> >> >the code and not a misbehaving GPU.
> >> >
> >> > When I did MD using exact same random seed(irest=1 to 0, ntx=5 to 1,
> >> >ig=-1
> >> >to 71277), error occurred at exact same time step.
> >> >Here are the mdinfo file right before and after error occurred.
> >> >
> >> > NSTEP = 116500 TIME(PS) = 273.000 TEMP(K) = 299.88 PRESS =
> >> >0.0
> >> > Etot = -290241.5794 EKtot = 73194.3125 EPtot =
> >> >-363435.8919
> >> > BOND = 4886.6630 ANGLE = 288.5639 DIHED =
> >> >357.0713
> >> > 1-4 NB = -290.2780 1-4 EEL = 207.0313 VDWAALS =
> >> >52299.7656
> >> > EELEC = -421184.7088 EHBOND = 0.0000 RESTRAINT =
> >> >0.0000
> >> >
> >>
> >>>------------------------------------------------------------------------
> >>>--
> >> >----
> >> >
> >> >check COM velocity, temp: 0.000000 0.00(Removed)
> >> >
> >> >
> >> > NSTEP = 117000 TIME(PS) = 274.000 TEMP(K) = 299.95 PRESS =
> >> >0.0
> >> > Etot = -290251.4099 EKtot = 73211.3984 EPtot =
> >> >-363462.8083
> >> > BOND = 4843.7191 ANGLE = 306.5830 DIHED =
> >> >344.0662
> >> > 1-4 NB = -282.1788 1-4 EEL = 209.5822 VDWAALS =
> >> >51954.7377
> >> > EELEC = -420839.3177 EHBOND = 0.0000 RESTRAINT =
> >> >0.0000
> >> >
> >>
> >>>------------------------------------------------------------------------
> >>>--
> >> >----
> >> >
> >> >wrapping first mol.: NaN NaN NaN
> >> >wrapping first mol.: NaN NaN NaN
> >> >
> >> >
> >> >NSTEP = 117500 TIME(PS) = 275.000 TEMP(K) = NaN PRESS =
> >> >0.0
> >> > Etot = NaN EKtot = NaN EPtot =
> >> >**************
> >> > BOND = 0.0000 ANGLE = 70230.8688 DIHED =
> >> >0.0000
> >> > 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
> >> >-1006.2814
> >> > EELEC = ************** EHBOND = 0.0000 RESTRAINT =
> >> >0.0000
> >> >
> >>
> >>>------------------------------------------------------------------------
> >>>--
> >> >----
> >> >check COM velocity, temp: NaN NaN(Removed)
> >> >wrapping first mol.: NaN NaN NaN
> >> >wrapping first mol.: NaN NaN NaN
> >> >
> >> >Regards,
> >> >
> >> >Hoshin Kim
> >> >
> >> >
> >> >On Mon, Aug 4, 2014 at 3:14 PM, Ross Walker <ross.rosswalker.co.uk>
> >> wrote:
> >> >
> >> >> Hi Hoshin,
> >> >>
> >> >> You are probably hitting some assumption we made in the GPU code.
> >> >> Certainly I've never tried doing simulations of Gold surfaces with it
> >> >>and
> >> >> that is way outside the scope of what most people would do.
> >> >>
> >> >> Firstly, please confirm that you are using AMBER 14 with all the
> >>latest
> >> >> patches. Look in your mdout file for the section that begins:
> >> >> --------------------- INFORMATION ----------------------
> >> >> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> >> >>
> >> >> And paste in the reported version and date here.
> >> >>
> >> >> Next try running your heating and initial equilibration on the CPU
> >>and
> >> >> then switch to the GPU and see if that helps.
> >> >>
> >> >> Finally confirm that if you use the exact same input with the exact
> >>same
> >> >> random seed (set ig explicitly) that the situation yields NANs at
> >> >>exactly
> >> >> the same point. This is critical and will establish that it is a bug
> >>in
> >> >> the code and not a misbehaving GPU.
> >> >>
> >> >> Once you have done this and have a reproducible test case that shows
> >> >>this
> >> >> behavior please post it here and we can try to figure out what the
> >> >>problem
> >> >> is.
> >> >>
> >> >> All the best
> >> >> Ross
> >> >>
> >> >>
> >> >> On 8/4/14, 12:04 PM, "Hoshin Kim" <85hskim.gmail.com> wrote:
> >> >>
> >> >> >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
> >> >> >error:
> >> >> >
> >> >> >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 =
> >> >> >0.0
> >> >> > Etot = NaN EKtot = NaN EPtot =
> >> >> >**************
> >> >> > BOND = 0.0000 ANGLE = 70230.8688 DIHED =
> >> >> >0.0000
> >> >> > 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
> >> >> >**************
> >> >> > EELEC = ************** EHBOND = 0.0000 RESTRAINT =
> >> >> >0.0000
> >> >> >
> >> >>
> >>
> >>>>>----------------------------------------------------------------------
> >>>>>--
> >> >>>--
> >> >> >----
> >> >> >
> >> >> >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.
> >> >> >
> >> >> >Regards,
> >> >> >
> >> >> >Hoshin
> >> >> >_______________________________________________
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> >> >>
> >> >>
> >> >>
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Received on Wed Aug 06 2014 - 12:30:02 PDT
