Dear Le Grand,
No. there are no hydrogen atoms connected to Au.
Regards,
Hoshin
On Sat, Aug 9, 2014 at 11:23 AM, Scott Le Grand <varelse2005.gmail.com>
wrote:
> Are there any H atoms connected to gold atoms here? And if so, what's the
> maximum coordination number of attached hydrogen atoms? The GPU code can
> only handle up to 4.
>
>
>
>
> On Fri, Aug 8, 2014 at 10:54 AM, Hoshin Kim <85hskim.gmail.com> wrote:
>
> > Dear Dr. Walker and Le Grand,
> >
> > I am not using SHAKE on the gold but using only on H atoms (ntf=2).
> >
> > As I already mentioned, this error occurred at 275 ps on GPU, when I set
> > same random seed (ig=71277). So, I am doing MD simulation on CPU using
> > exact same input parameters, and it already reached at 600 ps, without
> NaN
> > and asterisks errors.
> >
> > I will keep running it on CPU to see if same error occurs.
> >
> > Regards,
> >
> > Hoshin
> >
> >
> >
> > On Wed, Aug 6, 2014 at 3:24 PM, Scott Le Grand <varelse2005.gmail.com>
> > wrote:
> >
> > > 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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> > > > >> >> >AMBER.ambermd.org
> > > > >> >> >http://lists.ambermd.org/mailman/listinfo/amber
> > > > >> >>
> > > > >> >>
> > > > >> >>
> > > > >> >> _______________________________________________
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Received on Mon Aug 11 2014 - 10:00:02 PDT
