Your GPU is very old, and the out of memory problem means just that: there
is not enough memory on the card. If your system has more than a few
hundred thousand atoms, this is going to happen on those old cards. A
newer GTX-1080Ti, Titan-V, or RTX card will handle any system that tleap
can generate (up to a few million atoms) just fine. If you have only 680
residues, the issue might be that your complex is very spread out or
unfolded.
If you're stuck with that old card, there are still things you can try. A
single 680 residue globular protein will typically fit in a water box of
150k atoms. You might be able to switch to an octahedral box (rebuild in
tleap) and save a little bit of volume that way. Otherwise, look at how
much water you're trying to place around the whole thing and how far the
complex is separated at the beginning of the run.
Dave
On Mon, Aug 19, 2019 at 8:55 AM Giulia Paiardi <g.paiardi.unibs.it> wrote:
> It's a Tesla K20c.
> Could there be problem with compatibility?
>
> Giulia
>
> Il giorno lun 19 ago 2019 alle ore 13:11 Jacopo Sgrignani <
> sgrigna.gmail.com>
> ha scritto:
>
> > Dear Giulia
> > Which hardware (GPU model) are you using ?
> >
> >
> > Jacopo
> >
> > Il lun 19 ago 2019, 13:01 Giulia Paiardi <g.paiardi.unibs.it> ha
> scritto:
> >
> > > Hi amber users,
> > > I try to set up a production for accellerated MD using amber 14.
> > > I'm following the concepts of tutorial 22 of amber because my complex
> is
> > > bigger than that of the example (680 residue vs 58 of the example).
> > > I obtained a stable equilibration process but when I start the
> > production
> > > with the following script
> > >
> > > AVP dt=2.0fs with SHAKE, NPT aMD boost pot and dih
> > > &cntrl
> > > imin=0, irest=1, ntx=5,
> > > dt=0.002, ntc=2, ntf=2, tol=0.000001,iwrap=1,
> > > ntb=2, cut=12.0, ntp=1,igb=0,ntwprt = 0,ioutfm = 1,
> > > ntt=3, temp0=310.0, gamma_ln=1.0, ig=-1,
> > > ntpr=1000, ntwx=1000, ntwr=1000, nstlim=2000000,
> > > iamd=3, EthreshD=11481,
> > > alphaD=544,EthreshP=-2705594,
> > > alphaP=204136,
> > > /
> > > &ewald
> > > dsum_tol=0.000001,
> > > /
> > >
> > > the resulting error using pmemd.cuda is
> > > cudaMalloc GpuBuffer::Allocate failed out of memory
> > > Someone can help me resolving with problem?
> > >
> > > Thanks
> > > Giulia
> > >
> > > --
> > >
> > >
> > > Informativa sulla Privacy: http://www.unibs.it/node/8155
> > > <http://www.unibs.it/node/8155>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
>
>
> Informativa sulla Privacy: http://www.unibs.it/node/8155
> <http://www.unibs.it/node/8155>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 19 2019 - 10:30:02 PDT
