Thank you all. I could start the calculation
On 24 March 2014 16:46, Brian Radak <radak004.umn.edu> wrote:
> It might also be worth noting that, especially for small QM regions,
> parallelization can actually diminish performance. I've seen this happen
> with as few as 8 processors. As far as I know, this is a limitation of the
> algorithms, not the sander implementation. There is probably a similar
> problem for GPU accelerated QM/MM.
>
> On a separate note, has anyone been following the GPU developments in
> MOPAC? I'm sure there are some difficulties just with using the special GPU
> linear algebra libraries, etc. Are there any plans to bring this to SQM
> (obviously *very* long term)?
>
> Regards,
> Brian
>
>
> On Mon, Mar 24, 2014 at 12:35 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > On Mon, 2014-03-24 at 16:17 +0000, John Smith wrote:
> > > Hi AMBER users
> > >
> > > I am trying to run a QM/MM MD simulation on a protein ligand complex
> (431
> > > amino acid protein). I used Antechamber initially for the prepin and
> > frcmod
> > > files. I then used xLeap to generate the prmtop and inpcrd files. I am
> > > trying to run a QM/MM simulation where the quantum region would include
> > the
> > > ligand and a key residue in the protein (CYS123). I am using AMBER12
> and
> > > have a GPU machine. I noticed that I cannot use the PMEMD to run QM/MM
> > and
> > > I have to use Sander, even with Sander I am getting the error message
> > > "Internal namelist read error" and the calculation stops. The input
> files
> > > is as follows:
> > >
> > > Initial minimisation
> > > &cntrl
> > > imin=1, maxcyc=2000, ncyc=1000,
> > > cut=12, ntb=1, igb=0, ifqnt=1
> > > /
> > > &qmmm
> > > qmmask = '123, 432'
> > > qmcharge = 0,
> > > qm_theory = 'PM3'
> > > qmcut = 12.0
> > > /
> >
> > qmmask is not a valid mask. See Appendix C of the Amber manual for
> > details about the mask syntax. (I think you meant ':123,432')
> >
> > Also, putting commas after every variable in the input file might
> > prevent these kinds of errors with some compilers.
> >
> > > END
> > > END
> > >
> > > This input file is for the initial minimisation and I was planning to
> use
> > > the QM part on the MD stages as well but unfortunately I am being
> unable
> > to
> > > progress because of the aforementioned error message.
> > >
> > > Could you please help me with that?
> > >
> > > Also is there a command that I can use to run the calculations on the
> > GPU?
> >
> > No. The time-consuming part is the QM/MM part, anyway, so GPU
> > acceleration would not buy much speed enhancement. Semi-empirical QM/MM
> > is not well-suited for GPU acceleration (and only mopac can do it right
> > now, AFAIK).
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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Received on Mon Mar 24 2014 - 10:30:02 PDT
