[CP2K-user] [CP2K:12185] modelling protein crystals
Pierre-André Cazade
pierre.a... at gmail.com
Tue Sep 10 09:40:40 UTC 2019
Dear Juerg,
Thank you very much for your answer that helps me understand better how to
efficiently use CP2K. I do realise that perhaps the reason why my system
was going wrong using LS_SCF was I tried to use it together with OT.
Apparently, these methods are not meant to be use together. It is one or
the other. Am I correct?
Best regards,
Pierre
On Tuesday, September 10, 2019 at 8:46:41 AM UTC+1, jgh wrote:
>
> Hi
>
> yes, LS_SCF is for very large systems, but
> - it has a large prefactor that is strongly dependent on the
> method and system (basis set etc)
> - it needs much more care and should only be used after
> extensively study the system properties using smaller systems.
>
> Depending on the QM method you are using (I assume here a GGA KS-DFT
> with a DZVP basis) I would guess
>
> - protein crystal of 10000 atoms -> use OT
> - 100000 atom system -> use LS_SCF and a very large supercomputer
>
> regards
>
> Juerg Hutter
> --------------------------------------------------------------
> Juerg Hutter Phone : ++41 44 635 4491
> Institut für Chemie C FAX : ++41 44 635 6838
> Universität Zürich E-mail: h... at chem.uzh.ch
> <javascript:>
> Winterthurerstrasse 190
> CH-8057 Zürich, Switzerland
> ---------------------------------------------------------------
>
> -----c... at googlegroups.com <javascript:> wrote: -----
> To: c... at googlegroups.com <javascript:>
> From: "Pierre Cazade"
> Sent by: c... at googlegroups.com <javascript:>
> Date: 09/06/2019 10:44AM
> Subject: Re: [CP2K:12185] modelling protein crystals
>
> Dear Juerg,
>
> Thank you for your answer. Could you please elaborate? Is not Linear
> Scaling SCF meant to make it feasible running QM calculation for large
> systems? It was my understanding from the workshops presentations and
> the tutorials. What would you recommend for a protein crystal of 10000
> atoms and another of 100000 with different heme groups (A and B) and
> ions bridges? Simply OT?
>
> Thank you again,
> Pierre
>
> On 06/09/2019 09:37, h... at chem.uzh.ch <javascript:> wrote:
> > Hi
> >
> > I would not start using the LS_SCF optimizer, but use a standard
> > OT setup.
> >
> > regards
> >
> > Juerg Hutter
> > --------------------------------------------------------------
> > Juerg Hutter Phone : ++41 44 635 4491
> > Institut für Chemie C FAX : ++41 44 635 6838
> > Universität Zürich E-mail: h... at chem.uzh.ch
> <javascript:>
> > Winterthurerstrasse 190
> > CH-8057 Zürich, Switzerland
> > ---------------------------------------------------------------
> >
> > -----c... at googlegroups.com <javascript:> wrote: -----
> > To: "cp2k" <c... at googlegroups.com <javascript:>>
> > From: "Pierre-André Cazade"
> > Sent by: c... at googlegroups.com <javascript:>
> > Date: 09/04/2019 12:29PM
> > Subject: [CP2K:12182] modelling protein crystals
> >
> > Dear CP2K users,
> >
> > Aside for my previous post, I am also interested in using CP2K to model
> protein crystals. Some of the proteins I am interested in are
> metalloproteins. Using again my test system, beta glycine, I am simply
> adding the following block to an input that works to preform a CELL_OPT.
> Please find part of this input below:
> >
> > &FORCE_EVAL
> > METHOD QS
> > STRESS_TENSOR ANALYTICAL
> > &DFT
> > BASIS_SET_FILE_NAME /usr/local/src/cp2k/data/GTH_BASIS_SETS
> > POTENTIAL_FILE_NAME /usr/local/src/cp2k/data/GTH_POTENTIALS
> > MULTIPLICITY 0
> > CHARGE 0
> > &SCF
> > MAX_SCF 20
> > EPS_SCF 1.e-7
> > SCF_GUESS ATOMIC
> > &OT T
> > MINIMIZER CG
> > PRECONDITIONER FULL_SINGLE_INVERSE
> > &END OT
> > &OUTER_SCF T
> > EPS_SCF 1.e-6
> > MAX_SCF 50
> > &END OUTER_SCF
> > &END SCF
> > &QS
> > LS_SCF T
> > EPS_DEFAULT 1.0000000000000000E-10
> > EPS_PGF_ORB 1.0000000000000000E-08
> > METHOD GPW
> > &END QS
> > &MGRID
> > NGRIDS 4
> > CUTOFF 5.0000000000000000E+02
> > REL_CUTOFF 8.0000000000000000E+01
> > &END MGRID
> > &XC
> > DENSITY_CUTOFF 1.0000000000000000E-10
> > GRADIENT_CUTOFF 1.0000000000000000E-10
> > TAU_CUTOFF 1.0000000000000000E-10
> > &XC_FUNCTIONAL NO_SHORTCUT
> > &PBE T
> > &END PBE
> > &END XC_FUNCTIONAL
> > &END XC
> > &POISSON
> > POISSON_SOLVER PERIODIC
> > PERIODIC XYZ
> > &END POISSON
> > &END DFT
> >
> > So I tried to add this block:
> >
> > &LS_SCF
> > PURIFICATION_METHOD TRS4
> > EPS_FILTER 1E-6
> > EPS_SCF 1E-7
> > MAX_SCF 20
> > S_PRECONDITIONER ATOMIC
> > &END
> >
> > and it does not work. Then, I tried:
> >
> > &LS_SCF
> > PURIFICATION_METHOD TRS4
> > EPS_FILTER 1E-6
> > EPS_SCF 1E-7
> > MAX_SCF 30
> > S_PRECONDITIONER NONE
> > &CURVY_STEPS
> > &END CURVY_STEPS
> > &END
> >
> > And again, it failed. In both cases, at first the optimization goes
> well, I reach a point where the system is almost optimized and then
> everything goes wrong. If anyone can tell me what I am doing wrong, I would
> be grateful. More generally, if anyone could tell me which algorithms I
> should use to maximize the efficiency of the calculation for large systems
> (up to about 100000 atoms), while having decent accuracy and stability, I
> would be grateful. I have checked the various options in SCF, OT,
> OUTER_SCF, LS_SCF and MOTION, but it is unclear which ones are the most
> suitable and can work well together.
> >
> > Thank you,
> > Pierre
> >
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "cp2k" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> an email to c... at googlegroups.com <javascript:>.
> > To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/ea4192e6-fe57-4ecd-99eb-e1cb6430c365%40googlegroups.com.
>
> >
> >
>
> --
> Dr Pierre Cazade, PhD
> AD3-023, Bernal Institute,
> University of Limerick,
> Plassey Park Road,
> Castletroy, co. Limerick,
> Ireland
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to c... at googlegroups.com <javascript:>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/47f4bdba-74cc-ab74-bf18-53a2dea287ea%40gmail.com.
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20190910/756ea2e4/attachment.htm>
More information about the CP2K-user
mailing list