[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 
> > 
> >     
> >    -- 
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>
> >   
> > 
>
> -- 
> Dr Pierre Cazade, PhD 
> AD3-023, Bernal Institute, 
> University of Limerick, 
> Plassey Park Road, 
> Castletroy, co. Limerick, 
> Ireland 
>
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