[CP2K-user] [CP2K:12196] modelling protein crystals
hut... at chem.uzh.ch
hut... at chem.uzh.ch
Tue Sep 10 10:53:41 UTC 2019
Yes
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Juerg Hutter Phone : ++41 44 635 4491
Institut für Chemie C FAX : ++41 44 635 6838
Universität Zürich E-mail: hut... at chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
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-----cp... at googlegroups.com wrote: -----
To: "cp2k" <cp... at googlegroups.com>
From: "Pierre-André Cazade"
Sent by: cp... at googlegroups.com
Date: 09/10/2019 11:40AM
Subject: Re: [CP2K:12196] modelling protein crystals
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
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------
-----c... at googlegroups.com wrote: -----
To: c... at googlegroups.com
From: "Pierre Cazade"
Sent by: c... at googlegroups.com
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 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
> Winterthurerstrasse 190
> CH-8057 Zürich, Switzerland
> ---------------------------------------------------------------
>
> -----c... at googlegroups.com wrote: -----
> To: "cp2k" <c... at googlegroups.com>
> From: "Pierre-André Cazade"
> Sent by: c... at googlegroups.com
> 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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