[CP2K:1581] Re: Isotopic dilution study
irti
irtazah... at gmail.com
Tue Feb 20 19:52:08 UTC 2018
Dear Teo,
Hi, kind section for D does not seems to work in QMMM setup. I am trying to
set up QMMM simulation for di-peptide in D2O and also I want to deuterate
certain H atoms of dipeptide.
After preparing coorinates and topology file with AMBER tools, I have
modifiled it with PARMED . CP2K reads the topology correctly with masses as
intended for dipeptide (also D2O) in the FIST module. But in the Quickstep
and QM section of QMMM _QM_ atoms which are deuterated in the MM does seem
to be not deuterated.
For example (copied from the output file)
MODULE FIST: ATOMIC COORDINATES IN ANGSTROM
Atom Kind ATM_TYP X Y Z q(eff)
Mass
1 1 _QM_ 3.971530 11.274613 5.974515 0.00
14.0100
* 2 2 _QM_ 4.861530 11.734613 6.124515 0.00
2.0140 #deuteated 3 2 _QM_ 3.401530 12.004613
5.574515 0.00 2.0140 4 2 _QM_ 3.581530
11.074613 6.884515 0.00 2.0140*
5 3 _QM_ 4.211530 10.104613 5.124515 0.00
12.0100
6 4 _QM_ 3.481530 9.344613 5.394515 0.00
1.0080
7 5 _QM_ 4.131530 10.454613 3.634515 0.00
12.0100
8 6 _QM_ 3.211530 10.964613 3.384515 0.00
1.0080
9 6 _QM_ 4.921530 11.134613 3.324515 0.00
1.0080
10 6 _QM_ 4.291530 9.514613 3.104515 0.00
1.0080
11 7 _QM_ 5.551530 9.434613 5.384515 0.00
12.0100
12 8 _QM_ 6.581530 10.014613 5.734515 0.00
16.0000
13 9 _QM_ 5.511530 8.094613 5.304515 0.00
14.0100
14 10 _QM_ 4.621530 7.744613 4.984515 0.00
2.0140
15 11 _QM_ 6.681530 7.254613 5.444515 0.00
12.0100
16 12 _QM_ 7.171530 7.674613 6.314515 0.00
1.0080
17 13 _QM_ 6.221530 5.884613 5.954515 0.00
12.0100
18 14 _QM_ 5.681530 6.034613 6.884515 0.00
1.0080
19 14 _QM_ 5.581530 5.364613 5.244515 0.00
1.0080
20 15 _QM_ 7.381530 4.954613 6.324515 0.00
12.0100
21 16 _QM_ 8.111530 5.544613 6.874515 0.00
1.0080
22 17 _QM_ 8.081530 4.224613 5.174515 0.00
12.0100
23 18 _QM_ 8.691530 4.984613 4.684515 0.00
1.0080
24 18 _QM_ 8.751530 3.474613 5.574515 0.00
1.0080
25 18 _QM_ 7.401530 3.834613 4.414515 0.00
1.0080
26 17 _QM_ 6.701530 3.804613 7.064515 0.00
12.0100
27 18 _QM_ 7.421530 3.014613 7.294515 0.00
1.0080
28 18 _QM_ 6.231530 4.094613 7.994515 0.00
1.0080
29 18 _QM_ 5.891530 3.394613 6.454515 0.00
1.0080
30 19 _QM_ 7.661530 7.274613 4.284515 0.00
12.0100
31 20 _QM_ 8.841530 7.664613 4.474515 0.00
16.0000
MODULE QM/MM first QM, then MM (0 charges): ATOMIC COORDINATES IN angstrom
Atom Kind Element X Y Z Z(eff)
Mass
1 1 H 1 4.861530 11.734613 6.124515 1.00
1.0079 # 4 H's were deuteraated but here it does not look like that
2 1 H 1 3.401530 12.004613 5.574515 1.00
1.0079
3 1 H 1 3.581530 11.074613 6.884515 1.00
1.0079
4 1 H 1 3.481530 9.344613 5.394515 1.00
1.0079
5 1 H 1 3.211530 10.964613 3.384515 1.00
1.0079
6 1 H 1 4.921530 11.134613 3.324515 1.00
1.0079
7 1 H 1 4.291530 9.514613 3.104515 1.00
1.0079
8 1 H 1 4.621530 7.744613 4.984515 1.00
1.0079
9 1 H 1 7.171530 7.674613 6.314515 1.00
1.0079
10 1 H 1 5.681530 6.034613 6.884515 1.00
1.0079
11 1 H 1 5.581530 5.364613 5.244515 1.00
1.0079
12 1 H 1 8.111530 5.544613 6.874515 1.00
1.0079
13 1 H 1 8.691530 4.984613 4.684515 1.00
1.0079
14 1 H 1 8.751530 3.474613 5.574515 1.00
1.0079
15 1 H 1 7.401530 3.834613 4.414515 1.00
1.0079
16 1 H 1 7.421530 3.014613 7.294515 1.00
1.0079
17 1 H 1 6.231530 4.094613 7.994515 1.00
1.0079
18 1 H 1 5.891530 3.394613 6.454515 1.00
1.0079
19 2 C 6 4.211530 10.104613 5.124515 4.00
12.0107
20 2 C 6 4.131530 10.454613 3.634515 4.00
12.0107
21 2 C 6 5.551530 9.434613 5.384515 4.00
12.0107
22 2 C 6 6.681530 7.254613 5.444515 4.00
12.0107
23 2 C 6 6.221530 5.884613 5.954515 4.00
12.0107
24 2 C 6 7.381530 4.954613 6.324515 4.00
12.0107
25 2 C 6 8.081530 4.224613 5.174515 4.00
12.0107
26 2 C 6 6.701530 3.804613 7.064515 4.00
12.0107
27 2 C 6 7.661530 7.274613 4.284515 4.00
12.0107
28 3 O 8 6.581530 10.014613 5.734515 6.00
15.9994
29 3 O 8 8.841530 7.664613 4.474515 6.00
15.9994
30 3 O 8 7.201530 6.854613 3.204515 6.00
15.9994
31 4 N 7 3.971530 11.274613 5.974515 5.00
14.0067
32 4 N 7 5.511530 8.094613 5.304515 5.00
14.0067
I have also tried to read in coorinates using &COORD section and label D
for deuterated atoms (with corresponding kind section the input) but there
is no change in output.
As QM atoms are defined using MM indexes I was wondering does CP2K uses
same mass as defined in the forcefield ?
How I can solve this technical issue? Thanks in advance.
I have attached the input and output file and basic working folder which
contains all the required files to run the simulation.
------------------------------------------------------------------
CP2K version 4.1
SVN source code revision svn:17462
cp2kflags: libint fftw3 libxc elpa3 parallel mpi3 scalapack
------------------------------------------------------------------
Best,
Irtaza
On Friday, November 28, 2008 at 9:45:54 PM UTC+1, Teo wrote:
>
> here's the way to fix this problem:
>
> &KI ND D
> BASIS_SET TZV2P-GTH
> POTENTIAL GTH-BLYP-q1
> MASS 2.0
> ELEMENT H
> &END KIND
>
> teo
>
> On 28 Nov 2008, at 21:43, Eric Shamay wrote:
>
> >
> > Here's the error I receive when trying the following:
> >
> > *** Unknown element for KIND <D>. This problem can be fixed
> > specifying ***
> > *** properly elements in PDB or specifying a KIND section or getting
> > in ***
> > *** touch with one of the
> > developers! ***
> >
> >
> > My KIND section is as follows:
> >
> > &KIND H
> > BASIS_SET TZV2P-GTH
> > POTENTIAL GTH-BLYP-q1
> > &END KIND
> > &KIND D
> > BASIS_SET TZV2P-GTH
> > POTENTIAL GTH-BLYP-q1
> > MASS 2.0
> > &END KIND
> > &KIND O
> > BASIS_SET TZV2P-GTH
> > POTENTIAL GTH-BLYP-q6
> > &END KIND
> > &KIND N
> > BASIS_SET TZV2P-GTH
> > POTENTIAL GTH-BLYP-q5
> > &END KIND
> >
> >
> > It's the error I received when trying that out before, but forgot what
> > the problem was. Any insight on this?
> >
> > ~Eric
> >
> >
> >
> > On Nov 21, 2:52 pm, Laino Teodoro <teodor... at gmail.com> wrote:
> >> Ciao Erick,
> >>
> >> sure it is possible. Please, follow this pseudo-input..
> >>
> >> &COORD
> >> D x y z
> >> D x y z
> >> O x y z
> >> H x y z
> >> H x y z
> >> O x y z
> >> &END
> >>
> >> &KIND H
> >> BASIS_SET ..
> >> POTENTIAL ..
> >> &END
> >>
> >> &KIND D
> >> BASIS_SET ..
> >> POTENTIAL ..
> >> MASS 2.0
> >> &END
> >>
> >> ...etc..
> >>
> >> ciao,
> >> Teo
> >>
> >> On 21 Nov 2008, at 23:46, Eric Shamay wrote:
> >>
> >>> Does anyone know of how I would specify this in my input file for
> >>> cp2k? Is this possible to do?
> > >
>
>
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