Isotopic dilution study
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Eric Shamay
Nov 21, 2008, 5:46:04 PM11/21/08
to cp2k
Hello cp2k users,
I am starting a study that requires the use of deuterium to make D2O
instead of water in my aqueous phase. I'd like to specify certain
atoms to use the normal hydrogen definitions (with a mass of 1.0), and
other atoms to have the same but with mass=2.0. For instance, I wish
to model nitric acid, and keep the acid proton as a hydrogen, but
change all the waters around it to D2O.
Does anyone know of how I would specify this in my input file for
cp2k? Is this possible to do?
Thanks,
~Eric
I am starting a study that requires the use of deuterium to make D2O
instead of water in my aqueous phase. I'd like to specify certain
atoms to use the normal hydrogen definitions (with a mass of 1.0), and
other atoms to have the same but with mass=2.0. For instance, I wish
to model nitric acid, and keep the acid proton as a hydrogen, but
change all the waters around it to D2O.
Does anyone know of how I would specify this in my input file for
cp2k? Is this possible to do?
Thanks,
~Eric
Laino Teodoro
Nov 21, 2008, 5:52:32 PM11/21/08
to cp...@googlegroups.com
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
Eric Shamay
Nov 24, 2008, 1:12:56 PM11/24/08
to cp2k
Teo,
thanks for the response. Are you suggesting using the same basis set
and potential for D as for H but only changing the mass?
thanks.
thanks for the response. Are you suggesting using the same basis set
and potential for D as for H but only changing the mass?
thanks.
Teodoro Laino
Nov 24, 2008, 1:15:28 PM11/24/08
to cp...@googlegroups.com
Well.. "chemically" speaking they are the same.. I'm not aware of any
particular influence on the
basis set / potential due to the additional neutron. Do you?
Teo
particular influence on the
basis set / potential due to the additional neutron. Do you?
Teo
Eric Shamay
Nov 26, 2008, 2:05:18 PM11/26/08
to cp2k
Nope :) Thanks for the help.
~Eric
~Eric
Eric Shamay
Nov 28, 2008, 3:43:55 PM11/28/08
to cp2k
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
*** 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
Laino Teodoro
Nov 28, 2008, 3:45:54 PM11/28/08
to cp...@googlegroups.com
here's the way to fix this problem:
&KI ND D
&END KIND
teo
&KI ND D
BASIS_SET TZV2P-GTH
POTENTIAL GTH-BLYP-q1
MASS 2.0
ELEMENT H
POTENTIAL GTH-BLYP-q1
MASS 2.0
&END KIND
teo
Eric Shamay
Dec 1, 2008, 11:55:33 AM12/1/08
to cp2k
Thanks Teo, adding the ELEMENT tag works!
~Eric
~Eric
Eric Shamay
Dec 1, 2008, 7:46:45 PM12/1/08
to cp2k
One last issue on this - When the trajectories are printed (i.e. when
doing geo_opt or MD) the output XYZ file contains the name of the
element H again. I.e. my input coordinates specify that the atom name
is 'D', but then the output, instead of printing 'D' for each atom, it
prints out 'H' as if I had never changed the KIND. Is the output based
on the 'ELEMENT' parameter? Is there a way to force it to output the
name associated with the 'KIND' and not the 'ELEMENT' of each atom?
doing geo_opt or MD) the output XYZ file contains the name of the
element H again. I.e. my input coordinates specify that the atom name
is 'D', but then the output, instead of printing 'D' for each atom, it
prints out 'H' as if I had never changed the KIND. Is the output based
on the 'ELEMENT' parameter? Is there a way to force it to output the
name associated with the 'KIND' and not the 'ELEMENT' of each atom?
Laino Teodoro
Dec 2, 2008, 1:54:49 AM12/2/08
to cp...@googlegroups.com
Hi Eric,
On 2 Dec 2008, at 01:46, Eric Shamay wrote:
>
> One last issue on this - When the trajectories are printed (i.e. when
> doing geo_opt or MD) the output XYZ file contains the name of the
> element H again. I.e. my input coordinates specify that the atom name
> is 'D', but then the output, instead of printing 'D' for each atom, it
> prints out 'H' as if I had never changed the KIND. Is the output based
of course you never changed the KIND, but the "standard" of XYZ is to
have:
ELEMENT X Y Z
and not
KIND x y z
If you want to be able to track the "D", then I suggest you to
exploit the
capabilities of VMD, first loading an XYZ with the names you like and
loading
on the top of that molecule the whole trajectory you like (since the
order of the atoms
in the trajectory is the same as the one in input).
Instead of the original XYZ, you can as well use PSF or PDB.
Teo
On 2 Dec 2008, at 01:46, Eric Shamay wrote:
>
> One last issue on this - When the trajectories are printed (i.e. when
> doing geo_opt or MD) the output XYZ file contains the name of the
> element H again. I.e. my input coordinates specify that the atom name
> is 'D', but then the output, instead of printing 'D' for each atom, it
> prints out 'H' as if I had never changed the KIND. Is the output based
have:
ELEMENT X Y Z
and not
KIND x y z
If you want to be able to track the "D", then I suggest you to
exploit the
capabilities of VMD, first loading an XYZ with the names you like and
loading
on the top of that molecule the whole trajectory you like (since the
order of the atoms
in the trajectory is the same as the one in input).
Instead of the original XYZ, you can as well use PSF or PDB.
Teo
Eric Shamay
Dec 2, 2008, 2:43:53 PM12/2/08
to cp2k
Teo,
thanks for your help on this. I've just output the first 1000
timesteps and verified that the system is doing what it should be
doing, and convinced myself that even though the output says H, it's
still behaving like a D. I just generated some IR data from the system
dipole autocorrelation function and the spectra look convincing.
thanks a lot!
~Eric
thanks for your help on this. I've just output the first 1000
timesteps and verified that the system is doing what it should be
doing, and convinced myself that even though the output says H, it's
still behaving like a D. I just generated some IR data from the system
dipole autocorrelation function and the spectra look convincing.
thanks a lot!
~Eric
irti
Feb 20, 2018, 2:52:08 PM2/20/18
to cp2k
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
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
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