Hi Leila,
r.ndx would be the index file indeed. Sorry for not explicitly mentioning
that. For the rest, the most important question is 'did it work?' Knowing
python is not so important, unless you're determined to understand how it
works :) As for the numbers, python always goes up to, not includi
Dear Tsjerk
thanks for your reply
I have not experience in using python.
in [python -c
'r,a,b,c=range,1868,24086,24100;open("r.ndx","w").write("[x]\n"+"\n".join([str(i)
for i in r(1,a)+r(b,c)+r(a,b)]))'].
r.ndx contains all the atoms. is it true?
why did you use r,a,b,c=range,1868,24086,24100
Hey Leila,
Why all the fuzz? You can do this with trjconv using an index file.
The following oneliner (:$) should write you the index file you need.
python -c
'r,a,b,c=range,1868,24086,24100;open("r.ndx","w").write("[x]\n"+"\n".join([str(i)
for i in r(1,a)+r(b,c)+r(a,b)]))'
Hope it helps,
Tsj
for example ordering in final.pdb is as follows:
ATOM 1856 N2 DG3 X 86 15.620 47.770 21.660 1.00
0.00
ATOM 1857 H21 DG3 X 86 16.480 48.290 21.560 1.00
0.00
ATOM 1858 H22 DG3 X 86 15.010 48.060 22.420 1.00
0.00
ATOM 1859 N3 DG3 X 86 14.160 46.250 20.
Dear Justin and Chris
very thanks for your reply and guidance.
I did all the steps successfully. then I used (./my_tool -f final.xtc -o
final.pdb -b 300 -e 350), the final.pdb file was created without problem.
when I opened final.pdb file by text editor, order of waters and ions in
final.pdb was
leila karami wrote:
Dear Chris
very thanks for your time and attention.
only difference between what you said and what I did is in the
location of template directory:
for me gromacs-4.0.7/share/template
for you gromacs-4.0.7/exec/share/gromacs/template
in my gromac
Dear Chris
very thanks for your time and attention.
only difference between what you said and what I did is in the
location of template directory:
for me gromacs-4.0.7/share/template
for you gromacs-4.0.7/exec/share/gromacs/template
in my gromacs there is not exec dire
Dear Chris
I found gmx_trjconv.c file, It is in gromacs-4.0.7/src/tools.
since location of template directory is as follows:
gromacs-4.0.7/share/template,
I used cp gmx_trjconv.c ../../share/template/my_tool.c.
is it true?
I did those changes you said in my_tool.c file.
I created makefile without
Dear Chris
Happy new year
thanks for your reply.
please clarify these more:
cd src/tools
cp gmx_trjconv.c ../../exec/share/gromacs/template/my_tool.c
1) where is exact location of gmx_trjconv.c file?
when I enter cd /src, in src directory, there is not tools directory.
2) in my linux, gromacs
Dear Leila:
Perhaps I took the long way around, but I am not aware of any such
tool. You can make custom modifications to things like trjconv as
follows.
!!! Please note: I didn't test this except to see that it compiles.
You should run some analyses before and after switching the order t
Dear gromacs users
My simulation system contains protein, dna, water molecules and Na+
ions respectively.
I want to reorder water molecules with Na+ ions in final xtc file as
at first
1-1867 complex (protein and dna)
1868 - 24085 SOL (water molecules)
24086 -
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