Hi Jones,
I'm not sure what you mean with "shape" and "that integer". There's
> > nothing much redundant in the .xtc file and there are no integers
> > having to do with box shape. In fact, there is no "shape"...
>
>
> Well, by "shape" I meant "cubic" and "truncated octahedral", for example.
> But
Hi Mark.
> I think those three can become yes in a really easy way: some kind of
> > "state machine" would easily do the trick and "count" them properly.
> Yes, but now you have to infer molecule changes from residue name
> changes, which is doable, but messy.
Forgot about this slice of the prob
Jones de Andrade wrote:
>From .gro or .pdb file in the standard way.
> number of molecules types,
No
> number of molecules of each type,
No
> number of atoms of each molecule type,
No
I think those three can become yes in a really easy way: some kind of
"state ma
Hi all.
First of all, I would really want want to apologize if I somehow
missunderstood any previous message from anyone, and made myself a bit
annoying because of this fact.
Second, I would like to say thanks again to eferybody for all help in these
matters.
On 10/1/07, Tsjerk Wassenaar <[EMAIL
Jones de Andrade wrote:
Hi all.
First: ok, lets stop the C X Fortran issue here: this kind of subject
always look like a "ready to become flamme war" one. ;) Sorry for
rising the subject a bit in the previous email.
The point is: when this project started, almost 4 years ago, I already
kne
Jones de Andrade wrote:
Hi Mark.
Wait a second, you mean that editconf would allow me to have both
charges and masses on a .pdb file directly from command line (having
other matters asking for my presence absolutelly now, so please forgive
me if this message becomes somehow strange)
No, nob
Hi Jones,
> I can already do that for .xtc files. Seems that, unfortunatelly, the least
> odd way is to find a way to get the last pieces of information needed
> (atomic charges and masses) from the .tpr files. Other ways would include
> lots of file translations, or adaptions in the codes themsel
Hi all.
First: ok, lets stop the C X Fortran issue here: this kind of subject always
look like a "ready to become flamme war" one. ;) Sorry for rising the
subject a bit in the previous email.
The point is: when this project started, almost 4 years ago, I already knew
very well frotran90, and gro
Jones de Andrade wrote:
Hi Mark.
Wait a second, you mean that editconf would allow me to have both
charges and masses on a .pdb file directly from command line (having
other matters asking for my presence absolutelly now, so please forgive
me if this message becomes somehow strange)
So, I w
Hi Mark.
Wait a second, you mean that editconf would allow me to have both charges
and masses on a .pdb file directly from command line (having other matters
asking for my presence absolutelly now, so please forgive me if this message
becomes somehow strange)
So, I would have atom names, number o
Jones de Andrade wrote:
Hi all.
Firstly, thanks a lot for all the help! ;)
First, about reading the atom-names from a .gro file, I don't think it
would "so painfull". It would "look like" a bit to having a well
programmed "state machine" in the code.
About the language, yes, I admit that b
Hi all.
Firstly, thanks a lot for all the help! ;)
First, about reading the atom-names from a .gro file, I don't think it would
"so painfull". It would "look like" a bit to having a well programmed "state
machine" in the code.
About the language, yes, I admit that bor reads and writes, fortran
David van der Spoel wrote:
the box is in the xtc file, if you need the atom names a corresponding
pdb or gro file should do the trick. don't try to read tpr files or
gmxdumps of it, that's a complete waste of time. you can e.g. use
editconf to dump a pdb file with charges in the b-factor field
Mark Abraham wrote:
Jones de Andrade wrote:
Hi Tsjerk.
Thanks for the prompt answer.
Good idea, I can take the atom names from a .gro file, nad, probably
some strange algorithm can also get the number of atoms per molecule
and number of molecules from there, am I right? That would help a lot
Jones de Andrade wrote:
Hi Tsjerk.
Thanks for the prompt answer.
Good idea, I can take the atom names from a .gro file, nad, probably
some strange algorithm can also get the number of atoms per molecule and
number of molecules from there, am I right? That would help a lot.
Simplest is to wr
Hi Tsjerk.
Thanks for the prompt answer.
Good idea, I can take the atom names from a .gro file, nad, probably some
strange algorithm can also get the number of atoms per molecule and number
of molecules from there, am I right? That would help a lot.
But: I'll still be unable to get atomic masses
Hi Jones,
You probably only need to read the atoms and such from a .pdb or .gro
file, unless you really want to have topology information (bondedness,
molecule definitions, etc). Then you do have to read the topology file
or a .tpr file directly. Don't recall having seen the fortran
implementation
Hi Bert.
Thanks a lot for the help. I've found the mistakes, one programming minor
issue and a compiler configuration a bit of "hidden" in the config files.
Old time mistakes just choose to arise at its worst moments. :)
At the moment, I already can read the coordinates, number of atoms, box
coor
On Sat, 29 Sep 2007, Jones de Andrade wrote:
> Hi Bert.
>
> Thank you for the prompt answer.
>
> Just did as instructed, but got the following:
>
> CruNumMac src/own/B/9/xtc 286% ifort xtciof.f90 test_xtc.f90
> -L/home/johannes/src/own/B/9/xtc/xtc/ -lxrdf -lg2c
> IPO link: can not find -lxrdf
we
Hi Bert.
Thank you for the prompt answer.
Just did as instructed, but got the following:
CruNumMac src/own/B/9/xtc 286% ifort xtciof.f90 test_xtc.f90
-L/home/johannes/src/own/B/9/xtc/xtc/ -lxrdf -lg2c
IPO link: can not find -lxrdf
ifort: error: problem during multi-file optimization compilation
Hi,
try:
download
http://www.mpibpc.gwdg.de/groups/de_groot/xtc.tar.gz
(and optionally issue a 'make' in the xtc directory after unpacking)
in the linking stage, use something like
ifort -blabla -lxdrf -L/wherever/xtc -lg2c
your smalll test code looks OK apart from the fact that I don't know
Hi all.
I'm writing this beucase I'm having terrible problems in trying to deal with
gromacs trajectory files with my own programs, originally written on
fortran90.
The codes themselves are enoughly big to make it out of question to try to
"translate" them. What leads to some sort of mixed langua
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