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
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