Re: Patchfile? Re: [gmx-users] gromacs 3.3.2

Allen Smith wrote: In message <[EMAIL PROTECTED]> (on 30 September 2007 22:09:21 +0200), [EMAIL PROTECTED] (David van der Spoel) wrote: Hi, it is my pleasure to let you all know that 3.3.2 is now available for download from the usual source: http://www.gromacs.org and ftp://ftp.gromacs.org

Re: [gmx-users] Reading XTC files from fortran90

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

Patchfile? Re: [gmx-users] gromacs 3.3.2

In message <[EMAIL PROTECTED]> (on 30 September 2007 22:09:21 +0200), [EMAIL PROTECTED] (David van der Spoel) wrote: >Hi, > >it is my pleasure to let you all know that 3.3.2 is now available for >download from the usual source: http://www.gromacs.org and >ftp://ftp.gromacs.org Will a patch be av

[gmx-users] gromacs 3.3.2

Hi, it is my pleasure to let you all know that 3.3.2 is now available for download from the usual source: http://www.gromacs.org and ftp://ftp.gromacs.org It contains a lot of small bug fixes. Cheers, -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala

Re: [gmx-users] Reading XTC files from fortran90

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

Re: [gmx-users] MPIRUN problem when switched to 8 np (searched the list)

Thanks Mark But there's no standard error output at all for my problem, it seems mdrun stagnated at this point, I dont know if anybody had met this situation before...and now I'm compiling LAMMPI as you suggested, hope this works for me. On 10/1/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > li

Re: [gmx-users] Reading XTC files from fortran90

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

Re: [gmx-users] Reading XTC files from fortran90

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

Re: [gmx-users] MPIRUN problem when switched to 8 np (searched the list)

liu xin wrote: Dear GMXers my mdrun stops when I try to do it with 8 nodes, but there's no error message, here's the end of the md0.log: The log file won't be helpful if the problem is outside of GROMACS, and the fact that it isn't helpful is strongly diagnostic of that. You need the standa

Re: [gmx-users] Reading XTC files from fortran90

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

Re: [gmx-users] Reading XTC files from fortran90

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

Re: [gmx-users] Reading XTC files from fortran90

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

Re: [gmx-users] Reading XTC files from fortran90

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

[gmx-users] MPIRUN problem when switched to 8 np (searched the list)

Dear GMXers my mdrun stops when I try to do it with 8 nodes, but there's no error message, here's the end of the md0.log: "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije LINCS: A Linear Constraint Solver for molecular simulations J. Comp. Chem. 18 (1997) pp. 1463-1472 --

Re: [gmx-users] Reading XTC files from fortran90

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

Re: [gmx-users] Reading XTC files from fortran90

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