[gmx-users] xtc files from fortran on 64 bit architecture

[Rahul Godawat]

Hi all, 

 

I need library to read xtc files on a 64 bit architecture (Intel Xeon) from
my fortran codes. Any hints on this wll help, I am currently using the 32
bit library (libxdrf_lnx.a) to do this which has a size limitation of 2 GB. 

 

Regards,

Rahul 

 

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Re: [gmx-users] xtc files

[YOLANDA SMALL]

Thanks David,
That works!

On Tue, 14 Mar 2006 08:49:43 +0100, David van der Spoel wrote:

 YOLANDA SMALL wrote:
  Hi All,
  
  How do I convert xtc files exported for a subset of atoms in my system to
pdb
  files?
  
  When I run trjconv, I get the following error message:
  
  Fatal error: Index[0] 3611 is larger than the number of atoms in the
trajectory
  file (3152)
  
  In my mdp file I specify the option 'xtc_grps' to export a subset of solvent
and
  protein atoms to an xtc file. This subset of atoms is defined in my index
file
  and contains 3152 atoms. Then I discard the .trr files to save space.  It
looks
  like the atom index gets renumbered from 1 in the new .xtc file so that the
new
  atom indeces no longer correspond to the atoms in the original coordinate
file.
   How do I recover the coordinates with matching atom names from the .xtc
file?
  
 Sorry I misread your question.
 You make a pdb file from your original tpr using the same index group 
 you used for the xtc-grps, then you use this pdb file as reference for 
 trjconv on the xtc to pdb conversion.
  Thanks,
  Yolanda
  
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 -- 
 David.
 
 David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
 Dept. of Cell and Molecular Biology, Uppsala University.
 Husargatan 3, Box 596,75124 Uppsala, Sweden
 phone:46 18 471 4205  fax: 46 18 511 755
 [EMAIL PROTECTED] [EMAIL PROTECTED]   http://folding.bmc.uu.se
 
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