[gmx-users] memory problems with g_hbond

[Attilio Vargiu]

Hi all,
 I have some problems with memory in analyzing the h-bonds between a 
 molecule and waters. This is an extract of the output:
 ------------------------
 Select a group: 65
 Selected 65: 'O9_IMI'
 Select a group: 9
 Selected 9: 'WAT'
 Checking for overlap...
 Calculating hydrogen bonds between two groups of 1 and 24078 atoms
 Found 0 donors and 1 acceptors in group 'O9_IMI'
 Found 8026 donors and 8026 acceptors in group 'WAT'
 Going to allocate 1509953 kb of memory,  and that's only the beginning
 Killed
 -------------------------
 
 Does someone know how to fix this problem? Is there some possibility 
 (for example with trjconv) to reduce the size of  the box removing some 
 water molecule?
 
 Thanks in advance, any help will be greatly apprecied!!!!
 
 Attilio
 
 ---------
 Attilio Vittorio Vargiu
 Ph.D. Student at SISSA/ISAS, via Beirut 4 34014 Trieste, Italy
 Phone: +39-040-3787335, Fax  : +39-040-3787528
 




----------------------------------------------------------------
  SISSA Webmail https://webmail.sissa.it/
  Powered by Horde http://www.horde.org/