Certain options require an amount of memory that is proportional to na x
nd x t, where na and nd are number of acceptors and donors, and t is
time. You need more memory. Or you could do your calculation for a
subset of your solvent.
Erik
Chandan Choudhury skrev 2011-04-13 13.29:
I missed my Gromacs version. It's 4.0.7
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Wed, Apr 13, 2011 at 4:58 PM, Chandan Choudhury <iitd...@gmail.com
<mailto:iitd...@gmail.com>> wrote:
Hello gmx-users !!
I tried using g_hbond tool to analyse h-bonds on my system. I
could successfully execute the tool for two of my systems. But the
third system should the memory problem. Below I have pasted my
command and its output.
/*$ g_hbond -s ../md0-20.tpr -f 40-50.trr -n index_2.ndx -num
hbnum.xvg -dist hbdist.xvg -ang hbang.xvg -life hblife.xvg -nice 0
-xvgr
*
No option -sel
Reading file ../md0-20.tpr, VERSION 4.0.7 (single precision)
Specify 2 groups to analyze:
Group 0 ( System) has 95687 elements
Group 1 ( HNP) has 10 elements
Group 2 ( PE) has 192 elements
Group 3 ( HP) has 216 elements
Group 4 ( CPE) has 9 elements
Group 5 ( SOL) has 95235 elements
Group 6 ( Cl) has 25 elements
Group 7 ( N_H) has 126 elements
Select a group: 5
Selected 5: 'SOL'
Select a group: 7
Selected 7: 'N_H'
Checking for overlap in atoms between SOL and N_H
Calculating hydrogen bonds between SOL (95235 atoms) and N_H (126
atoms)
Found 31795 donors and 31795 acceptors
-------------------------------------------------------
Program g_hbond, VERSION 4.0.7
Source code file: smalloc.c, line: 147
Fatal error:
Not enough memory. Failed to calloc 31795 elements of size 4 for
hb->hbmap[i]
(called from file gmx_hbond.c, line 186)
-------------------------------------------------------
"I Solve Problems" (Pulp Fiction)
: Cannot allocate memory
Making hbmap structure.../
Kindly help.
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
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