I missed my Gromacs version. It's 4.0.7<br clear="all"><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Wed, Apr 13, 2011 at 4:58 PM, Chandan Choudhury <span dir="ltr"><<a href="mailto:iitdckc@gmail.com">iitdckc@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello gmx-users !!<br><br>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.<br>
<br><i><b>$ 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<br></b><br clear="all">No option -sel<br>Reading file ../md0-20.tpr, VERSION 4.0.7 (single precision)<br>
Specify 2 groups to analyze:<br>Group 0 ( System) has 95687 elements<br>Group 1 ( HNP) has 10 elements<br>Group 2 ( PE) has 192 elements<br>Group 3 ( HP) has 216 elements<br>
Group 4 ( CPE) has 9 elements<br>Group 5 ( SOL) has 95235 elements<br>Group 6 ( Cl) has 25 elements<br>Group 7 ( N_H) has 126 elements<br>Select a group: 5<br>Selected 5: 'SOL'<br>
Select a group: 7<br>Selected 7: 'N_H'<br>Checking for overlap in atoms between SOL and N_H<br>Calculating hydrogen bonds between SOL (95235 atoms) and N_H (126 atoms)<br>Found 31795 donors and 31795 acceptors<br>
<br>-------------------------------------------------------<br>Program g_hbond, VERSION 4.0.7<br>Source code file: smalloc.c, line: 147<br><br>Fatal error:<br>Not enough memory. Failed to calloc 31795 elements of size 4 for hb->hbmap[i]<br>
(called from file gmx_hbond.c, line 186)<br>-------------------------------------------------------<br><br>"I Solve Problems" (Pulp Fiction)<br>: Cannot allocate memory<br>Making hbmap structure...</i><br><br><br>
Kindly help.<br><font color="#888888"><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
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