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Today's Topics:
1. Re: g_principal: memory corruption (David van der Spoel)
----------------------------------------------------------------------
Message: 1
Date: Sat, 03 Jul 2010 09:36:58 +0200
From: David van der Spoel <sp...@xray.bmc.uu.se>
Subject: Re: [gmx-users] g_principal: memory corruption
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4c2ee89a.2070...@xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2010-07-03 02.40, kulleperuma.kulleper...@utoronto.ca wrote:
Hi all,
I am using Gromacs-4.0.5 g_principal for a system with a protein of 132
resiudes, ~450 octane molecules and ~9000 water molecules, as below,
g_principal -f pos_Rep.xtc -s em.tpr -n index.ndx (Protein was the
selected group ).
I get the follwing message soon after I selected Protein
Reading frame 0 time 0.000 *** glibc detected *** g_principal: malloc():
memory corruption: 0x000000000646c250 ***
======= Backtrace: =========
/lib64/libc.so.6[0x2b4788cd24ac]
/lib64/libc.so.6(__libc_calloc+0xc0)[0x2b4788cd3ce0]
g_principal[0x41071c]
g_principal[0x471aff]
g_principal[0x472237]
g_principal[0x410539]
g_principal[0x40251f]
g_principal[0x402139]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x2b4788c7d974]
g_principal[0x402079]
======= Memory map: ========
.................
This error didn't occur and ran smoothly when .gro file was selected for
-f flag, but failed even for a shorter trajectory file.
What is the way around for this problem
Thank you in advance!
Please submit a bugzilla with a short trajectory (since it crashes at
time 0 one frame is enough).
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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End of gmx-users Digest, Vol 75, Issue 18
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Thank you David and sorry for the late reply, The problem is fixed.
It's my mistake, I have been using a xtc file from a position
restrained equilibration, where the protein was fixed
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