[gmx-users] Re: gmx-users Digest, Vol 75, Issue 18

[kulleperuma.kulleperuma at utoronto.ca]

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>    1. Re: g_principal: memory corruption (David van der Spoel)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 03 Jul 2010 09:36:58 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] g_principal: memory corruption
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4C2EE89A.2070105 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 2010-07-03 02.40, kulleperuma.kulleperuma at 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.
> spoel at 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