<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt">Hi,<br>I have got a segmentation fault error when I run mdrun for 1ns. I would be glad if you let me know what is going on and how can I solve it.<br>Thank you very much.<br><br>Best,<br><br><div> </div>Jahanshah Ashkani,<br>PhD student of Biotechnology & Genetics,<br>University of the Western Cape,<br>Biotechnology Department,<br>Private Bag X17,<br>7735 Bellville,<br>Cape Town,<br>South Africa<br>jashkani@mail.biotech.uwc.ac.za<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original Message ----<br>From: Justin A. Lemkul <jalemkul@vt.edu><br>To: JMandumpal <jesbman@rediffmail.com><br>Cc: gmx-users@gromacs.org<br>Sent: Tuesday, December 4, 2007
4:07:36 AM<br>Subject: Re: Re: Re: [gmx-users] Energy minimisation<br><br>
Quoting JMandumpal <<a ymailto="mailto:jesbman@rediffmail.com" href="mailto:jesbman@rediffmail.com">jesbman@rediffmail.com</a>>:<br><br>><br>> Dear Justin,<br>><br>> I made some changes in my .mdp file, but the result is same.<br>><br>> My box size, as mentioned in the previous mail, is 20.1 A. The cut
off I used<br>> is 8 angstrom.<br>><br>> I attach the input file here.<br>> **************************************<br>><br>> cpp = /lib/cpp<br>> define = -DPOSRES-DFLEX_SPC<br>> constraints = none<br>> morse = no<br>> integrator = steep<br>> nsteps = 2000<br>> ; Energy minimizing<br>> emtol = 100<br>> emstep = 0.00001<br>> nstcomm = 1<br>> ns_type = grid<br>> rlist = 0.8<br>> coulumbtype = pme<br>> rcoulomb = 0.8<br>> vdw-type = cut-off<br>> rvdw = 0.8<br>> nstenergy
= 10<br>> Tcoupl = no<br>> Pcoupl = no<br>> gen_vel = no<br>> *************************************************<br>><br>> And the output message is :<br>><br>>
---------------------------------------------------------------------------<br>> creating statusfile for 1 node...<br>><br>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#<br>> checking input for internal consistency...<br>> calling /lib/cpp...<br>> processing topology...<br>> Generated 332520 of the 332520 non-bonded parameter combinations<br>> Generating 1-4 interactions: fudge = 0.5<br>> Generated 332520 of the 332520 1-4 parameter combinations<br>> Excluding 2 bonded neighbours for SOL 258<br>> NOTE:<br>> System has non-zero total charge: -2.580000e-01<br>><br>> processing coordinates...<br>> double-checking input for internal consistency...<br>> ERROR: The cut-off length is longer than half the shortest box vector
or<br>> longer than the smallest box diagonal element. Increase the box size
or<br>> decrease rlist.<br>> -------------------------------------------------------<br>> Program grompp, VERSION 3.3.2<br>> Source code file: grompp.c, line: 1111<br>><br>> Fatal error:<br>> There were 1 error(s) processing your input<br>> -------------------------------------------------------<br>><br>> "Stop Drinking My Beer !" (The Amps)<br>>
----------------------------------------------------------------------<br>><br>><br>> HOW CAN I SETTLE THIS ISSUE?<br><br>Did you read Tsjerk's message from this morning? His suggestions
regarding PBC<br>and verifying your box dimensions are good ones that I had not
considered.<br><br>Also note that you probably have a broken topology, as the net charge
on your<br>system is non-integral. This has nothing to do with the problem at
hand, but<br>it will likely be problematic later.<br><br>-Justin<br><br>><br>><br>> REGARDS<br>> JESTIN<br>><br><br><br><br>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br><a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/</a><br><br>========================================<br>_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a
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