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Hi,<br><br>You should be much more precise in describing your problems.<br>gmxdump does not seem to give a segv at all.<br>Also you did not mail me your Gromacs version.<br><br>mdrun immediately gives a warning:<br>Warning: 1-4 interaction between 1 and 28 at distance 0.982 which is larger than the 1-4 table size 0.500 nm<br>These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br><br>You seem to have reduced the table size from the default 1.0 to 0.5.<br>But if interactions are beyond the table size, you need to increase the table.<br><br>Also your cut-off's are 0.1 nm, which is much smaller than the size of your atoms.<br>This simulation setup is complete nonsens.<br>You can never expect a system to run propely with these kind of settings.<br><br>Berk<br><br><hr id="stopSpelling">Date: Mon, 16 Feb 2009 12:57:50 +0400<br>From: varsha.gautham88@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] .mdp file for polymer<br><br>Hello sir,<br><br>On giving gmxdump its giving me an error saying "segmentation fault.My box size is 6x6X6.Am trying to run it it vaccum for 250 ps wit 50000 timesteps and with columb type=PME. I read from mailing list that PME calculations requires large amount of memory space.Is this an issue with dimension of box or with the system memory allocation ?Here's my log file.<br>
<br>T-Coupling : 106 (total 106 atoms)<br>Energy Mon. : 106 (total 106 atoms)<br>Acceleration: 106 (total 106 atoms)<br>Freeze : 106 (total 106 atoms)<br>User1 : 106 (total 106 atoms)<br>
User2 : 106 (total 106 atoms)<br>VCM : 106 (total 106 atoms)<br>XTC : 106 (total 106 atoms)<br>Or. Res. Fit: 106 (total 106 atoms)<br>QMMM : 106 (total 106 atoms)<br>ben-nch0.xtc frame 0:<br>
natoms= 1 step= 0 time=-2.9120485e-05 prec=2.8026e-45<br> box (3x3):<br> box[ 0]={-2.89059e-05, 3.98821e-34, -2.39380e-05}<br> box[ 1]={ 3.98770e-34, 1.40130e-45, -2.91168e-05}<br>
box[ 2]={-1.96789e+00, -2.91207e-05, -1.96789e+00}<br> x (1x3):<br>Segmentation fault<br> <br><br><br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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