<div dir="ltr"><br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">sapna sarupria</b> <<a href="mailto:sapna.sarupria@gmail.com">sapna.sarupria@gmail.com</a>><br>
Date: Tue, Jul 15, 2008 at 9:16 AM<br>Subject: Using user-tables for simulations in vacuum<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br><br><br><div dir="ltr">
Hello users,<br><br>I am trying to do a simulation of a polymer chain (which is simply a bead of unified methane molecules) in vacuum using user-defined tables. The interactions are Weeks-Chandler-Andersen instead of Lennard-Jones. However, when I run the simulations, mdrun gives me a segmentation fault. When I run simulations for the exact same configurations without the tables (and therefore using VdW) the simulations run fine. In addition, the starting configurations were obtained after 3ns simulations of the polymer in water.<br>
<br>So I was wondering if there is any issue with using user-defined tables with simulations in vacuum. If not do you have any idea what could be going wrong. <br>Some details of the mdp file:<br>1. pbc is turned off.<br>
2. there is no pressure coupling.<br>3. center of mass removal is set to angular.<br>4. temperature is 298 K and berendsen thermostat is used.<br>5. energy groups and table are defined (correctly).<br>6. the cut-offs are set to 1.0nm (box size is larger than 4 nm).<br>
7. no constraints are being used.<br><br>Thank you<br><br>Regards<br>Sapna<br></div>
</div><br><br clear="all"><br>-- <br>Sapna Sarupria<br>Ph.D. Student - Chemical Engineering<br>Rensselaer Polytechnic Institute<br>Troy, New York 12180<br>U.S.A.<br>Ph#: (518)276-3031<br>Life isn't about finding yourself. Life is about creating yourself. <br>
George Bernard Shaw. <br>Dare to Dream
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