Hi,<div><br></div><div>don't send user questions to the developer list!</div><div><br></div><div>Roland<br><br><div class="gmail_quote">On Tue, May 8, 2012 at 9:11 PM, Prakash Chapain <span dir="ltr"><<a href="mailto:pchapain@gmail.com" target="_blank">pchapain@gmail.com</a>></span> wrote:<br>
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<div class="gmail_quote"><span>Hello, </span><br>
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<span>I am very new to GROMACS and needed some help with simple MD simulations. I have amyloid beta peptide (pdb code 1IYT) monomer that I need to place side by side in a water box, energy minimize and run the simulation. I have problems putting them together
and creating the new necessary files for the simulation. I can work it out for a single peptide in a solvated system but can't figure out how to run the simulations for both together to see any â-sheet/dimer formation.</span><br>
<span>Please help and be as detailed as possible as I am very new to GROMACS. </span>
<div>I found an exact similar situation as mine on a thread which is listed below, but even following the thread did not provide the needed help:</div>
<div><a href="http://lists.gromacs.org/pipermail/gmx-users/2007-September/029541.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2007-September/029541.html</a> <br>
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<span>Thanks, Prakash.</span></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>
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