Just a note concerning dihedral restraints documentation -- the function and default behavior of dihre-fc needs to be documented somewhere in the manual. I just spent a couple hours (and my student a couple of days!) trying to track down the source of some crashes which ended up being due to the difference between specifying<div>
<br></div><div>dihre-fc = 1</div><div><br></div><div>in our topology file, and not specifying anything at all.</div><div><br></div><div>THis how-to documents what dihre-fc DOES (<a href="http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints">http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints</a>) but it is not mentioned anywhere in the gromacs manual at all. It turns out dihre-fc defaults to 1000, so the difference between dihre-fc = 1 and omitting dihre-fc is a factor of 1000 in dihedral restraint strength. This is enough (since it's a multiplier!) to make the difference between simulations reliably crashing and simulations not crashing at all... </div>
<div><br></div><div>This clearly should be documented in the manual since (with this behavior) knowing what value of dihre-fc one is using is critical to knowing what dihedral restraint strength one is using.</div><div><br>
</div><div>Thanks.</div><div><br></div><div><div><br></div>-- <br>David Mobley<br><a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a><br>504-383-3662<br><br><br>
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