On Mon, Jun 06, 2016, Thomas Pochapsky wrote:
> Thanks, Dave. Meanwhile, we are trying to optimize the alignment
> tensors for two sets of RDCs in an explicitly solvated protein using
> Amber 14. The .prmtop and .rst files we are using have worked fine for
> heating (at constant V) and equilibration (first constant V, then
> constant P) runs. When I add the RST.dip file, and hold the structure
> constant (freezemol=.true.), I get a sander bomb message:
Oooh...don't do this! With freezemol=.true., I not surprised that
constant pressure runs will crash. The purpose of freezemol is to
optimize the alignment tensor: for that, just do minimization (with
ntb=1). Then copy the optimized alignment tensor to your MD input file,
turn off freezemol, and continue the MD run (where you can set ntb back to
2).
....good luck....dac
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Received on Tue Jun 07 2016 - 01:30:03 PDT
