Thanks, dac, this is what happens when you let an experimentalist
loose. I will keep the list posted.
Tom
On 6/7/16 4:04 AM, David A Case wrote:
> 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 - 06:00:02 PDT
