[gmx-users] six member ring won't stay flat

Justin Lemkul jalemkul at vt.edu
Thu Jan 18 13:54:01 CET 2018

On 1/18/18 7:51 AM, MD wrote:
> On Thu, Jan 18, 2018 at 7:43 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 1/17/18 6:11 PM, Mark Abraham wrote:
>>> Hi,
>>> If you poke your finger into something, it isn't going to stay flat. :-)
>> And to add on to this, in the CHARMM parametrization protocol, the first
>> step is always an in vacuo geometry optimization (QM vs. MM comparison) to
>> make sure the topology is sensible. If that doesn't check out, there are
>> problems that can be easily spotted before subjecting the new residue to
>> any other complicating factors like water and other parts of the protein.
>> -Justin
> ​​Thank you Justin. What would you look at to make a judgement to see if
> the topology is sensible after the vacuo geometry optimization? Or as long
> as there were no errors or bad notes along the run it should be good?

You look at the structure to see if it is sensible (and here, sensible 
is defined as properly reproducing QM-optimized geometries and/or known 
high-resolution experimental geometries - start with QM and compare 
against empirical evidence later).

The absence of errors or notes when executing grompp tells you precisely 
nothing about the integrity of the physical model; it only tells you if 
you've forgotten to do something. I can populate every parameter field 
with absolute garbage and grompp will happily carry on preparing my 
doomed simulation :)



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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