[gmx-developers] soft-core atom selection
hess at kth.se
Thu Nov 20 12:49:56 CET 2014
But this can not explain your crashes. If all interactions with a
perturbed atom without LJ are soft-cored, there is never a singularity,
since all interactions are soft-cored.
Just to be sure, what have you set sc-coul to? This parameters is
causing lots of headaches and I still have not fully understood the
behavior. We need clear documentation here. I will add this soft-coring
selection to the manual.
On 11/20/2014 12:37 PM, dmobley at gmail.com wrote:
> Hi, all,
> OK, to follow up on this - I think this is incorrect at least in part,
> and explains a crash I’ve had on my list of things to track down.
> Specifically, if I simulate multiple carboxylic acids in solution and
> attempt a hydration free energy calculation (as a specific example,
> let’s take a case I’ve done where I have neutral benzoic acid at a
> finite concentration in water, and I am attempting to compute the free
> energy of turning one of the benzoic acid solutes into dummy atoms) I
> simply CANNOT get the calculation to run stably, even with reduced
> time steps, etc. In every respect it behaves like the type of crash I
> would expect if I had charged sites overlapping one another, but I had
> been unable to figure out how this could possibly happen. I WAS,
> however, able to determine that if I added nonzero LJ parameters to
> the hydroxyl hydrogen on the carboxylic acid (which is a GAFF hydrogen
> and hence had zero LJ parameters) the crashes go away.
> I believe this is explained by your statement about “for atoms without
> LJ, all perturbed interactions are soft-cored”. Specifically, I am
> turning off the solute (carboxylic acid) and so its perturbed
> interactions with the REMAINING, non-perturbed solutes are soft-cored,
> meaning that charge sites can overlap. At least, that’s my reading of
> what you’re saying and it would perfectly explain the crashes I’m seeing.
> I’ve also seen essentially identical crashes I was unable to
> understand for binding free energy calculations in a
> carboxylic-acid-rich host-guest system, presumably again because the
> REMAINING hydroxyl hydrogens on the host end up being able to overlap
> with charge sites on the guest which is being turned into dummies.
> Again I can “fix” it by adding nonzero LJ parameters to the hydrogens
> on the host, though this is incorrect since it is not “allowed” by the
> force field.
> Unless I’m missing something, this is a substantial mistake, and
> clearly a better solution is needed.
> Thanks so much,
> David Mobley
> dmobley at gmail.com <mailto:dmobley at gmail.com>
> On Wed, Nov 19, 2014 at 3:36 AM, Berk Hess <hess at kth.se
> <mailto:hess at kth.se>> wrote:
> Soft-core is not decided on an atom basis. A pair interaction is
> soft-cored when at least one of the two atoms is perturbed and at
> least one of the atoms has c12=0 at lambda=0 or lambda=1. So for
> atoms with LJ, interactions are only soft-cored when strictly
> necessary. For atoms without LJ, e.g. many hydrogens in many force
> fields, all perturbed interactions are soft-cored. For such atoms
> soft-coring is necessary when connected to a heavy atom that is
> decoupled. So the only cases where some interactions are
> soft-cored that are not strictly necessary is in a system where
> some atoms are decoupled and others are modified, then
> interactions with hydrogens connected to modified atoms would not
> need to be soft-cored.
> On 11/18/2014 11:45 PM, David Mobley wrote:
>> I wanted to ask concerning soft-core potentials in GROMACS: How
>> is it determined which atoms are soft core? Specifically, some
>> other code bases allow the option to select specific atoms which
>> are going to be treated with LJ soft core potentials, while other
>> atoms are not treated in this way and maintain their normal
>> potential or a linear mix of their A and B state potentials. In
>> GROMACS, there is no option to select this that I am aware of, so
>> I'm assuming that soft core is applied to all atoms, or to all
>> atoms which have different A and B states or different A and B
>> state LJ parameters?
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