[gmx-developers] soft-core atom selection

David Mobley dmobley at gmail.com
Wed Nov 26 01:59:20 CET 2014


Sorry for the delay. Our computer cluster was down for maintenance and I
just got access to the files, at least for now.

We do not specify sc-coul in our mdp files, which apparently means it is
set to its default value (sc-coul = no).

Our normal procedure is to first turn off charge interactions, then turn
off vdW interactions separately after-the-fact, and we have never needed
sc-coul with this procedure, so we have never used it. (Our protocol dates
to before this was added).

I'm guessing that this particular case, where there is a perturbed atom
with a charge but zero LJ parameters, is a special case where there is
"unexpected" behavior unless sc-coul is used?

I'll upload files shortly to Redmine.


On Thu, Nov 20, 2014 at 3:49 AM, Berk Hess <hess at kth.se> wrote:

>  Hi,
> 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.
> Cheers,
> Berk
> 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
> David Mobley
> dmobley at gmail.com
> 949-385-2436
>  On Wed, Nov 19, 2014 at 3:36 AM, Berk Hess <hess at kth.se> wrote:
>> Hi,
>> 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.
>> Cheers,
>> Berk
>> On 11/18/2014 11:45 PM, David Mobley wrote:
>> Hi,
>> 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?
>> Thanks!
>> David

David Mobley
dmobley at gmail.com
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