[gmx-developers] soft-core atom selection

Berk Hess 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
> David Mobley
> dmobley at gmail.com <mailto:dmobley at gmail.com>
> 949-385-2436
> On Wed, Nov 19, 2014 at 3:36 AM, Berk Hess <hess at kth.se 
> <mailto: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

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