[gmx-developers] soft-core atom selection

Berk Hess hess at kth.se
Wed Nov 26 09:31:20 CET 2014

On 11/26/2014 01:59 AM, David Mobley wrote:
> Hi,
> 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?
No, this should always work.
Lets continue this discussion on redmine.


> I'll upload files shortly to Redmine.
> Thanks.
> On Thu, Nov 20, 2014 at 3:49 AM, Berk Hess <hess at kth.se 
> <mailto: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
>     <mailto: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 <tel: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
> -- 
> David Mobley
> dmobley at gmail.com <mailto:dmobley at gmail.com>
> 949-385-2436

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20141126/e21a3db2/attachment-0001.html>

More information about the gromacs.org_gmx-developers mailing list