<span id="mailbox-conversation"><div>Hi, all,</div>
<div><br></div>
<div>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. </div>
<div><br></div>
<div>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.</div>
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<div>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.</div>
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<div>Unless I’m missing something, this is a substantial mistake, and clearly a better solution is needed. </div>
<div><br></div>
<div>Thanks so much,</div>
<div>David</div>
<div><br></div></span><div class="mailbox_signature">
<br><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; line-height: normal; background-color: rgb(255, 255, 255);">David Mobley</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; line-height: normal;"><a href="mailto:dmobley@gmail.com" target="_blank" style="font-family: arial, sans-serif; font-size: 13px; line-height: normal;">dmobley@gmail.com</a><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; line-height: normal;"><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; line-height: normal; background-color: rgb(255, 255, 255);">949-385-2436</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; line-height: normal;"></div>
<br><br><div class="gmail_quote"><p>On Wed, Nov 19, 2014 at 3:36 AM, Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span> wrote:<br></p><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="moz-cite-prefix">Hi,<br><br>
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.<br><br>
Cheers,<br><br>
Berk<br><br>
On 11/18/2014 11:45 PM, David Mobley wrote:<br></div>
<blockquote cite="mid:CAPCBi1-g0=+3Co=efQ=E0j8n1Kt8gu0iM-1zkRSEnZJi2ytCEQ@mail.gmail.com" type="cite">
<p dir="ltr">Hi,</p>
<p dir="ltr">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?</p>
<p dir="ltr">Thanks!<br>
David<br></p>
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