<div dir="ltr">Hi,<div><br></div><div>Sorry for the delay. Our computer cluster was down for maintenance and I just got access to the files, at least for now.</div><div><br></div><div>We do not specify sc-coul in our mdp files, which apparently means it is set to its default value (sc-coul = no). </div><div><br></div><div>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). </div><div><br></div><div>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?</div><div><br></div><div>I'll upload files shortly to Redmine.</div><div><br></div><div>Thanks.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Nov 20, 2014 at 3:49 AM, Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div>Hi,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Cheers,<br>
<br>
Berk<div><div class="h5"><br>
<br>
On 11/20/2014 12:37 PM, <a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a> wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<span>
<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>
<div><br>
</div>
<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>
<div><br>
</div>
<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>
<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" style="font-family:arial,sans-serif;font-size:13px;line-height:normal" target="_blank">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)"><a href="tel:949-385-2436" value="+19493852436" target="_blank">949-385-2436</a></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>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 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>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</blockquote>
</div>
<br>
</blockquote>
<br>
</div></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature">David Mobley<br><a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a><br>949-385-2436<br></div>
</div>