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<div class="moz-cite-prefix">On 11/26/2014 01:59 AM, David Mobley
wrote:<br>
</div>
<blockquote
cite="mid:CAPCBi1_JsHg9+iybG2e9BnBQwk--FuCy-6QSk2PF7_jms3Jmkg@mail.gmail.com"
type="cite">
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<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>
</blockquote>
No, this should always work.<br>
Lets continue this discussion on redmine.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<blockquote
cite="mid:CAPCBi1_JsHg9+iybG2e9BnBQwk--FuCy-6QSk2PF7_jms3Jmkg@mail.gmail.com"
type="cite">
<div dir="ltr">
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true" 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 moz-do-not-send="true"
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>
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<br clear="all">
<div><br>
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-- <br>
<div class="gmail_signature">David Mobley<br>
<a moz-do-not-send="true" href="mailto:dmobley@gmail.com"
target="_blank">dmobley@gmail.com</a><br>
949-385-2436<br>
</div>
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