<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<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">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<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 class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>