<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
Hi Erik,<br>
<br>
What was the issuse you metion with the BSC0 parameters (I take it
you are referring to the contributed force field that I added to the
GROMACS website)? I tested the conversion of the new dihedrals by
looking at single-point energies between AMBER and GROMACS and they
matched up. If there is a problem, I would like to know so as to be
able to take a look at it.<br>
<br>
Cheers<br>
<br>
Tom<br>
<br>
<div class="moz-cite-prefix">On 14/02/14 16:47, Erik Lindahl wrote:<br>
</div>
<blockquote
cite="mid:CC4ECD17-AFE1-42C0-9362-E0627105A7B6@scilifelab.se"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
Hi,
<div><br>
</div>
<div>I would strongly prefer that we do NOT ship forcefields that
haven’t had (1) plenty of testing, (2) somebody named who is
responsible for each of them, (3) specifics on how to repeat the
testing.</div>
<div><br>
</div>
<div>The second we ship something with official Gromacs people
will start using it, and then they will instantly blame Gromacs
if there are errors in the force field. This is exactly why we
have separate contributed sections, to make it clear it is not
our responsibility.</div>
<div><br>
</div>
<div>BSC0 is a concrete example: It was only a week ago I got a
mail from Eric Sorin about BSC0 not reproducing some results.
For a contributed force field that is the problem of the
contributor. If we are shipping it with Gromacs-5.0, it will
tarnish our reputation.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Erik</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<div>On 14 Feb 2014, at 08:38, Rossen Apostolov <<a
moz-do-not-send="true" href="mailto:rossen@kth.se">rossen@kth.se</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div class="moz-cite-prefix" style="font-family: Helvetica;
font-size: 12px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: start; text-indent:
0px; text-transform: none; white-space: normal; widows:
auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><br
class="Apple-interchange-newline">
On 14/02/14 17:12, Mark Abraham wrote:<br>
</div>
<blockquote
cite="mid:CAMNuMAS1=yvHh73==5N3uXMa3baF5HQ64_OMV9niPmeV_CnNmQ@mail.gmail.com"
type="cite" style="font-family: Helvetica; font-size:
12px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: start; text-indent:
0px; text-transform: none; white-space: normal; widows:
auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<div dir="ltr">Removing encad and gmx sounds good.
Probably don't have time to rip out the code that
supported encad.
<div><br>
</div>
</div>
</blockquote>
<span style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); float: none;
display: inline !important;">I can look at that.</span><br
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<br style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<blockquote
cite="mid:CAMNuMAS1=yvHh73==5N3uXMa3baF5HQ64_OMV9niPmeV_CnNmQ@mail.gmail.com"
type="cite" style="font-family: Helvetica; font-size:
12px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: start; text-indent:
0px; text-transform: none; white-space: normal; widows:
auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<div dir="ltr">
<div>We're happy to add forcefields that are used by
more than one person, have been extensively tested,
have an associated publication record, etc. Any
particular suggestions, Alexey? Others?</div>
<div><br>
</div>
</div>
</blockquote>
<span style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); float: none;
display: inline !important;">I vote also for Stockholm
lipids, it can be quite useful, but hasn't got much
publicity.</span><br style="font-family: Helvetica;
font-size: 12px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: start; text-indent:
0px; text-transform: none; white-space: normal; widows:
auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<br style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<span style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); float: none;
display: inline !important;">Rossen</span><br
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<br style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<blockquote
cite="mid:CAMNuMAS1=yvHh73==5N3uXMa3baF5HQ64_OMV9niPmeV_CnNmQ@mail.gmail.com"
type="cite" style="font-family: Helvetica; font-size:
12px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: start; text-indent:
0px; text-transform: none; white-space: normal; widows:
auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<div dir="ltr">
<div>Off the top of my head, Charmm36 would be an
obvious thing to add. My reservation here is that
there's not really ever been a good way to run
CHARMM-style non-bondeds in GROMACS. I suspect this
will change in 5.0 with Verlet-kernel support for
switch functions, but perhaps a fully validated
forcefield and workflow port for 5.1 would be a good
joint project. Thoughts, Justin?</div>
<div><br>
</div>
<div>Mark</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Fri, Feb 14, 2014 at 4:39
PM, Alexey Shvetsov<span class="Apple-converted-space"> </span><span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:alexxy@omrb.pnpi.spb.ru"
target="_blank">alexxy@omrb.pnpi.spb.ru</a>></span><span
class="Apple-converted-space"> </span>wrote:<br>
<blockquote class="gmail_quote" style="margin: 0px 0px
0px 0.8ex; border-left-width: 1px;
border-left-color: rgb(204, 204, 204);
border-left-style: solid; padding-left: 1ex;">Hi
all!<br>
<br>
Its good idea to drop deprecated force fields!<br>
<br>
BTW are there any plans to add some new forcefields
from contributuions pages?<br>
<br>
Peter Kasson писал 14-02-2014 18:47:<br>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left-width: 1px;
border-left-color: rgb(204, 204, 204);
border-left-style: solid; padding-left: 1ex;">
<div class="">Sounds good to me! If anyone has a
burning need to use them, they<br>
can still of course do so, but having them part
of the supported<br>
distribution doesn't seem like a good idea at
this point.<br>
<br>
--Peter<br>
<br>
----------------------------------------------------------------------<br>
Peter Kasson, MD, PhD<br>
Assistant Professor<br>
Departments of Molecular Physiology and
Biological Physics<br>
and of Biomedical Engineering<br>
University of Virginia<br>
<br>
On Fri, Feb 14, 2014 at 6:39 AM, Erik Lindahl<br>
<<a moz-do-not-send="true"
href="mailto:erik.lindahl@scilifelab.se"
target="_blank">erik.lindahl@scilifelab.se</a>>
wrote:<br>
<br>
</div>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left-width: 1px;
border-left-color: rgb(204, 204, 204);
border-left-style: solid; padding-left: 1ex;">
<div class="">Agreed!<br>
<br>
On 14 Feb 2014, at 06:37, Rossen Apostolov
<<a moz-do-not-send="true"
href="mailto:rossen@kth.se" target="_blank">rossen@kth.se</a>>
wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:
0px 0px 0px 0.8ex; border-left-width: 1px;
border-left-color: rgb(204, 204, 204);
border-left-style: solid; padding-left:
1ex;">Hi,<br>
<br>
Encad and GmxFF have been deprecated for a
while. Now before 5.0<br>
</blockquote>
is a good time for cleanup, if nobody is using
them.<br>
<blockquote class="gmail_quote" style="margin:
0px 0px 0px 0.8ex; border-left-width: 1px;
border-left-color: rgb(204, 204, 204);
border-left-style: solid; padding-left:
1ex;"><br>
Any objections?<br>
<br>
Rossen<br>
_______________________________________________<br>
Gromacs Core Developers mailing list<br>
<a moz-do-not-send="true"
href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-core"
target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-core</a><br>
</blockquote>
</div>
[1]
<div class=""><br>
<br>
_______________________________________________<br>
Gromacs Core Developers mailing list<br>
<a moz-do-not-send="true"
href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-core"
target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-core</a><br>
</div>
[1]<br>
</blockquote>
<br>
<br>
<br>
Links:<br>
------<br>
[1]<span class="Apple-converted-space"> </span><a
moz-do-not-send="true"
href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-core"
target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-core</a><span
class="HOEnZb"><font color="#888888"><br>
</font></span></blockquote>
<span class="HOEnZb"><font color="#888888"><br>
--<span class="Apple-converted-space"> </span><br>
Best Regards,<br>
Alexey 'Alexxy' Shvetsov<br>
Petersburg Nuclear Physics Institute, NRC
Kurchatov Institute, Gatchina, Russia<br>
Department of Molecular and Radiation Biophysics<br>
Gentoo Team Ru<br>
Gentoo Linux Dev<br>
mailto:<a moz-do-not-send="true"
href="mailto:alexxyum@gmail.com"
target="_blank">alexxyum@gmail.com</a><br>
mailto:<a moz-do-not-send="true"
href="mailto:alexxy@gentoo.org"
target="_blank">alexxy@gentoo.org</a><br>
mailto:<a moz-do-not-send="true"
href="mailto:alexxy@omrb.pnpi.spb.ru"
target="_blank">alexxy@omrb.pnpi.spb.ru</a></font></span>
<div class="HOEnZb">
<div class="h5"><br>
--<span class="Apple-converted-space"> </span><br>
Gromacs Developers mailing list<br>
<br>
* Please search the archive at<span
class="Apple-converted-space"> </span><a
moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a><span
class="Apple-converted-space"> </span>before
posting!<br>
<br>
* Can't post? Read<span
class="Apple-converted-space"> </span><a
moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
* For (un)subscribe requests visit<br>
<a moz-do-not-send="true"
href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers"
target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a><span
class="Apple-converted-space"> </span>or send
a mail to<span class="Apple-converted-space"> </span><a
moz-do-not-send="true"
href="mailto:gmx-developers-request@gromacs.org"
target="_blank">gmx-developers-request@gromacs.org</a>.</div>
</div>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<span style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); float: none;
display: inline !important;">--<span
class="Apple-converted-space"> </span></span><br
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<span style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); float: none;
display: inline !important;">Gromacs Developers mailing
list</span><br style="font-family: Helvetica; font-size:
12px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: start; text-indent:
0px; text-transform: none; white-space: normal; widows:
auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<br style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<span style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); float: none;
display: inline !important;">* Please search the archive
at<span class="Apple-converted-space"> </span></span><a
moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List"
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a><span
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); float: none;
display: inline !important;"><span
class="Apple-converted-space"> </span>before posting!</span><br
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<br style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<span style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); float: none;
display: inline !important;">* Can't post? Read<span
class="Apple-converted-space"> </span></span><a
moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">http://www.gromacs.org/Support/Mailing_Lists</a><br
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<br style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<span style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); float: none;
display: inline !important;">* For (un)subscribe requests
visit</span><br style="font-family: Helvetica; font-size:
12px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: start; text-indent:
0px; text-transform: none; white-space: normal; widows:
auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<a moz-do-not-send="true"
href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers"
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a><span
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); float: none;
display: inline !important;"><span
class="Apple-converted-space"> </span>or send a mail to<span
class="Apple-converted-space"> </span></span><a
moz-do-not-send="true"
href="mailto:gmx-developers-request@gromacs.org"
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;">gmx-developers-request@gromacs.org</a><span
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); float: none;
display: inline !important;">.</span></blockquote>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Dr Thomas Piggot
University of Southampton, UK.
</pre>
</body>
</html>