<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv=Content-Type content="text/html; charset=iso-8859-7">
<meta name=Generator content="Microsoft Word 12 (filtered medium)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0cm;
margin-right:0cm;
margin-bottom:0cm;
margin-left:36.0pt;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
span.EmailStyle18
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:windowtext;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:1960838241;
mso-list-type:hybrid;
mso-list-template-ids:-2118887862 1033940678 201916441 201916443 201916431 201916441 201916443 201916431 201916441 201916443;}
@list l0:level1
{mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:54.0pt;
text-indent:-18.0pt;}
@list l0:level2
{mso-level-tab-stop:72.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level3
{mso-level-tab-stop:108.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level4
{mso-level-tab-stop:144.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level5
{mso-level-tab-stop:180.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level6
{mso-level-tab-stop:216.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level7
{mso-level-tab-stop:252.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level8
{mso-level-tab-stop:288.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level9
{mso-level-tab-stop:324.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang=EN-AU link=blue vlink=purple>
<div class=WordSection1>
<p class=MsoNormal><span lang=EN-US>Hi,<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>I am doing a partition coefficient of
solute between 1-Octanol and water using gromacs ffG53a6 force field. Actually
I am trying to reproduce Garrido et al’ s paper (J. Chem Theory Comput.
2009). The first thing I have done is to predict the Gibbs free energy of
salvation of pentane (my solute) in 1-Octanol by thermodynamics integration
method using 16 </span><span lang=EN-US style='font-family:"Times New Roman","serif"'>ë</span><span
lang=EN-US> (lambda) values. It works well for<span style='color:#1F497D'> </span></span><span
lang=EN-US style='font-family:"Times New Roman","serif"'>ë</span><span
lang=EN-US> =0. 0.05, 0.1, 0.2, 0.3, 0.4 and 0.5. The problem ha<span
style='color:#1F497D'>s</span> stated <span style='color:#1F497D'>at</span> </span><span
lang=EN-US style='font-family:"Times New Roman","serif"'>ë=0.6 and it is LINCS
error which says as follows:</span><span lang=EN-US><o:p></o:p></span></p>
<p class=MsoNormal style='text-indent:36.0pt'><span lang=EN-US>Fatal error:<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:72.0pt'><span lang=EN-US>Too many LINCS
warnings (1001)<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:72.0pt'><span lang=EN-US>If you know what
you are doing you can adjust the lincs warning threshold in your mdp file or
set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better
to fix the problem<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>The atoms that make the problem are pentane
atoms.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>I have put the parameter file that I am
using on this link <a
href="http://hydra.pharm.monash.edu.au/md_project/production.txt">http://hydra.pharm.monash.edu.au/md_project/production.txt</a><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>Before I run the production simulation I minimized
the system well as exactly stated on the paper.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>After I got the error I have tried to run
it again by changing the time step and the soft core value i.e sc_alpha and run
three jobs independently<o:p></o:p></span></p>
<p class=MsoListParagraph style='margin-left:54.0pt;text-indent:-18.0pt;
mso-list:l0 level1 lfo2'><![if !supportLists]><span lang=EN-US><span
style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US>With 1fs time step and sc_alpha
= 1.51<o:p></o:p></span></p>
<p class=MsoListParagraph style='margin-left:54.0pt;text-indent:-18.0pt;
mso-list:l0 level1 lfo2'><![if !supportLists]><span lang=EN-US><span
style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US>With 2fs time step changing
sc_alpha to 0.5 and<o:p></o:p></span></p>
<p class=MsoListParagraph style='margin-left:54.0pt;text-indent:-18.0pt;
mso-list:l0 level1 lfo2'><![if !supportLists]><span lang=EN-US><span
style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span lang=EN-US>With 1fs time step and 0.5
sc_alpha<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>The same problem happened for 2 and 3 but 1
works well, but the average dVpot/d</span><span lang=EN-US style='font-family:
"Times New Roman","serif"'> ë is not what I expected, its >+7. I could not
figure it out where exactly the problem is.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>Thanks
in advance for your advise.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>Cheers,<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>Emanuel</span><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
</div>
</body>
</html>