<html 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=utf-8">
<meta name="Title" content="">
<meta name="Keywords" content="">
<meta name="Generator" content="Microsoft Word 15 (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:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
p.Times, li.Times, div.Times
{mso-style-name:Times;
margin:0cm;
margin-bottom:.0001pt;
text-indent:1.0cm;
font-size:12.0pt;
font-family:"Times New Roman";}
span.EmailStyle18
{mso-style-type:personal-compose;
font-family:Calibri;
color:windowtext;}
span.msoIns
{mso-style-type:export-only;
mso-style-name:"";
text-decoration:underline;
color:teal;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:Calibri;}
@page WordSection1
{size:595.0pt 842.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style>
</head>
<body bgcolor="white" lang="EN-US" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri">Dear Sir or Madam:</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri"> </span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri">I’m a new GROMACS user, and I’m interested in the study of solutions of small molecules, like ionic liquids.</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri">At this moment I’m trying to ma</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri"> </span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri">ke a simulation of a molecule called bicalutamide. As a first step, I tested the force field (OPLS-AA) with DL-POLY, and everything run without problems. However,
when I changed to GROMACS, the simulations start to blow up.</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri">To understand what was happening, I made the input files only for one bicalutamide molecule and I run a small simulation. The files I used are attached to this
e-mail. The analysis of the simulation results revealed that the problem is related with two hydrogen atoms (one connected to a nitrogen atoms and the other belonging to a hydroxyl group), that come very close to each other and, when this happens, the system
goes crazy! What eludes me, is the fact that the parametrization works really good with DL-POLY (being able to reproduce the crystal structures parameters and the energetics of this molecule very accurately), but fails with GROMACS. Furthermore, when I compare
the single point energies computed by the two programs for the same starting configuration, the following differences are obtained (data in kJ/mol):</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri"> </span><o:p></o:p></p>
<table class="MsoNormalTable" border="1" cellspacing="0" cellpadding="0" width="723" style="margin-left:-5.4pt;border-collapse:collapse;border:none">
<tbody>
<tr>
<td width="115" valign="bottom" style="width:86.6pt;border:none;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal" align="center" style="text-align:center;text-autospace:none">
<span style="font-family:Calibri">Bond</span><o:p></o:p></p>
</td>
<td width="106" valign="bottom" style="width:79.6pt;border:none;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal" align="center" style="text-align:center;text-autospace:none">
<span style="font-family:Calibri">Angle</span><o:p></o:p></p>
</td>
<td width="95" valign="bottom" style="width:71.6pt;border:none;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal" align="center" style="text-align:center;text-autospace:none">
<span style="font-family:Calibri">Dih.</span><o:p></o:p></p>
</td>
<td width="97" valign="bottom" style="width:72.6pt;border:none;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal" align="center" style="text-align:center;text-autospace:none">
<span style="font-family:Calibri">LJ</span><o:p></o:p></p>
</td>
<td width="97" valign="bottom" style="width:72.6pt;border:none;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal" align="center" style="text-align:center;text-autospace:none">
<span style="font-family:Calibri">Coulomb</span><o:p></o:p></p>
</td>
<td width="97" valign="bottom" style="width:72.6pt;border:none;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal" align="center" style="text-align:center;text-autospace:none">
<span style="font-family:Calibri">Potential</span><o:p></o:p></p>
</td>
</tr>
<tr>
<td width="115" valign="bottom" style="width:86.6pt;border:none;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal" align="center" style="text-align:center;text-autospace:none">
<span style="font-family:Calibri">0.02</span><o:p></o:p></p>
</td>
<td width="106" valign="bottom" style="width:79.6pt;border:none;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal" align="center" style="text-align:center;text-autospace:none">
<span style="font-family:Calibri">-0.04</span><o:p></o:p></p>
</td>
<td width="95" valign="bottom" style="width:71.6pt;border:none;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal" align="center" style="text-align:center;text-autospace:none">
<span style="font-family:Calibri">-0.05</span><o:p></o:p></p>
</td>
<td width="97" valign="bottom" style="width:72.6pt;border:none;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal" align="center" style="text-align:center;text-autospace:none">
<span style="font-family:Calibri">-98.24</span><o:p></o:p></p>
</td>
<td width="97" valign="bottom" style="width:72.6pt;border:none;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal" align="center" style="text-align:center;text-autospace:none">
<span style="font-family:Calibri">59.97</span><o:p></o:p></p>
</td>
<td width="97" valign="bottom" style="width:72.6pt;border:none;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal" align="center" style="text-align:center;text-autospace:none">
<span style="font-family:Calibri">-158.28</span><o:p></o:p></p>
</td>
</tr>
</tbody>
</table>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri"> </span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri">i.e., the bonds, angles and dihedrals energies computed by the two programs are approximately the same, but the Coulomb and LJ are significantly different. Initially,
I thought this could be related with the 1-4 interactions, but I did not find anything suspicious error in the input files (maybe because I’m new with GROMACS). However, if this was the problem, it does not explain the strange attraction between two highly
positively charged hydrogen atoms (~+0.3e each), since they are 5 bonds apart from each other.</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri">At this point, I do not know what I can check more, and I’m not sure if the problem is related with my input files or if is something intrinsic of GROMACS and
the routines LINCS or SHAKE (the behavior is similar with both algorithms). Can you give me a help on this?</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri"> </span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri">Best regards,</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:11.0pt;font-family:Calibri"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">CB</span><span style="font-size:11.0pt;font-family:Calibri"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
</div>
</body>
</html>