<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=us-ascii"><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:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
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;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri",sans-serif;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></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-US link="#0563C1" vlink="#954F72"><div class=WordSection1><p class=MsoNormal>Hi!<o:p></o:p></p><p class=MsoNormal> I just signed up for this list, and I’d like to contribute to GROMACS. I’m a Ph.D. student, with relevant background in physics, biochemistry, and engineering.<o:p></o:p></p><p class=MsoNormal> I’m interested in extending GROMACS’ abilities to impose user-defined electric fields, and specifically interested in spatially constant time-varying fields. I looked at calc_f_el in sim_util.cpp, having read “Patching mdrun” on the GROMACS website, and see that it would be fairly easy to modify. But I’m concerned about this “WARNING” in the comment lines above the function definition, which state that there “can be problems with the virial.”<o:p></o:p></p><p class=MsoNormal> The solution proposed there is to implement the “externally imposed” field directly in PME. I’m not an expert yet, but I read the relevant section in Berendsen’s book and the ’95 smooth PME paper to get up to speed; I haven’t yet got to a detailed study of pme.c.<o:p></o:p></p><p class=MsoNormal> What is the best place to begin? I suppose that a linearly increasing potential mapped to each charge along with the FT lattice sum terms in the PME routine(s) would do it? May I please ask for any suggestions, ideas or hints (possibly including relevant spots in the code)?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Tim<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>