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On 5/08/2011 1:17 PM, DeChang Li wrote:
<blockquote
cite="mid:CAB0HCkKq2XuD91YUS=zEj+g01bq1So8+gP9KYUxxZOeBiYEJLw@mail.gmail.com"
type="cite">
<p class="MsoNormal"><span lang="EN-US">Dear all,</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<span
style="font-size:10.5pt;mso-bidi-font-size:12.0pt;font-family:
"Times New
Roman";mso-fareast-font-family:宋体;mso-font-kerning:1.0pt;mso-ansi-
language:
EN-US;mso-fareast-language:ZH-CN;mso-bidi-language:AR-SA"
lang="EN-US"><span style="mso-spacerun:yes"> </span>I want to
use Gromacs to run an enhanced
sampling molecular dynamics (ESMD) proposed by Karplus’s group
(J. Am. Chem. Soc.
(1990) 112, 9161-9175. & J. Mol. Biol. (1999) 291, 101-115).
In the ESMD simulation,
we need to exclude the interactions (especially the Coulomb
interactions)
between some small molecules (e.g. ligand A and its replica).
How can Gromacs
to do this? Any suggestion will be very appreciated.</span></blockquote>
<br>
See energy groups and energy group exclusions in 3.3 and 7.3.19 of
the manual.<br>
<br>
Mark<br>
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