<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>You can use positional restrained, this will introduce some harmonic force which will retain the atoms to a specific position.</div><div><br></div><div>Itamar.</div><div><br><div><div>On 10/10/2011, at 6:22 PM, <a href="mailto:auryn_valemig@libero.it">auryn_valemig@libero.it</a> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; ">Hi to everybody!!!</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; ">I'd like to know if it is possible to "simulate" with gromacs a crystal lattice where the atoms are just kept "almost fixed" in their crystallographic structure positions and they are allowed just to vibrate around this positions. This is not a real MD simulation but I need it just to calculated radial distrubution function among the atoms in the crystal. </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; ">Tahnk you in advance </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; ">valentina<br></div>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div>-- </div><div><br></div><div>"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut</div><div><br></div><div>===========================================</div><div>| Itamar Kass, Ph.D.</div><div>| Postdoctoral Research Fellow</div><div>|</div><div>| Department of Biochemistry and Molecular Biology</div><div>| Building 77 Clayton Campus</div><div>| Wellington Road</div><div>| Monash University,</div><div>| Victoria 3800</div><div>| Australia</div><div>|</div><div>| Tel: +61 3 9902 9376</div><div>| Fax: +61 3 9902 9500</div><div>| E-mail: <a href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a></div><div>============================================</div><br><br></span>
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