<html><head><base href="x-msg://693/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ehud!<div><br></div><div>Your settings are correct.</div><div>However, you can also use domain decomposition with GB,</div><div>and I at least usually bypass the editconf stage, and do pdb2gmx->grompp->mdrun, when you do not want any pbc.</div><div><br></div><div>/Per</div><div><br></div><div><br></div><div><br><div><div>7 okt 2010 kl. 12.29 skrev Ehud Schreiber:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; 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 lang="EN-US" link="blue" vlink="purple"><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Dear GROMACS users,<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">I try to compute energies of a small peptide-domain complex and of its constituents using implicit solvent, so that I can get the binding Delta E. I need the accuracy to be high enough so that I can reliably measure the Delta Delta E between the wildtype peptide and a mutation of it.<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">I would like to get advice as to the best setting and parameters to use; are the ones given below the correct and best ones (most in an mdp file, some run control parameters of GROMACS commands)? Are other defaults in need to be changed?<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">As the GBSA method necessitates using the inexact cut-off interactions, and my system is rather small, I consider using no cut-off at all, i.e. an all-vs.-all approach. For that I understand the parameters should be<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">nstlist=0<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">ns_type=simple<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">-pd ; in mdrun<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">coulombtype=cut-off<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">rcoulomb=0<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">vdwtype=cut-off<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">rvdw=0<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">rlist=0<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Then, there are the implicit solvent parameters themselves:<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">implicit_solvent=GBSA<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">gb_algorithm= Still<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">sa_algorithm=Ace-approximation<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">rgbradii=0<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Finally, regarding the simulation box, I see no need for periodic boundary conditions, and I pick some big margin around the system (as there are no water molecules, no need to spare):<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">pbc=no<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">-d 5.0 ; in editconf<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">What do you say?<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Thanks,<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Ehud.<o:p></o:p></div></div>--<span class="Apple-converted-space"> </span><br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" style="color: blue; text-decoration: underline; ">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" style="color: blue; text-decoration: underline; ">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/Support/Mailing_Lists/Search" style="color: blue; text-decoration: underline; ">http://www.gromacs.org/Support/Mailing_Lists/Search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org" style="color: blue; text-decoration: underline; ">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/Support/Mailing_Lists" style="color: blue; text-decoration: underline; ">http://www.gromacs.org/Support/Mailing_Lists</a></div></span></blockquote></div><br></div></body></html>