<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>Indeed we are lucky then! <div>In the mean field there no periodic boundary, the system is spherical.<div><br></div><div>Thanks.</div><div>XAvier.</div><div><br><div><div>On Mar 16, 2009, at 7:05 PM, Berk Hess wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: 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; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">Hi,<br><br>I think you are lucky.<br>The angular comm code only does not work with DD when molecules are partially over the periodic boundaries.<br>But I guess that in your case molecules will never cross the boundary<br>and therefore the comm code will work as it should.<br><br>Berk<br><br><hr id="stopSpelling">From:<span class="Apple-converted-space"> </span><a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a><br>To:<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Subject: Re: [gmx-users] angular removal of COM and domain decomposition<br>Date: Mon, 16 Mar 2009 18:58:24 +0100<br><br><div><blockquote><span class="EC_Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div class="EC_hmmessage" style="font-size: 10pt; font-family: Verdana; "><br>> mdrun complains when I am asking for the angular removal of the COM<span class="EC_Apple-converted-space"> </span><br>> together<br>> with dynamic load balance on (with gmx-4.0.4). It says the combination<span class="EC_Apple-converted-space"> </span><br><br>You mean domain decomposition.<br></div></span></blockquote>Yes, sorry!</div><div><br></div><div>By imposed I mean that the flags are explicitly changed to do angular removal of </div><div>COM (remove the rotational momentum) even if it is not the case in the mdp file. </div><div>The code itself of not modified to do implement it!</div><div><br></div><div>You'd find in the lines like this:</div><div><br></div><div>if ( mean_field ) {</div><div> ir->comm_mode = ecmANGULAR;</div><div> ir->nstcomm = 1;</div><div>}</div><div><br></div><div>The question really what the code is then doing is asked to remove the rotational momentum</div><div>while not implemented! The code is stable for micro seconds!</div><div><br></div><div>It is so as the mean field stuff was imported from earlier gmx versions where the particule/domain </div><div>decomposition were not implemented I guess.</div><div><br></div><div>XAvier.</div><div><br><blockquote><span class="EC_Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div class="EC_hmmessage" style="font-size: 10pt; font-family: Verdana; ">> is not<br>> implemented and suggests to use particle decomposition, which is<span class="EC_Apple-converted-space"> </span><br>> unfortunately<br>> much much slower.<br>><span class="EC_Apple-converted-space"> </span><br>> What would happen if the use of angular removal of the COM was<span class="EC_Apple-converted-space"> </span><br>> "imposed" in a<br>> subroutine implemented in an in house version (mean field boundary<span class="EC_Apple-converted-space"> </span><br>> potential)?<br>> The code does not through the check_dd_restrictions so it is actually<span class="EC_Apple-converted-space"> </span><br>> running but<br>> it is actually difficult to see what the removal of the COM does.<br>><span class="EC_Apple-converted-space"> </span><br>> Anyone would have an idea? may be Berk?<br>><span class="EC_Apple-converted-space"> </span><br>> Thanks,<br>> XAvier.<br><br>What do you mean with "imposed"?<br>If you impose it correctly, it would of course work.<br><br>Berk<br><br><br><hr>Express yourself instantly with MSN Messenger!<span class="EC_Apple-converted-space"> </span><a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/">MSN Messenger</a><span class="EC_Apple-converted-space"> </span>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="EC_Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="EC_Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. 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