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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>Here tau_p=4, which is already quite large.<br>But there are no "real" problems in the system, the results should be fine.<br>But the relative ling tau_p might be the reason for the strange scaling.<br>This would make the scaling factor always close to 1 plus or minus one bit.<br>I have not done the binary math, so I can not see if somehow this would<br>make numbers slightly below 20 scale down and above 20 scale up.<br><br>Berk.<br><br></div><br><hr id="stopSpelling">> Date: Thu, 24 Jul 2008 13:40:02 +0200<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] box size changing during isotropic pressure coupling<br>> <br>> Berk Hess wrote:<br>> > <br>> > Hi,<br>> > <br>> > Hmm... this is a (seemingly( really systematic decrease in x and y and <br>> > increase in z.<br>> > <br>> > But is x at the start really EXACTLY identical to y?<br>> > Because in that case I would think they should always stay identical.<br>> > But looking at the code I see that it is always uses triclinic scaling.<br>> > Thus x and y are treated differently (although adding only zeros),<br>> > so depending on the compiler, the results could differ by a bit.<br>> > What system and compiler are you using?<br>> > <br>> <br>> Pressure coupling artifacts may be enhance by short coupling constants <br>> as well. We recently had a problem that systems consisting of simple <br>> liquids would not equilibrate with tau_p = 1 ps and isotropic scaling. <br>> With tau_p = 5 ps it was fine. For more complicated systems like yours <br>> tau_p might need to be larger. I realize this is somewhat separate from <br>> the issue you are presenting. By the way the website doesn't seem to <br>> exist anymore.<br>> <br>> > Berk.<br>> > <br>> > <br>> > > Date: Fri, 18 Jul 2008 13:54:19 -0400<br>> > > From: chris.neale@utoronto.ca<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: [gmx-users] box size changing during isotropic pressure coupling<br>> > ><br>> > > Hello,<br>> > ><br>> > > I have a system of 750,000 atoms consisting of detergent in water.<br>> > > Although this run has been carried out using isotropic pressure<br>> > > coupling, I see significant drift in the box dimensions over 150 ns.<br>> > > This run was carried out using gromacs version 3.3 and 3.3.1. I used the<br>> > > -shuffle and -sort options and an in-house g_desort. This means that my<br>> > > restarts are via grompp, not tpbconv, although I do use the .trr and<br>> > > .edr with gen_vel=no and unconstrained-start=yes for a proper restart.<br>> > ><br>> > > My system is rectangular, starting with an x=y!=z and a=b=c=90. When I<br>> > > view the .xtc file, it is clear that the system is shrinking in the x/y<br>> > > and growing in the z. However, while turning on PBC images it looks like<br>> > > a totally normal simulation in that there is no net drift or anything<br>> > > else obviously problematic.<br>> > ><br>> > > I have posted some images here<br>> > > http://www.pomeslab.com/CN_GromacsPost_071808.html that show the box<br>> > > dimensions over time and also the total volume. The initial rapid volume<br>> > > change, and its asymptotic continuation, is an aggregation effect and is<br>> > > expected. Other than this, the volume is generally stable to the changes<br>> > > in the box lengths along single dimensions. I can not explain any of the<br>> > > features of the individual x/y/z plots, nor can I explain why they level<br>> > > out, why y levels out before x and z, or guess if this will continue to<br>> > > stay (relatively) flat.<br>> > ><br>> > > I am interested to know if anybody else has experienced this. Also, it<br>> > > seems to me like this is simply an output format thing and will not<br>> > > cause problems unless the x/y shrinks so much that cutoff effects cause<br>> > > me problems.<br>> > ><br>> > > my .mdp file follows.<br>> > ><br>> > > title = seriousMD<br>> > > cpp = cpp<br>> > > integrator = md<br>> > > nsteps = 25000<br>> > > tinit = 153200<br>> > > dt = 0.002<br>> > > comm_mode = linear<br>> > > nstcomm = 1<br>> > > comm_grps = System<br>> > > nstxout = 25000<br>> > > nstvout = 25000<br>> > > nstfout = 25000<br>> > > nstlog = 5000<br>> > > nstlist = 10<br>> > > nstenergy = 500<br>> > > nstxtcout = 5000<br>> > > ns_type = grid<br>> > > pbc = xyz<br>> > > coulombtype = PME<br>> > > rcoulomb = 0.9<br>> > > fourierspacing = 0.12<br>> > > pme_order = 4<br>> > > vdwtype = cut-off<br>> > > rvdw_switch = 0<br>> > > rvdw = 1.4<br>> > > rlist = 0.9<br>> > > DispCorr = no<br>> > > Pcoupl = Berendsen<br>> > > pcoupltype = isotropic<br>> > > compressibility = 4.5e-5<br>> > > ref_p = 1.<br>> > > tau_p = 4.0<br>> > > tcoupl = Berendsen<br>> > > tc_grps = DPC SOL<br>> > > tau_t = 0.1 0.1<br>> > > ref_t = 300. 300.<br>> > > annealing = no<br>> > > gen_vel = no<br>> > > unconstrained-start = yes<br>> > > gen_temp = 300.<br>> > > gen_seed = 9896<br>> > > constraints = all-bonds<br>> > > constraint_algorithm= lincs<br>> > > lincs-iter = 1<br>> > > lincs-order = 4<br>> > > ;EOF<br>> > ><br>> > > #########<br>> > ><br>> > > many thanks,<br>> > > Chris.<br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before <br>> > 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/mailing_lists/users.php<br>> > <br>> > Express yourself instantly with MSN Messenger! MSN Messenger <br>> > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php<br>> <br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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