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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>Hmm... this is a (seemingly( really systematic decrease in x and y and 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>Berk.<br></div><br><br><hr id="stopSpelling">> 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 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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