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Hi,<br><br>I have no clue why you would want to fix the peptide in the middle of the box.<br>But what you want seems to be more like com removal for the peptide only<br>with the comm options.<br>The pull code will do approximately what you want, but with pressure coupling<br>there is the problem that your peptide will stay fixed in space, while the rest<br>of the system has to scale around it.<br><br>In general there are problems with absolute reference pulling, because you just<br>fix the location of the pull group, whereas the rest of the system can freely move,<br>thus the net effect is zero, except for lots of nasty artifacts when you change<br>the pull position too fast.<br><br>Berk<br><br>> Date: Thu, 16 Apr 2009 10:27:04 -0400<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] pull code absolute reference artifacts<br>> <br>> Hello,<br>> <br>> I have a question about the following grompp 4.0.4 warning:<br>> <br>> "You are using an absolute reference for pulling, but the rest of the <br>> system does not have an absolute reference. This will lead to <br>> artifacts."<br>> <br>> While I do realize that this is an excellent error message containing <br>> lots of information, I am still unclear about how to proceed. Why does <br>> my system not have an absolute reference? Is it because I have pbc and <br>> center of mass motion removal? Exactly what types of artifacts are <br>> expected? Is there a simple solution?<br>> <br>> I am trying to hold my peptide in the center of a water box. I realize <br>> that there is no "center" and everything in pbc, but I need to do it <br>> nevertheless.<br>> <br>> Here are my .mdp options:<br>> <br>> pull = umbrella<br>> pull_geometry = distance<br>> pull_dim = Y Y Y<br>> pull_ngroups = 1<br>> ;pull_group0 =<br>> pull_group1 = peptide_A<br>> pull_k1 = 500<br>> pull_init1 = 0.00<br>> <br>> nsteps = 250000 ; REMOVE_FOR_EM<br>> tinit = 49000 ; REMOVE_FOR_EM<br>> dt = 0.004 ; REMOVE_FOR_EM<br>> nstxout = 250000 ; REMOVE_FOR_EM<br>> nstvout = 250000 ; REMOVE_FOR_EM<br>> nstfout = 250000 ; REMOVE_FOR_EM<br>> nstenergy = 25000 ; REMOVE_FOR_EM<br>> nstxtcout = 25000 ; REMOVE_FOR_EM<br>> nstlog = 250000 ; REMOVE_FOR_EM<br>> gen_vel = no<br>> unconstrained-start = yes<br>> <br>> integrator = sd<br>> gen_seed = -1<br>> comm_mode = linear<br>> nstcomm = 1<br>> comm_grps = System<br>> nstlist = 5<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 = EnerPres<br>> Pcoupl = Berendsen ; REMOVE_FOR_EM<br>> pcoupltype = isotropic ; REMOVE_FOR_EM<br>> compressibility = 4.5e-5 ; REMOVE_FOR_EM<br>> ref_p = 1. ; REMOVE_FOR_EM<br>> tau_p = 4.0 ; REMOVE_FOR_EM<br>> tc_grps = System ; REMOVE_FOR_EM<br>> tau_t = 1.0 ; REMOVE_FOR_EM<br>> ld_seed = -1 ; REMOVE_FOR_EM<br>> ref_t = 300. ; REMOVE_FOR_EM<br>> gen_temp = 300. ; REMOVE_FOR_EM<br>> constraints = all-bonds ; REMOVE_FOR_EM<br>> constraint_algorithm= lincs ; REMOVE_FOR_EM<br>> lincs-iter = 1 ; REMOVE_FOR_EM<br>> lincs-order = 6 ; REMOVE_FOR_EM<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 /><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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