Hello Gmx-users,<br> can it be true that it is not possible to constrain the vector between 2 molecules defined as constrain group and reference group in a ppa file?<br> <br> After a longer struggle it seems to me that one can only constrain _one_ of the<br> following: I. The length of the vector II.,III.,IV., The length of the vector onto the x, y, and z, coordinate axis, respectively.<br> <br> This means that setting: <br> "constraint_direction = 0.0 1.0 1.0" or <br> "constraint_direction = 1.0 1.0 1.0"<br> <br> in the ppa file will constrain _anything_!<br> Why is that?<br> <br> Best regards<br> -Soren<br> <br> <br> <br><br><b><i>Soren Enemark <blegbirk@yahoo.dk></i></b> skrev:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> <div>Dear Gromacs users,</div> <div>I have difficulties to get the distance between two molecules constraint using</div> <div>a .ppa file as
described in Chapter 6 in the manual. I tried to combine the</div> <div>different options in almost all ways but nothing seems to constraint the</div> <div>distance.</div> <div>To check that the inter molecular distance is unchanged I use g_dist. Is it</div> <div>unprecise? Can the inter molecular constraint be used together with the</div> <div>normal bond/angle constraints set in the mdp file, or are they somehow</div> <div>working against each other?</div> <div>I include a test md.mdp file, my constraint.ppa file and a piece of the dist.xvg</div> <div>file generated with g_dist</div> <div> </div> <div> </div> <div>md.mdp</div> <div>-----------------------</div> <div>title = FWS</div> <div>integrator = md<br>dt =
0.001<br>nsteps = 2000 ; 2 ps<br>ns_type = grid</div> <div>pbc = xyz<br>nstlist = 1<br>rlist = 1.1</div> <div>nstxout = 10<br>nstvout = 10<br>nstfout = 10<br>nstlog = 10<br>nstenergy = 10<br>nstxtcout = 0<br>energygrps = Complex_A Complex_B</div> <div>comm_mode = Linear<br>nstcomm =
1<br>comm_grps = Complex_All</div> <div>coulombtype = PME<br>optimize_fft = yes<br>fourierspacing = 0.12<br>pme_order = 4<br>rcoulomb = 1.1<br>vdwtype = Switch<br>rvdw_switch = 1.1<br>rvdw = 1.2</div> <div>tcoupl = berendsen<br>tc_grps = Complex_All SOL_NA+<br>tau_t = 0.1 0.1<br>ref_t = 300 300</div> <div>pcoupl = berendsen<br>pcoupltype =
isotropic<br>tau_p = 5<br>compressibility = 4.5e-5<br>ref_p = 1.1</div> <div>gen_vel = no<br>gen_temp = 300<br>genseed = 42</div> <div>;constraints = hbonds<br>;constraint_algorithm = lincs<br>;unconstrained_start = no</div> <div> </div> <div> </div> <div> </div> <div>constraint.ppa</div> <div>--------------------------------<br>verbose = yes<br>runtype = constraint<br>group_1 = Complex_A<br>reference_group = Complex_B<br>;reftype = com_t0<br>;reflag = 1<br>pulldim = Y Y Y<br>constraint_direction = 1.0 1.0 1.0<br>;constraint_tolerance = 0.010</div> <div> </div> <div> </div> <div> <div>dist.xvg</div> <div>--------------------------------<br></div>
<div># This file was created Fri Apr 21 10:37:52 2006<br># by the following command:<br># g_dist -f traj.trr -s topol.tpr -n index.ndx -o dist.xvg<br>#<br># g_dist is part of G R O M A C S:<br>#<br># God Rules Over Mankind, Animals, Cosmos and Such<br>#<br>@ title "Distance"<br>@ xaxis label "Time (ps)"<br>@ yaxis label "Distance (nm)"<br>@TYPE xy<br>@ view 0.15, 0.15, 0.75, 0.85<br>@ legend on<br>@ legend box on<br>@ legend loctype view<br>@ legend 0.78, 0.8<br>@ legend length 2<br>@ s0 legend "|d|"<br>@ s1 legend "d\sx\N"<br>@ s2 legend "d\sy\N"<br>@ s3 legend "d\sz\N"<br> 0.000 4.39150 4.39143 -0.00756 0.02317<br> 0.010 4.39139 4.39132 -0.00756 0.02328<br> 0.020 4.39129 4.39122
-0.00755 0.02338<br> 0.030 4.39119 4.39112 -0.00756 0.02349<br> 0.040 4.39110 4.39103 -0.00759 0.02360<br> 0.050 4.39102 4.39095 -0.00763 0.02372<br> 0.060 4.39094 4.39087 -0.00767 0.02384<br> 0.070 4.39086 4.39079 -0.00770 0.02395<br> 0.080 4.39079 4.39071 -0.00772 0.02405<br> 0.090 4.39071 4.39063 -0.00773 0.02414<br> 0.100 4.39062 4.39054
-0.00774 0.02424<br> 0.110 4.39052 4.39044 -0.00775 0.02435<br> 0.120 4.39042 4.39034 -0.00778 0.02448<br>......</div> <div> </div> <div> 0.900 4.38858 4.38848 -0.00831 0.02686<br> 0.910 4.38866 4.38857 -0.00831 0.02677<br> 0.920 4.38875 4.38866 -0.00830 0.02668<br> 0.930 4.38883 4.38874 -0.00828 0.02658<br> 0.940 4.38890 4.38881 -0.00826 0.02649<br> 0.950 4.38898
4.38889 -0.00824 0.02639</div> <div>......</div> <div> </div></div> <div> 1.930 4.39870 4.39867 -0.00592 0.01429<br> 1.940 4.39872 4.39870 -0.00591 0.01425<br> 1.950 4.39874 4.39871 -0.00589 0.01422<br> 1.960 4.39874 4.39871 -0.00586 0.01419<br> 1.970 4.39874 4.39871 -0.00584 0.01417<br> 1.980 4.39874 4.39872 -0.00581 0.01413<br> 1.990 4.39876 4.39874 -0.00577 0.01408<br>
2.000 4.39880 4.39878 -0.00575 0.01401</div> <div> </div> <div> </div> <div> </div> <div>Finding the max and min distance shows that the molecules move 0.1 Ång</div> <div>over a period of 1 ps. I am simply demanding too much from the program,</div> <div>since each of the molecules are about 450 aa?</div> <div> </div> <div>Can U plz help me to solve this problem! I also have one question to the</div> <div>constraint-direction, if I set this to "0 0 0" then what do I constraint??</div> <div> </div> <div> Thanks,</div> <div> Soren</div><!-- type = text -->_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<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
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