<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 -->