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Hi guys,<BR> <BR>When I did my SMD simulation by applying load to a certain group of atoms and fixing certain atoms by modifying the topology file, the points that i have fixed moved from there original position. I don't know what the problem is!<BR> <BR>Any suggestion!<BR> <BR> <BR>To make what I was doing clear, I started the equilibrium by creating a box and filling it with water. Then I did the energy minimization. After that I heated up and pressurized the structure. Every thing is good so far. After that, I modified the topology file by adding four points that i want to fix as following:<BR>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>1330 1 1000 1000 1000 <--------- my 1st point<br>1426 1 1000 1000 1000 <--------- my 2nd point<br>1437 1 1000 1000 1000 <--------- my 3rd point<BR>1548 1 1000 1000 1000 <--------- my 4th point<br>#endif<BR>This only what I did to fix the points.<BR> <BR>The results have shown that the fixid points moved from their original position.<BR> <BR> <BR> <BR>Here is my topology file:<BR> <BR>;<br>; File '3gm1a.top' was generated<br>; By user: onbekend (0)<br>; On host: onbekend<br>; At date: Sat Jul 2 14:03:14 2011<br>;<br>; This is a standalone topology file<br>;<br>; It was generated using program:<br>; pdb2gmx - VERSION 4.5.3<br>;<br>; Command line was:<br>; pdb2gmx -f 3gm1a.pdb -o 3gm1a.gro -p 3gm1a.top<br>;<br>; Force field data was read from:<br>; /opt/apps/pgi7_2/mvapich1_1_0_1/gromacs/4.5.3/share/gromacs/top<br>;<br>; Note:<br>; This might be a non-standard force field location. When you use this topology, the<br>; force field must either be present in the current directory, or the location<br>; specified in the GMXLIB path variable or with the 'include' mdp file option.<br>;<BR> <BR>; Include forcefield parameters<br>#include "gromos53a6.ff/forcefield.itp"<BR> <BR>; Include chain topologies<br>#include "3gm1a_Protein_chain_A.itp"<br>#include "3gm1a_Protein_chain_E.itp"<br>#include "3gm1a_Protein_chain_F.itp"<BR> <BR>; Include water topology<br>#include "gromos53a6.ff/spc.itp"<BR>#ifdef POSRES_WATER<br><BR>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>1330 1 1000 1000 1000<br>1426 1 1000 1000 1000<br>1437 1 1000 1000 1000<br>1548 1 1000 1000 1000<br><BR>#endif<BR> <BR>; Include topology for ions<br>#include "gromos53a6.ff/ions.itp"<BR> <BR>[ system ]<BR>; Name<br>PROTEIN TYROSINE KINASE 2 BETA; 5 RESIDUES 861-1009; PAXILLIN in water<BR> <BR>[ molecules ]<BR>; Compound #mols<br>Protein_chain_A 1<br>Protein_chain_E 1<br>Protein_chain_F 1<br>SOL 8788<br>NA 25<br>CL 18<br><BR> <BR>And Here is my mdp file:<BR> <BR>title = smd_120 ; 120 pN<br>; this is loosely based off of the VT pulling tutorial; heavily modified <br>; Run parameters<br>integrator = md<br>dt = 0.002<br>tinit = 0<br>nsteps = 2500000 ; 5 ns<br>; Output parameters<br>nstxout = 1000 ; every 2 ps<br>nstvout = 1000<br>nstfout = 5000<br>nstxtcout = 5000 ; every ps<br>nstenergy = 1000<br>; Bond parameters<br>constraint_algorithm = lincs<br>constraints = hbonds<br>lincs_iter = 1 ; accuracy of LINCS<br>lincs_order = 4 ; also related to accuracy<BR>; Single-range cutoff scheme<br>nstlist = 5<br>ns_type = grid<br>rlist = 1.4<br>rcoulomb = 1.4<br>rvdw = 1.4<br>; PME electrostatics parameters<br>coulombtype = PME<br>fourierspacing = 0.16<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = Nose-Hoover<br>tc_grps = Protein Non-Protein<br>tau_t = 0.2 0.2<br>ref_t = 310 310<br>; Pressure coupling is on<br>Pcoupl = Parrinello-Rahman<br>pcoupltype = isotropic<br>tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocities is off<br>gen_vel = no<br>; Periodic boundary conditions are on in all directions<br>pbc = xyz<br>; Long-range dispersion correction<br>DispCorr = EnerPres<br>; COM motion removal<br>; These options remove comm motion of the constraint / freeze group<br>nstcomm = 1<br>comm_mode = Linear<br>comm_grps = System<br>; pull parameters<br>pull = constant_force<br>pull_geometry = direction<br>pull_nstxout = 500 ; will print the c.o.m. coordinates<br>pull_nstfout = 500 ; forces on group<br>pull_ngroups = 1<br>pull_group0 = Protein ;<br>pull_group1 = group_B ;<br>pull_pbcatom1 = 100 ; the CA of the 10th residue<br>pull_vec1 = -2.63 -16.48 -14.95 ; direction of pull, will be normalized<br>pull_k1 = 72.29 ; pull_k1*1.66 = pN; units: [kJ / (mol * nm^2)]<BR> <BR> <BR> <BR> <BR> <BR>What should I do?<BR> <BR> <BR>Thanks,<BR>Talal<BR> <BR> </div></body>
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