<br clear="all">hi all<br><br> i have done protein protein interaction and the complex structure<br>
was taken for MD simulation using Gromacs.while performing mdrun step for position restrain i got error. i have carried out mdrun for 1ps and the command given for mdrun<br>
and position restrain are<br>
grompp -f *.pdb -c *.gro -p top.top -o *.tpr
<br>
mdrun -v -deffnm pr<br>my em.mdp file<br><br>title = com<br>cpp = /usr/local/gromacs/share/gromacs/cpp ; the c pre-processor<br>define = -DFLEXIBLE<br>constraints = none<br>
integrator = steep<br>dt = 0.002 ; ps !<br>nsteps = 3000<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>
rcoulomb = 1.0<br>vdwtype = cut-off<br>rvdw = 1.4<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>
pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 1000.0<br>emstep = 0.01.<br><br>
here i have given nsteps 3000. but while doing energy minimization it considers only 1000 steps and the energy was minimized for only 1000 steps. then i gone for position restrain step while doing Mdrun i got error like this<br>
<br>starting mdrun 'Protein in water'<br>500 steps, 1.0 ps.<br>step 400, remaining runtime: 132 s <br>Step 402, time 0.804 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.000119, max 0.006712 (between atoms 2873 and 2875)<br>
bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 2873 2875 64.4 0.0989 0.1007 0.1000<br><br>t = 0.868 ps: Water molecule starting at atom 93766 can not be settled.<br>
Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates<br><br>wat should i do now. how can i progress this.could any one help me plz. thank in advance<br><br>Cheers,<br>
Manjula Kasinathan.<br><br>