Dear Gromacs users,<br><br>I am trying to run a urea+protein simulation and encountering a few problems at various stages.<br><br>I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 300K)<br>
<br>I am using this equilibrated box to add to a globular protein of about 250 residues using following commands :<br><br><br>editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron (Giving me a dodecahedron with Vol = 407.98nm^3, so for this volume, for 10M urea the number of urea above box should add is 2448.)<br>
<br>genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro (<b>This adds 2064 Urea only, shouldnt it be adding 2448 urea molecules, corresponding to 10M urea box i have solvated with??)</b><br><br><br>When i try to minimize this using the following em.mdp <br>
<br><br>cpp = /usr/bin/cpp<br>constraints = none<br>integrator = steep<br>nsteps = 5000<br>coulombtype = PME<br>pme_order = 4<br>nstlist = 5<br>ns_type = grid<br>rlist = 1.0<br>
rcoulomb = 1.0<br>rvdw = 1.0<br>Tcoupl = no<br>Pcoupl = no<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>; Energy minimizing stuff<br>
;<br>emtol = 100<br>emstep = 0.01<br><br><br><b>It gives me the following output</b><br><br><br>Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+02<br> Number of steps = 5000<br>
Warning: 1-4 interaction between 2796 and 2801 at distance 2.727 which is larger than the 1-4 table size 2.000 nm<br>These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br>
or with user tables increase the table size<br><br>t = 0.015 ps: Water molecule starting at atom 34477 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>Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>but not to the requested precision Fmax < 100<br><br>Double precision normally gives you higher accuracy.<br>You might need to increase your constraint accuracy, or turn<br>
off constraints alltogether (set constraints = none in mdp file)<br><br>writing lowest energy coordinates.<br><br>Steepest Descents converged to machine precision in 34 steps,<br>but did not reach the requested Fmax < 100.<br>
Potential Energy = -1.3092671e+22<br>Maximum force = inf on atom 12598<br>Norm of force = inf<br><br>gcq#160: "The Microsecond is Within Reach" (P.J. Van Maaren)<br><br><br><br><i>When i look at the file in VMD, the protein is completely out of the box + There are unusual bonds between a lot of UREA and SOL molecules</i>. ( The unusual bonds are artifcats after minimization which are not there when i initially look at my P48_10Mrea.gro, that is the gro generated after genbox wth -cs as 10M urea)<br>
<br>I tried constraining hbonds as well in em.mdp bit to no effect.<br><br><br>I used the above em.gro to run a production run, with following pr.mdp<br><br><br>cpp = /usr/bin/cpp<br>define = -DPOSRES<br>constraints = hbonds<br>
integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 100000 ; total 200 ps<br>nstcomm = 1<br>nstxtcout = 50 ; collect data every 1 ps<br>nstxout = 100<br>nstvout = 100<br>nstfout = 100<br>nstlog = 100<br>nstenergy = 100<br>nstlist = 5<br>
ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>rvdw = 1.0<br>pbc = xyz<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>
Tcoupl = V-rescale<br>tau_t = 0.1 0.1 ; use items in bold if you have Cl ions<br>tcgrps = Protein Non-protein<br>ref_t = 300 300<br>; Pressure coupling is on<br>Pcoupl = berendsen<br>tau_p = 1<br>compressibility = 4.5e-5<br>
ref_p = 1.0<br>; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br><br><br><br><br><b>the simulation stops after following error</b><br><br>t = 0.002 ps: Water molecule starting at atom 36943 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><br><br><br>Can anyone pls suggest what should i modify to effectively simulate my system? <br><br><br><br>
Any suggestions regarding how i can run a urea+protein simulation with the exact desired concentration will be highly appreciated. <br><br><br><br><br>Thanks for all the time and pateince,<br>Regards<br>Karan<br> <br><br>
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