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<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Dear all,</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">I am trying to simulate a ligand at the cavity of CB receptor with the dmso environment. Even if I used very large number of steps for the geometry optimization before simulation, I have some LINCS problem for the solvent, I changed the solvent from dmso to water, but it didn't help the solution.</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">The input and output files are in below.</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">I deeply appreciate any comment.</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Serdar Durdagi</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"><FONT size=2>
<P>title = FWS</P>
<P>cpp = /usr/bin/cpp</P>
<P>define = -DFLEXIBLE</P>
<P>constraints = none</P>
<P>integrator = steep</P>
<P>dt = 0.002 ; ps !</P>
<P>nsteps = 15000</P>
<P>nstlists = 10</P>
<P>ns_type = grid</P>
<P>rlist = 1.0</P>
<P>coulombtype = PME</P>
<P>rcoulomb = 1.0</P>
<P>vdwtype = cut-off</P>
<P>rvdw = 1.4</P>
<P>fourierspacing = 0.12</P>
<P>fourier_nx = 0</P>
<P>fourier_ny = 0</P>
<P>fourier_nz = 0</P>
<P>pme_order = 4</P>
<P>ewald_rtol = 1e-5</P>
<P>optimize_fft = yes</P>
<P>;</P>
<P>; Energy minimizing stuff</P>
<P>;</P>
<P>emtol = 100.0</P>
<P>emsteps = 0.01</P>
<P> </P>
<P> </P><FONT size=2>
<P>title = CB1_conf_a MD</P>
<P>cpp = /usr/bin/cpp</P>
<P>constraints = all-bonds</P>
<P>integrator = md</P>
<P>dt = 0.002 ; ps !</P>
<P>nsteps = 50000 ; total 100.0 ps</P>
<P>nstcomm = 1</P>
<P>nstxout = 500 ; collect data every 1 ps</P>
<P>nstvout = 0</P>
<P>nstfout = 0</P>
<P>nstlist = 10</P>
<P>ns_type = grid</P>
<P>rlist = 1.0</P>
<P>coulombtype = PME</P>
<P>rcoulomb = 1.0</P>
<P>vdwtype = cut-off</P>
<P>rvdw = 1.4</P>
<P>fourierspacing = 0.12</P>
<P>fourier_nx = 0</P>
<P>fourier_ny = 0</P>
<P>fourier_nz = 0</P>
<P>pme_order = 6</P>
<P>ewald_rtol = 1e-5</P>
<P>optimize_fft = yes</P>
<P>; Berendsen temperature coupling is on</P>
<P>Tcoupl = berendsen</P>
<P>tau_t = 0.1 0.1</P>
<P>tc-grps = protein non-protein</P>
<P>ref_t = 310 310</P>
<P>; Pressure coupling is on</P>
<P>Pcoupl = no</P>
<P>tau_p = 0.5</P>
<P>compressibility = 4.5e-5</P>
<P>ref_p = 1.0</P>
<P>Generate velocities is on at 310 K.</P>
<P>gen_vel = yes</P>
<P>gen_temp = 310.0</P>
<P>gen_seed = 173529</P></FONT>
<P> </P>
<P> </P>
<P>Initializing LINear Constraint Solver<BR> number of constraints is 13769<BR> average number of constraints coupled to one constraint is 2.1</P>
<P> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.042545 312 313 0.003927<BR> After LINCS 0.002285 2001 2013 0.000107</P>
<P><BR>Constraining the coordinates at t0-dt (step -1)<BR> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.107883 1519 1521 0.008308<BR> After LINCS 0.000669 2001 2013 0.000021</P>
<P>Started mdrun on node 0 Sun Dec 2 16:36:58 2007<BR>Initial temperature: 309.003 K<BR> Step Time Lambda<BR> 0 0.00000 0.00000</P>
<P>Grid: 11 x 11 x 11 cells<BR>Configuring nonbonded kernels...<BR>Testing ia32 SSE2 support... present.</P>
<P><BR> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.094303 25 26 0.003893<BR> After LINCS 0.000728 2013 2014 0.000030</P>
<P> Energies (kJ/mol)<BR> Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<BR> 2.19260e+03 1.02313e+03 5.03050e+02 2.32594e+03 2.33275e+04<BR> LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Potential<BR> -1.38354e+05 -6.00776e+03 -5.27839e+04 -5.80598e+04 -2.25833e+05<BR> Kinetic En. Total Energy Temperature Pressure (bar)<BR> 5.05816e+04 -1.75252e+05 3.10987e+02 -5.12348e+03</P>
<P><BR>Step 7, time 0.014 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 0.001574 (between atoms 1445 and 1446) rms 0.000030<BR>bonds that rotated more than 30 degrees:<BR> atom 1 atom 2 angle previous, current, constraint length<BR> 1445 1446 30.2 0.1001 0.1002 0.1000<BR>Large VCM(group rest): -0.00154, -0.00147, -0.00146, ekin-cm: 1.09254e+00<BR>Large VCM(group rest): -0.00164, -0.00157, -0.00155, ekin-cm: 1.24116e+00<BR>Large VCM(group rest): -0.00175, -0.00168, -0.00167, ekin-cm: 1.41931e+00<BR>Large VCM(group rest): -0.00188,
-0.00182, -0.00180, ekin-cm: 1.65240e+00</P>
<P>Step 12, time 0.024 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 0.001220 (between atoms 964 and 966) rms 0.000032<BR>bonds that rotated more than 30 degrees:<BR> atom 1 atom 2 angle previous, current, constraint length<BR> 964 967 33.0 0.1000 0.1000 0.1000<BR>Large VCM(group rest): -0.00201, -0.00196, -0.00194, ekin-cm: 1.90904e+00</P>
<P>Step 13, time 0.026 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 0.001168 (between atoms 964 and 966) rms 0.000032<BR>bonds that rotated more than 30 degrees:<BR> atom 1 atom 2 angle previous, current, constraint length<BR> 964 967 33.3 0.1000 0.1000 0.1000<BR>Large VCM(group rest): -0.00215, -0.00209, -0.00208, ekin-cm: 2.18517e+00<BR>Large VCM(group rest): -0.00230, -0.00225, -0.00224, ekin-cm: 2.51731e+00<BR>Large VCM(group rest): -0.00243, -0.00240, -0.00237, ekin-cm: 2.83354e+00</P>
<P> </P></FONT></DIV></DIV></DIV></DIV></DIV></div><br>
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