[gmx-users] lincs problems

[serdar durdagi]

Dear all,
 
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.
 
The input and output files are in below.
 
I deeply appreciate any comment.
 
Serdar Durdagi
 
title = FWS
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 15000
nstlists = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 100.0
emsteps = 0.01
 
 
title = CB1_conf_a MD
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 50000 ; total 100.0 ps
nstcomm = 1
nstxout = 500 ; collect data every 1 ps
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on
Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 310 310
; Pressure coupling is on
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
Generate velocities is on at 310 K.
gen_vel = yes
gen_temp = 310.0
gen_seed = 173529
 
 
Initializing LINear Constraint Solver
  number of constraints is 13769
  average number of constraints coupled to one constraint is 2.1
   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.042545    312    313   0.003927
        After LINCS         0.002285   2001   2013   0.000107

Constraining the coordinates at t0-dt (step -1)
   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.107883   1519   1521   0.008308
        After LINCS         0.000669   2001   2013   0.000021
Started mdrun on node 0 Sun Dec  2 16:36:58 2007
Initial temperature: 309.003 K
           Step           Time         Lambda
              0        0.00000        0.00000
Grid: 11 x 11 x 11 cells
Configuring nonbonded kernels...
Testing ia32 SSE2 support... present.

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.094303     25     26   0.003893
        After LINCS         0.000728   2013   2014   0.000030
   Energies (kJ/mol)
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    2.19260e+03    1.02313e+03    5.03050e+02    2.32594e+03    2.33275e+04
        LJ (SR)        LJ (LR)   Coulomb (SR)   Coul. recip.      Potential
   -1.38354e+05   -6.00776e+03   -5.27839e+04   -5.80598e+04   -2.25833e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    5.05816e+04   -1.75252e+05    3.10987e+02   -5.12348e+03

Step 7, time 0.014 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.001574 (between atoms 1445 and 1446) rms 0.000030
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1445   1446   30.2    0.1001   0.1002      0.1000
Large VCM(group rest):     -0.00154,     -0.00147,     -0.00146, ekin-cm:  1.09254e+00
Large VCM(group rest):     -0.00164,     -0.00157,     -0.00155, ekin-cm:  1.24116e+00
Large VCM(group rest):     -0.00175,     -0.00168,     -0.00167, ekin-cm:  1.41931e+00
Large VCM(group rest):     -0.00188,     -0.00182,     -0.00180, ekin-cm:  1.65240e+00
Step 12, time 0.024 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.001220 (between atoms 964 and 966) rms 0.000032
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    964    967   33.0    0.1000   0.1000      0.1000
Large VCM(group rest):     -0.00201,     -0.00196,     -0.00194, ekin-cm:  1.90904e+00
Step 13, time 0.026 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.001168 (between atoms 964 and 966) rms 0.000032
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    964    967   33.3    0.1000   0.1000      0.1000
Large VCM(group rest):     -0.00215,     -0.00209,     -0.00208, ekin-cm:  2.18517e+00
Large VCM(group rest):     -0.00230,     -0.00225,     -0.00224, ekin-cm:  2.51731e+00
Large VCM(group rest):     -0.00243,     -0.00240,     -0.00237, ekin-cm:  2.83354e+00


      Heute schon einen Blick in die Zukunft von E-Mails wagen? Versuchen Sie´s mit dem neuen Yahoo! Mail. www.yahoo.de/mail
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071204/613af7cb/attachment.html>