[gmx-users] Errors

[ali.hassanali.1]

Dear GMX Users,

I have been simulating a tri-peptide (Lysine-Tryptophan-Lysine) in water
using the gmx Gromacs forcefield with SPC-E water. However, because of
some discrepancies in some dipole results I am getting, I am now trying
the OPLSAA forcefield with Tip4 water. I am using the same mdp file as I
did before with the same parameters but for some reason I get this common
error on the mailing list. My dynamics ran fine when I was using the gmx
forcefield with SPCE water. It looks like the tip4 water atoms seem to be
acting weird and I am not sure why. You can look at my mdp file below. Any
help will be appreciated. Thanks.

Ali


max 5.003917 (between atoms 2430 and 2429) rms 0.145496
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2430   2429  156.9    0.1514   0.9089      0.1514
   2431   2429  160.7    0.0957   0.5080      0.0957
   2431   2430  148.7    0.0957   0.5614      0.0957
Constraint error in algorithm Lincs at step 3294
Wrote pdb files with previous and current coordinates

Step 3295, time 0.03295 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 10.108601 (between atoms 2430 and 2429) rms 0.270667
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2430   2429  177.0    0.9089   1.6817      0.1514
   2431   2429  164.2    0.5080   0.8522      0.0957
   2431   2430  161.3    0.5614   0.8856      0.0957
Constraint error in algorithm Lincs at step 3295
Wrote pdb files with previous and current coordinates

Step 3296, time 0.03296 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 1755767119194559875121152.000000 (between atoms 2430 and 2429) rms
31165349486518914252800.0000$
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     86     85  175.6    0.1514 364.0574      0.1514
     87     85   89.4    0.0957 995.7734      0.0957
     87     86   89.4    0.0957 1006.7483      0.0957
    162    161   59.3    0.1514 12611.1527      0.1514
    163    161   76.8    0.0957 11399.5113      0.0957
    210    209   89.5    0.1514 33260.3727      0.1514
    211    209   82.1    0.0957 25570.4152      0.0957
    211    210   78.2    0.0957 17087.8195      0.0957
    274    273   84.1    0.1514 303582.7189      0.1514
    275    273   71.6    0.0957 110184.9472      0.0957
    275    274   82.7    0.0957 272943.0322      0.0957
    374    373   90.7    0.1514 813249229237845.1250      0.1514
    375    373   79.8    0.0957 238826823673644.3125      0.0957
    375    374   86.6    0.0957 705676995324273.2500      0.0957
    631    629   94.0    0.0957 163423215551323872.0000      0.0957
    631    630   99.7    0.0957 67088178150753240.0000      0.0957
    670    669  119.4    0.1514  54.8586      0.1514
    671    669  121.0    0.0957  30.6366      0.0957
    671    670  113.7    0.0957  39.2865      0.0957
    782    781  107.3    0.1514 1416267.3063      0.1514
    783    781   91.8    0.0957 1189154.7293      0.0957
    783    782   94.2    0.0957 514287.5213      0.0957
    894    893   87.1    0.1514 5727.3480      0.1514
    895    893   90.0    0.0957 12127.7095      0.0957
    895    894   90.0    0.0957 11978.0528      0.0957
    918    917   83.4    0.1514  68.0343      0.1514
    919    917   43.7    0.0957   4.1836      0.0957
    919    918   87.3    0.0957  64.8391      0.0957
   1054   1053   64.3    0.1514  60.5991      0.1514
   1055   1053   79.5    0.0957  56.5326      0.0957
   1118   1117   78.9    0.1514 1261743.0598      0.1514
   1119   1117   43.2    0.0957 99499.6755      0.0957
   1119   1118   86.7    0.0957 1241297.5635      0.0957

   Constraint error in algorithm Lincs at step 3296
Wrote pdb files with previous and current coordinates
Large VCM(group rest): 118586.13794, -60837.53308, -73652.31722, ekin-cm:
2.22372e+14


title                    = Polymer_Simulation
cpp                      = /lib/cpp
include                  = -I../top
define                   =
integrator               = md
dt                       = 0.00001
emstep                   = 0.01
emtol                    = 1000
nsteps                   = 50000
nstxout                  = 200
nstvout                  = 200
nstfout                  = 200
nstlog                   = 200
nstenergy                = 250
nstxtcout                = 250
xtc_grps                 = Protein SOL
energygrps               = Protein SOL
nstlist                  = 10
ns_type                  = grid
rlist                    = 1.1
coulombtype              = PME
rcoulomb                 = 0.9
rvdw                     = 0.9
tcoupl                   = nose-hoover
ref_t                    = 30 30 30
tau_t                    = 0.01 0.01 0.01
tc_grps                  = Protein SOL Cl
Pcoupl                   = no
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = no
gen_temp                 = 300
gen_seed                 = 173529
constraints              = all-bonds
lincs_iter               = 5
fourierspacing           = 0.15
optimize_fft             = yes
pme_order                = 4
vdwtype                  = shift