[gmx-users] umbrella sampling, LINCS WARNING

[rose rahmani]

Hello;

I'm doing umbrella sampling, protein is getting closer to ZnS, but i get
some step files and run crashed just 107sec to end. Would it be because of
protein got very close to ZnS? Would you please help me?

With regards


---------------------
this is pullf.xvg

0.0000  -0.000579208
0.0020  2.45011
0.0040  4.89696
0.0060  7.35804
0.0080  9.82449
0.0100  12.2863
0.0120  14.7352
0.0140  17.1628
0.0160  19.5634

.
.
.
1956.0480       -100532
1956.0500       -100532
1956.0520       -100531
1956.0540       -100530
1956.0560       -100529
1956.0580       -100528
1956.0600       -100527
1956.0620       -100526
-----------
this is pullx.xvg

0.0000  4.287   1.73577
0.1000  4.287   1.72023
0.2000  4.287   1.73131
0.3000  4.287   1.75326
0.4000  4.287   1.77348
0.5000  4.287   1.76939
0.6000  4.287   1.75636
0.7000  4.287   1.73677
0.8000  4.287   1.71755
0.9000  4.287   1.70901
1.0000  4.287   1.72336

.
.
.

1953.2000       4.287   0.324765
1953.3000       4.287   0.323972
1953.4000       4.287   0.326929
1953.5000       4.287   0.323881
1953.6000       4.287   0.323358
1953.7000       4.287   0.325145
1953.8000       4.287   0.32516
1953.9000       4.287   0.324791
1954.0000       4.287   0.325144
1954.1000       4.287   0.324902
1954.2000       4.287   0.324985
1954.3000       4.287   0.324877
1954.4000       4.287   0.323429
1954.5000       4.287   0.32637
1954.6000       4.287   0.324941
1954.7000       4.

-----------------------------------
this is md_pull.mdp;

integrator               = md
dt                       = 0.002
nsteps                   = 1000000
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 500
nstlog                   = 500
nstenergy                = 1000
nstxtcout                = 1000
nstlist                  = 10
rlist                    = 1.5
coulombtype              = pme
rcoulomb                 = 1.5
vdwtype                  = Switch
rvdw_switch              = 1.0
rvdw                     = 1.2
pcoupl                   = no
gen_vel                  = no
constraints              = h-bonds
ns_type                  = grid
pbc                      = xy
freezegrps               = WAL ZnS
freezedim                = Y Y Y Y Y Y
energygrp-excl           = WAL WAL ZnS ZnS
energygrps               = SOL WAL ZnS Protein NA CL
nwall                    = 2
wall-atomtype            = C C
wall-type                = 9-3
wall-density             = 150 150
wall-ewald-zfac          = 3
ewald-geometry           = 3dc
fourierspacing           = 0.12
tcoupl                   = v-rescale
tc-grps                  = System
tau-t                    = 0.1
ref-t                    = 300

; Pull code
pull                    = umbrella
pull_ngroups            = 1
pull_group0             = ZnS
pull_group1             = Protein
pull_geometry           = direction
pull_vec1               = 0 0 1
pull_dim                = N N Y
pull_rate1              = -0.011        ; 1 nm per  ns
pull_k1                 = 5000
pull_start              = yes
pull_nstxout            = 50

--------------------------
This is pull.job


Step 978195, time 1956.39 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000004, max 0.000010 (between atoms 782 and 780)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    770    769   61.4    0.1090   0.1090      0.1090
    779    778   42.0    0.1010   0.1010      0.1010

Step 978197, time 1956.39 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.429802, max 1.468930 (between atoms 783 and 780)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    773    771   90.0    0.1112   0.1202      0.1090
    770    769   32.8    0.1090   0.1090      0.1090
    779    778   90.0    0.1010   0.1232      0.1010
    783    780   90.0    0.1090   0.2691      0.1090
Wrote pdb files with previous and current coordinates

Step 978198, time 1956.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2.212948, max 5.521000 (between atoms 773 and 771)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    773    771   90.0    0.1202   0.7108      0.1090
    772    771   47.8    0.1105   0.1031      0.1090
    770    769   90.0    0.1090   0.1142      0.1090
    779    778   90.0    0.1232   0.6381      0.1010
    783    780   57.8    0.2691   0.1086      0.1090
Wrote pdb files with previous and current coordinates

Step 978199, time 1956.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.451943, max 1.210712 (between atoms 770 and 769)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    773    771   90.0    0.7108   0.1628      0.1090
    772    771   36.8    0.1031   0.1131      0.1090
    770    769   90.0    0.1142   0.2410      0.1090
    779    778   56.6    0.6381   0.1010      0.1010
    783    780   90.0    0.1086   0.2027      0.1090
Wrote pdb files with previous and current coordinates
vol 0.70  imb F 27%
Step 978200, time 1956.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 3.021436, max 9.508962 (between atoms 769 and 770)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    769    770   90.0    0.2410   1.1455      0.1090
    773    771   90.0    0.1628   0.6838      0.1090
    772    771   90.0    0.1131   0.6719      0.1090
    779    778   90.0    0.1010   0.2717      0.1010
    783    780   90.0    0.2027   0.1641      0.1090
    782    780   90.0    0.1112   0.1303      0.1090
    781    780   90.0    0.1097   0.2685      0.1090

step 978200: Water molecule starting at atom 991 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
^Mstep 978200, remaining runtime:   107 s