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虫号: 4282835
注册: 2015-12-11
专业: 高分子物理与高分子物理化

[求助] GROMCS出现错误

求助各位大佬，在用gromacs的时候出现了以下的错误该如何解决呢？体系已经做了能量优化，这个错误是在做nvt预平衡的时候出现的。谢谢各位大佬！！

Step 1325, time 1.325 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.035172, max 0.281169 (between atoms 142 and 145)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
143 144 31.2 0.1005 0.0989    0.1000

Step 1331, time 1.331 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 816.149048, max 9026.031250 (between atoms 143 and 144)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
103 127 48.7 0.1453 0.1471    0.1435
114 115 49.4 0.1566 0.0854    0.1435
114 124 98.6 0.1649 0.1101    0.1520
117 118 38.8 0.1835 0.3072    0.1520
117 141  106.8 0.1585 0.1745    0.1435
118 119 45.0 0.1661 0.0786    0.1435
118 126 67.7 0.1792 0.0449    0.1520
119 120 37.4 0.1027 0.1192    0.1000
121 124 35.8 0.1524 0.2155    0.1520
124 125 38.1 0.1444 0.1945    0.1435
125 126 30.7 0.1466 0.1670    0.1435
128 129  176.2 0.2776 5.3298    0.1435
128 131 69.7 0.5636 4.4779    0.1520
128 138 79.8 0.3747 3.8723    0.1520
129 130 93.1 0.0182 2.2967    0.1000
131 132 56.9 0.3678 1.8625    0.1520
131 155  118.5 1.1285 4.6649    0.1435
132 133  105.0 0.1806  15.4852    0.1435
132 140 48.7 0.0869 0.9637    0.1520
133 134 98.4 0.1397  15.0138    0.1000
135 136 87.5 0.1530 1.4493    0.1435
135 138 82.6 0.1740 2.9280    0.1520
136 137 92.0 0.1226 0.7336    0.1000
138 139  177.3 0.1450  16.4410    0.1435
139 140 59.1 0.1621  16.2713    0.1435
140 141 95.8 0.1300 0.8640    0.1435
142 145 99.8 4.3105  38.1381    0.1520
142 152  149.1 4.6295 6.3105    0.1520
145 146 31.5 2.1491  40.9124    0.1520
145 171 49.5 2.5563  41.1024    0.1435
146 147 93.5 3.6932 3.2399    0.1435
146 154 33.9 2.4452 7.8218    0.1520
147 148 89.6 1.6534 1.7318    0.1000
149 150 92.5 0.8919 0.8930    0.1435
149 152 86.2 4.6661  10.1095    0.1520
150 151 92.4 0.4329 1.0297    0.1000
152 153 64.5 5.4649  13.5725    0.1435
153 154  156.7 4.2225 6.0705    0.1435
154 155 31.8 3.5694 6.1695    0.1435
157 158  127.9 0.1700 0.2188    0.1000
159 162 34.4 0.7675 1.7566    0.1520
160 161 58.5 0.3207 0.2597    0.1000
162 163 62.7 0.5360 0.5178    0.1435
162 170 84.9 2.2265 4.8269    0.1520
163 164 74.8 0.6339 0.2147    0.1000
166 167 55.6 0.1750 0.0975    0.1000
168 169 69.1 0.4028 1.2414    0.1435
169 170 85.7 2.0814 3.6421    0.1435
170 171  124.3 1.6610 4.1818    0.1435
170 171  124.3 1.6610 4.1818    0.1435
170 171  124.3 1.6610 4.1818    0.1435

step 1331: Water molecule starting at atom 4837 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step1331b.pdb to ./#step1331b.pdb.1#

Back Off! I just backed up step1331c.pdb to ./#step1331c.pdb.1#
Wrote pdb files with previous and current coordinates
段错误
********************************************************************************************************************************************
以下为minim.mdp的参数
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0    ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep       = 0.01       ; Energy step size
nsteps = 50000       ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.4 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.4 ; Short-range electrostatic cut-off
rvdw = 1.4 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
*******************************************************************************************************************************************
以下为nvt restraint的预平衡参数nvt.mdp：
define = -DPOSRES ; position restrain the protein
integrator = sd
dt = 0.001 ; ps
nsteps =100000 ; =  tot
nstcomm = 10000
nstxout = 10000
nstvout = 10000
nstfout = 10000
nstlog =  10000
nstenergy = 1000
nstlist = 5

pbc = xyz
ns_type = grid
coulombtype = PME
rcoulomb  = 1.2
pme_order    = 5          ; cubic interpolation
fourierspacing  = 0.175       ; grid spacing for FFT
vdwtype = cut-off
rvdw    = 1.2
rlist    = 1.2
DispCorr = EnerPres
;optimize_fft = yes
;epsilon_r    = 80

;Couplig Temp
tcoupl = v-rescale
tau_t = 0.2
tc-grps = System
ref_t = 298

;Costrain Bond
constraints = all-bonds
constraint_algorithm = LINCS

;Coupling P
;Pcoupl = berendsen
;Pcoupltype = isotropic
;tau_p = 0.5
;compressibility = 4.5e-5
;ref_p=1

;Generate velocity
gen_vel = yes
gen_temp = 298.0
gen_seed = 333529@smutao@smutao@oxox6085@oxox6085

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