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本帖最后由 chwen 于 2024-12-11 11:36 编辑
我在做gromacs的模拟，在里面加入沥青质，C6,C7,C8H10,C25等分子。在跑模拟时一直崩溃，找不到解决方法。
输命令时没有warning提示，只有一个note
NOTE 1 [file eq.mdp]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing.
因为我之前跑过类似的，因为我用acpype生成不了沥青质拓扑文件，我改用sobtop生成。所有可能是文件出问题，但我用体系里每个组分都与沥青质单独跑时，C6H14,C7H16成功，C6H12,C8H10,C25H52失败，失败的我重新生成文件也没用，成功的重跑还是成功了,所以我找不到问题所在。
也有可能是mdp设置不合理，但我已经试过降低步长，减少温度，和精简组分等方法，也尝试过修改控压（温）时间常数等mdp设置但都没能稳定的运行，我们组偏应用，代码层面的问题几乎是不懂的，我找不到问题，希望有大佬可以帮忙找找问题。下面是各个mdp文件和warning，分子文件和生成分子的步骤都通过网盘挂在了评论区。本人一直找不到问题所在，希望大佬们指导一下
em.mdp
define =
integrator = cg
nsteps = 10000
emtol = 50.0
emstep = 0.01
;
nstxout =2000
nstlog = 2000
nstenergy = 2000
;
pbc = xyz
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
DispCorr = EnerPres
;
constraints = none
eq.mdp
define =
integrator = md
dt = 0.001 ; ps
nsteps = 50000000 ; 50ns
comm-grps = system
comm-mode = Linear
energygrps = system
;
nstxout = 100000
nstvout = 100000
nstfout = 100000
nstlog = 100000
nstenergy = 100000
nstxout-compressed = 100000
compressed-x-grps = system
;
pbc = xyz
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
DispCorr = EnerPres
;
Tcoupl = V-rescale
tau-t = 0.5
tc_grps = system
ref-t = 293
gen-vel = no
gen-temp= 100
;
Pcoupl = Berendsen
pcoupltype = isotropic
tau-p = 1.0
ref-p = 1.0
compressibility = 4.5e-5
;
annealing = single
annealing_npoints = 3
annealing_time = 0 3000 45000 ;ps
annealing_temp = 100 353.15 293.15
freezegrps =
freezedim =
constraints = hbonds
lincs_order =
prod.mdp
define =
integrator = md
dt = 0.001 ; ps
nsteps = 50000000 ; 50ns
comm-grps = system
energygrps =
refcoord-scaling = com
;
nstxout = 100000
nstvout = 100000
nstfout = 100000
nstlog = 100000
nstenergy = 100000
nstxout-compressed = 100000
compressed-x-grps = system
;
pbc = xyz
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
DispCorr = EnerPres
;
Tcoupl = V-rescale
tau-t = 0.5
tc-grps = system
ref-t = 293
gen-vel = no
gen-temp= 100
;
Pcoupl = parrinello-rahman
pcoupltype = isotropic
tau-p = 1.0
ref-p = 1.0
compressibility = 4.5e-5
;
annealing = single
annealing-npoints = 3
annealing-time = 0 3000 45000 ;ps
annealing-temp = 100 353.15 293.15
freezegrps =
freezedim =
constraints = hbonds
lincs_order =
下面是warning
GROMACS: gmx mdrun, version 2020.6-MODIFIED
Executable: C:\gmx2020.6_AVX2_CUDA_win64\gmx2020.6_GPU\bin\gmx.exe
Data prefix: C:\gmx2020.6_AVX2_CUDA_win64\gmx2020.6_GPU
Working dir: G:\chw\A1-C25
Command line:
gmx mdrun -v -deffnm eq
Reading file eq.tpr, VERSION 2020.6-MODIFIED (single precision)
Changing nstlist from 10 to 100, rlist from 1 to 1
1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
PP:0,PME:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread
Using 16 OpenMP threads
Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
starting mdrun 'mixbox'
50000000 steps, 50000.0 ps.
step 13300: timed with pme grid 84 84 84, coulomb cutoff 1.000: 148.0 M-cycles
step 13500: timed with pme grid 72 72 72, coulomb cutoff 1.157: 142.2 M-cycles
step 13700: timed with pme grid 64 64 64, coulomb cutoff 1.302: 188.1 M-cycles
step 13900: timed with pme grid 72 72 72, coulomb cutoff 1.157: 177.1 M-cycles
step 14100: timed with pme grid 80 80 80, coulomb cutoff 1.042: 165.1 M-cycles
step 14300: timed with pme grid 84 84 84, coulomb cutoff 1.000: 173.7 M-cycles
optimal pme grid 72 72 72, coulomb cutoff 1.157
step 6373800, will finish Thu Dec 5 15:53:59 2024
Step 6373899, time 6373.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000001, max 0.000012 (between atoms 756 and 784)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 44.9 0.0973 0.0973 0.0973
Step 6373900, time 6373.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000001, max 0.000018 (between atoms 756 and 784)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 39.6 0.0973 0.0973 0.0973
step 6373900, will finish Thu Dec 5 15:53:58 2024
Step 6373901, time 6373.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000002, max 0.000030 (between atoms 756 and 784)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 37.1 0.0973 0.0973 0.0973
Step 6373902, time 6373.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000002, max 0.000042 (between atoms 756 and 784)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 35.9 0.0973 0.0973 0.0973
Step 6373903, time 6373.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000002, max 0.000049 (between atoms 756 and 783)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 37.3 0.0973 0.0973 0.0973
Step 6374897, time 6374.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000002, max 0.000033 (between atoms 729 and 767)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 55.8 0.0973 0.0973 0.0973
Step 6374898, time 6374.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000002, max 0.000045 (between atoms 729 and 767)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 55.1 0.0973 0.0973 0.0973
-------------------------------------------------------
Program: gmx mdrun, version 2020.6-MODIFIED
Source file: src\gromacs\mdlib\constr.cpp (line 224)
Fatal error:
Too many LINCS warnings (1000)
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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发表于 Post on 2024-12-5 12:34:24
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发表于 Post on 2024-12-5 16:34:50
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