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标题: 求助运行md.mdp时报错：Bond length not finite. [打印本页]
作者Author: I150 时间: 2023-10-3 23:16
标题: 求助运行md.mdp时报错：Bond length not finite.
本帖最后由 I150 于 2023-10-4 07:35 编辑
老师您好。我做的是纳米粒自组装的分子动力学模拟，把7个某一短肽（ww）和1个紫杉醇(yy)（比例根据具体实验中的摩尔比）放在一个盒子里水作溶剂跑了100ns。
之前对各个mdp文件调调改改，（先nvt再npt）总算成功跑了100ns模拟。
现在由于要图形化π-π堆积作用，根据 “使用Multiwfn做aNCI分析图形化考察动态过程中的蛋白-配体间的相互作用” 本文，先npt再nvt，就又在md_fix.mdp里利用索引对yy加了冻结，在最后用md.mdp这一步运行gmx mdrun -deffnm md_0_1_fix时报这个错，修改md＿fix.mdp文件参数几次都是这样，还请sob老师指点。
按之前跑的100那样进行能量最小化、NVT、NPT平衡没报错，到了md.mdp这一步：
gmx grompp -f md_fix.mdp -c nvt.gro -t nvt.cpt -p ww.top -o md_0_1_fix.tpr -n index.ndx
GROMACS显示如下：
Command line:
gmx grompp -f md_fix.mdp -c nvt.gro -t nvt.cpt -p ww.top -o md_0_1_fix.tpr -n index.ndx
Ignoring obsolete mdp entry 'ns_type'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Setting the LD random seed to -538050843
Generated 3570 of the 3570 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3570 of the 3570 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'ww'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'yy'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
Cleaning up constraints and constant bonded interactions with virtual sites
NOTE 1 [file ww.top, line 21]:
The bond in molecule-type ww between atoms 9 C9 and 10 O10 has an
estimated oscillational period of 1.9e-02 ps, which is less than 10 times
the time step of 2.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
NOTE 2 [file md_fix.mdp]:
There are 113 atoms that are fully frozen and part of COMM removal
group(s), removing these atoms from the COMM removal group(s)
Number of degrees of freedom in T-Coupling group System is 117917.09
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.436 nm, buffer size 0.036 nm
Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
NOTE 3 [file md_fix.mdp]:
Removing center of mass motion in the presence of position restraints
might cause artifacts. When you are using position restraints to
equilibrate a macro-molecule, the artifacts are usually negligible.
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
Last frame -1 time 250.000
Using frame at t = 250 ps
Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 52x52x52, spacing 0.154 0.154 0.154
Estimate for the relative computational load of the PME mesh part: 0.08
NOTE 4 [file md_fix.mdp]:
This run will generate roughly 16127 Mb of data
There were 4 notes
GROMACS reminds you: "You Look Better Upside Down" (Throwing Muses)
然后输入 gmx mdrun -deffnm md_0_1_fix
GROMACS显示如下：
Command line:
gmx mdrun -deffnm md_0_1_fix
Reading file md_0_1_fix.tpr, VERSION 2020.6-MODIFIED (single precision)
Changing nstlist from 10 to 100, rlist from 1.4 to 1.547
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
WARNING: This run will generate roughly 16109 Mb of data
starting mdrun 'ww in water'
50000000 steps, 100000.0 ps.
Step 1, time 0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 191382067054039269376.000000 (between atoms 22543 and 22545)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 90.0 0.1095 inf 0.1095
-------------------------------------------------------
Program: gmx mdrun, version 2020.6-MODIFIED
Source file: src\gromacs\mdlib\lincs.cpp (line 2188)
Fatal error:
Bond length not finite.
For more information and tips for troubleshooting, please check the GROMACS
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作者Author: cgy 时间: 2024-5-20 22:33
您好，我也遇到了同样的问题，请问您解决了吗
作者Author: science_6 时间: 2024-6-10 11:09
您好，我也遇到了这种问题，请问您解决了吗？
作者Author: science_6 时间: 2024-6-22 11:34
楼主您好，我也遇到了bond length not finite 的问题，想请一下您是怎么解决的呢
作者Author: zyw0135 时间: 2025-4-9 22:02
楼主您好，我也遇到了bond length not finite 的问题，想请一下您是怎么解决的呢
作者Author: 那年冬天风在吹 时间: 3 day ago
我也遇到了
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