求助运行md.mdp时报错：Bond length not finite.

I150

    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

website at http://www.gromacs.org/Documentation/Errors

-------------------------------------------------------

cgy

您好，我也遇到了同样的问题，请问您解决了吗

science_6

cgy 发表于 2024-5-20 22:33
您好，我也遇到了同样的问题，请问您解决了吗

您好，我也遇到了这种问题，请问您解决了吗？

science_6

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

zyw0135

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

那年冬天风在吹

我也遇到了