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标题: 求助使用gromacs进入寡糖和糖苷酶的复合场模拟，在能量最小化时候体系会爆炸 [打印本页]

作者
Author: 王宝金 时间: 2025-11-5 17:21
标题: 求助使用gromacs进入寡糖和糖苷酶的复合场模拟，在能量最小化时候体系会爆炸
我想使用gromacs进行复合场的模拟（寡糖配体glycam力场，糖苷酶amberff99sb力场），我首先先使用了glycam-web生成了我的寡糖能量最小化分子的parm7和rest7文件，然后使用ambertools去除了两个文件中的tip3p水和离子，并使用autodock vina对接后的配体文件坐标替换parm7和rst7原始坐标文件，然后使用acpype转化成gro和topol文件
请问:后续在能量最小化时候体系会爆炸，无法完成nvt平衡，那该怎么样进行复合场的模拟，求指导是不是的的思路全错了

作者
Author: student0618 时间: 2025-11-5 18:24
检查转换及合并后的拓朴、座标文件原子序号是否正确。

VMD检查合并后有没有原子重叠。

能量最小化和平衡并不是同一步，究竟是那步崩溃？

没有实际输入输出文件或实际用过的指令无法解答。

作者
Author: 王宝金 时间: 2025-11-5 20:08
本帖最后由王宝金于 2025-11-5 20:14 编辑

student0618 发表于 2025-11-5 18:24
检查转换及合并后的拓朴、座标文件原子序号是否正确。

VMD检查合并后有没有原子重叠。

  gmx mdrun -v -deffnm nvt

Reading file nvt.tpr, VERSION 2020.6-MODIFIED (single precision)
Changing nstlist from 10 to 80, rlist from 1.001 to 1.147

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 12 OpenMP threads

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
starting mdrun 'Protein in water'
50000 steps, 100.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 4012.251221, max 261857.984375 (between atoms 8952 and 8953)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
8890 8891 90.0 0.1090 0.3030    0.1090
8900 8903 90.0 0.1090 0.3050    0.1090
8913 8914 56.4 0.1090 0.1090    0.1090
8918 8919 67.0 0.1090 0.1090    0.1090
8922 8923 33.7 0.0960 0.0960    0.0960
8924 8925 90.0 0.1090 1.2371    0.1090
8933 8934  170.6 0.1090  42.3432    0.1090
8935 8936 56.7 0.1090  38.7208    0.1090
8937 8938 90.0 0.1090 0.2064    0.1090
8939 8940 90.0 0.1090 5.6032    0.1090
8939 8941 81.0 0.1090 6.9713    0.1090
8939 8942 90.0 0.1090 4.6769    0.1090
8952 8953 35.8 0.1090 28542.6289    0.1090
8959 8960 43.6 0.1090 0.1090    0.1090
8963 8964 90.0 0.1090 0.1909    0.1090
8965 8966 55.6 0.0960 0.0960    0.0960
8968 8969 31.1 0.1090  18.3900    0.1090
8972 8973 90.0 0.1090 0.7382    0.1090
8974 8975 90.0 0.1090 0.1619    0.1090
8976 8977  135.4 0.1090  75.8789    0.1090
8978 8979 90.0 0.1090 0.1760    0.1090
8991 8992 90.0 0.1090 0.1090    0.1090
8996 8997  150.9 0.1090 135.5157    0.1090
8998 8999  113.3 0.0960  93.9556    0.0960
9000 9001  109.0 0.1090  97.1642    0.1090
9004 9005 90.0 0.1090 0.1850    0.1090
Wrote pdb files with previous and current coordinates
step 0
WARNING: Listed nonbonded interaction between particles 8915 and 8919
at distance 5.905 which is larger than the table limit 2.147 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 54623.601562, max 3579114.250000 (between atoms 9004 and 9005)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
2008 2010 90.0 0.1010 0.1428    0.1010
5227 5228 53.7 0.1090 0.1090    0.1090
8890 8891 55.5 0.3030 0.1090    0.1090
8894 8895 31.3 0.1090 0.1090    0.1090
8898 8899 36.7 0.1090 0.1090    0.1090
8900 8901 57.3 0.1086 0.1117    0.1090
8900 8902 90.0 0.1090 0.2145    0.1090
8900 8903 90.0 0.3050 0.3796    0.1090
8913 8914  124.0 0.1090  51.1628    0.1090
8918 8919 43.1 0.1090 0.1090    0.1090
8920 8921 76.6 0.1090  52.5909    0.1090
8924 8925 36.1 1.2371 0.1090    0.1090
8929 8930 34.4 0.1090 0.1090    0.1090
8937 8938  139.4 0.2064 446.8499    0.1090
8939 8940  105.9 5.6032 9.4713    0.1090
8939 8941 93.7 6.9713  10.2294    0.1090
8939 8942 90.0 4.6769 5.9409    0.1090
8959 8960 90.0 0.1090 0.3205    0.1090
8963 8964 63.5 0.1909 197.3380    0.1090
8965 8966 42.2 0.0960 0.0960    0.0960
8970 8971 90.0 0.1090 0.2836    0.1090
8972 8973  121.8 0.7382 1920.6566    0.1090
8974 8975 90.0 0.1619 5.4523    0.1090
8978 8979 61.7 0.1760 0.1090    0.1090
8991 8992 90.0 0.1090 0.2661    0.1090
9002 9003 31.5 0.0960 0.0960    0.0960
9004 9005  123.4 0.1850 390123.5625    0.1090

step 1: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
就是在nvt模拟时会出现结构错误，出现极端不合理的键长，实在是很抱歉，我没有完成过这种复合场的模拟，所以不太知道应该去怎么让两种力场以各自偏好性的原子书写方法兼容，为了保证后续模拟添加一个配体，我将左边的标号的糖名字都改成了连续的编号和统一的名字，但不知道我这么做是不是正确的 (, 下载次数 Times of downloads: 0)

作者
Author: sobereva 时间: 2025-11-9 03:56
参考http://sobereva.com/soft/Sobtop#FAQ8排查和解决

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