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本帖最后由 RC_Yume 于 2025-3-31 16:31 编辑
在运行命令gmx grompp -f pr.mdp -c em.gro -p topol.top -r em.gro -o pr.tpr后，出现note
NOTE 1 [file pr.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.
忽视后进行限制性分子动力学，出现LINCS WARNING并崩溃
Command line:
gmx mdrun -v -deffnm pr
Step 645, time 0.645 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 152.161194, max 7480.088867 (between atoms 218 and 219)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
198 199 90.0 3.2922 0.5548 0.1090
200 201 75.4 0.1124 0.1090 0.1090
210 211 90.0 0.1090 5.1442 0.1090
212 213 34.4 0.1089 0.1090 0.1090
216 217 90.0 0.1080 6.3588 0.1080
221 222 50.6 0.0960 0.0960 0.0960
223 224 37.5 0.1080 0.1080 0.1080
229 230 127.9 0.1034 28.0997 0.1010
233 234 74.8 0.1090 632.7576 0.1090
233 235 90.0 0.1090 0.1713 0.1090
236 237 90.0 0.1090 0.1556 0.1090
236 238 90.0 0.1090 0.2760 0.1090
392 393 90.0 0.1090 1.5829 0.1090
434 436 90.0 0.1091 0.1096 0.1090
step 645: 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
此前已进行多次能量极小化，使Fmax<100，还通过删除拓扑文件中[pairs]可能产生1,4 interaction的地方，消除了警告：
WARNING: Listed nonbonded interaction between particles 1836 and 1842
at distance 7.019 which is larger than the table limit 2.109 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.
此外mdp、结构文件和拓扑文件都没有找到明显的问题，但崩溃仍然没有解决。
请问接下来要怎么解决呢，请求老师们帮助。
em.gro是能量最小化后的结构文件
em.mdp
(386 Bytes, 下载次数 Times of downloads: 1)
em.zip
(4.11 MB, 下载次数 Times of downloads: 3)
pr.mdp
(666 Bytes, 下载次数 Times of downloads: 4)
topol.zip
(444.16 KB, 下载次数 Times of downloads: 1)
mol.itp
(13.98 KB, 下载次数 Times of downloads: 0)
posre.itp
(184.43 KB, 下载次数 Times of downloads: 0)
posre_mol.itp
(948 Bytes, 下载次数 Times of downloads: 0)
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发表于 Post on 2025-3-30 10:44:31
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发表于 Post on 2025-3-30 13:42:23
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