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本帖最后由 Jiang127127 于 2026-3-19 08:41 编辑
请教各位老师crest在Setting up backup calculato后停止计算的解决方法
我在生成轨迹文件后,投入crest进行优化,之后用molclus的isotate进行筛选,代码如下
run_mxyzMD.sh
(5.02 KB, 下载次数 Times of downloads: 0)
:
# 直接将 RDKit 生成的 trj 拷进去
cp "${NAME}.xtb.trj" "crest_${NAME}/"
cd "crest_${NAME}"
# CREST 使用 -mdopt 读取 RDKit 生成的轨迹进行优化
crest -mdopt "${NAME}.xtb.trj" -gfn0 -opt normal -chrg 0 -uhf 0 >> crest_out
isostat crest_ensemble.xyz << EOF
0.5
0.5
EOF
crest -mdopt cluster.xyz -gfn2 -opt normal -gbsa Toluene -chrg 0 -uhf 0 >> crest_out
isostat crest_ensemble.xyz << EOF > "${NAME}_isostat.out"
0.5
0.5
298.15
EOF
但是出现了一个很奇怪的crest_out.如下
crest_out
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:
Command line input:
$ crest -mdopt 1_rea_2.xtb.trj -gfn0 -opt normal -chrg 0 -uhf 0 -T 4
--gfn0 : Use of GFN0-xTB requested.
-opt normal
-chrg 0
-uhf 0
-T 4 (CPUs/Threads selected)
> Setting up backup calculator ...
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
第一次crest,> Setting up backup calculator ...就莫名其妙结束了,开始第二次crestl,但是我单独把这一部分拿出来运行:
nohup crest -mdopt "1_rea_2.xtb.trj" -gfn0 -opt normal -chrg 0 -uhf 0 > crest_out 2>&1 &
第一次crest就正常结束了,请问各位老师这是为什么呢?应该怎么解决呢?
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