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    <title>模拟之家-SimuHome - 模拟报错</title>
    <link>https://simuhome.cn/forum-2-1.html</link>
    <description>Latest 20 threads of 模拟报错</description>
    <copyright>Copyright(C) 模拟之家-SimuHome</copyright>
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    <lastBuildDate>Wed, 20 May 2026 22:08:38 +0000</lastBuildDate>
    <ttl>60</ttl>
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      <title>模拟之家-SimuHome</title>
      <link>https://simuhome.cn/</link>
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    <item>
      <title>在用 GAFF 力场模拟电解液时，Li⁺和 FSI⁻会发生明显聚集，不能均匀分布在 DME 里，</title>
      <link>https://simuhome.cn/thread-149-1-1.html</link>
      <description><![CDATA[在用 GAFF 力场模拟电解液时，Li⁺和 FSI⁻会发生明显聚集，不能均匀分布在 DME 里，请问怎么处理？]]></description>
      <category>模拟报错</category>
      <author>kuaij</author>
      <pubDate>Thu, 30 Apr 2026 02:12:04 +0000</pubDate>
    </item>
    <item>
      <title>用 CHARMM-GUI 搭建的纯 DPPC 脂质双分子层，在能量最小化阶段出现极大作用力.。。。</title>
      <link>https://simuhome.cn/thread-143-1-1.html</link>
      <description><![CDATA[用 CHARMM-GUI 搭建的纯 DPPC 脂质双分子层，在能量最小化阶段出现极大作用力，直接报错终止；但同样流程构建的 POPC 膜却能正常完成能量最小化。想问：CHARMM-GUI 构建时是否本身就可能出现这类问题？遇到这种情况通常该怎么排查和解决？


 ...]]></description>
      <category>模拟报错</category>
      <author>lucks</author>
      <pubDate>Mon, 27 Apr 2026 02:21:43 +0000</pubDate>
    </item>
    <item>
      <title>运行mdrun提示condition:stat=cudasuccess如何解决</title>
      <link>https://simuhome.cn/thread-133-1-1.html</link>
      <description><![CDATA[运行mdrun提示condition:stat=cudasuccess如何解决??]]></description>
      <category>模拟报错</category>
      <author>accs</author>
      <pubDate>Fri, 17 Apr 2026 02:35:34 +0000</pubDate>
    </item>
    <item>
      <title>我用 gmx hbond 分析氢键数量时，得到的平均氢键数异常，求助？</title>
      <link>https://simuhome.cn/thread-119-1-1.html</link>
      <description><![CDATA[我用 gmx hbond 分析氢键数量时，得到的平均氢键数为负值且数值异常巨大，明显不符合实际情况。请问可能是什么原因导致的？具体如下：

gmx hbond -s md.tpr -f md.xtc -num pcd.xvg -tu ns -n index.ndx


出现如下情况：
Checking for overlap in atoms between Prote ...]]></description>
      <category>模拟报错</category>
      <author>moou</author>
      <pubDate>Mon, 30 Mar 2026 02:34:08 +0000</pubDate>
    </item>
    <item>
      <title>老师我在进行npt平衡时出现了这个问题请问是什么原因呢</title>
      <link>https://simuhome.cn/thread-118-1-1.html</link>
      <description><![CDATA[wangzj@localhost 0329]$ gmx mdrun -deffnm npt -v
                      :-) GROMACS - gmx mdrun, 2023.2 (-:

Executable:   /data/hzwtech/gromacs-GPU-2023.2/bin/gmx_mpi
Data prefix:  /data/hzwtech/gromacs-GPU-2023.2
Working dir:  /data/wangzj/gromacs/0]]></description>
      <category>模拟报错</category>
      <author>114511</author>
      <pubDate>Mon, 30 Mar 2026 01:17:38 +0000</pubDate>
    </item>
    <item>
      <title>模拟报错</title>
      <link>https://simuhome.cn/thread-108-1-1.html</link>
      <description><![CDATA[老师好，请问一下生产模拟后的盒子长成这个样子正确吗？右侧的RDF峰值和教程相反？]]></description>
      <category>模拟报错</category>
      <author>糯米糖葫芦</author>
      <pubDate>Thu, 19 Mar 2026 07:22:01 +0000</pubDate>
    </item>
    <item>
      <title>用 GROMACS 计算 Zn²⁺ 与小分子氧原子的 RDF，结果如何判断是否合理？</title>
      <link>https://simuhome.cn/thread-104-1-1.html</link>
      <description><![CDATA[用 GROMACS 计算 Zn²⁺ 与小分子氧原子的 RDF，结果如何判断是否合理？]]></description>
      <category>模拟报错</category>
      <author>luxiaot</author>
      <pubDate>Wed, 18 Mar 2026 06:46:01 +0000</pubDate>
    </item>
    <item>
      <title>配置GPU加速时失败，提示CUDA架构不支持或版本不匹配</title>
      <link>https://simuhome.cn/thread-65-1-1.html</link>
      <description><![CDATA[我在配置GPU加速时失败，提示CUDA架构不支持或版本不匹配。请问大家应该如何解决呢？]]></description>
      <category>模拟报错</category>
      <author>xiaopacai</author>
      <pubDate>Tue, 10 Mar 2026 06:25:09 +0000</pubDate>
    </item>
    <item>
      <title>安装后无法运行 gmx 命令。请问大家应该如何解决呢？</title>
      <link>https://simuhome.cn/thread-64-1-1.html</link>
      <description><![CDATA[安装后无法运行 gmx 命令。请问大家应该如何解决呢？]]></description>
      <category>模拟报错</category>
      <author>xiaopacai</author>
      <pubDate>Tue, 10 Mar 2026 06:24:48 +0000</pubDate>
    </item>
    <item>
      <title>运行gromacs时候出现下面错误：There are probably atoms missing earlier in the pdb</title>
      <link>https://simuhome.cn/thread-63-1-1.html</link>
      <description><![CDATA[我在运行gromacs时候出现下面错误：There are probably atoms missing earlier in the pdb file。请问大家应该如何解决呢？]]></description>
      <category>模拟报错</category>
      <author>xiaopacai</author>
      <pubDate>Tue, 10 Mar 2026 06:24:30 +0000</pubDate>
    </item>
    <item>
      <title>错误：Invalid order for directive \'xxx\'</title>
      <link>https://simuhome.cn/thread-62-1-1.html</link>
      <description><![CDATA[我在运行gromacs时候出现下面错误：Invalid order for directive \'xxx\'。请问大家应该如何解决呢？]]></description>
      <category>模拟报错</category>
      <author>xiaopacai</author>
      <pubDate>Tue, 10 Mar 2026 06:24:10 +0000</pubDate>
    </item>
    <item>
      <title>Fatal error: number of coordinates in coordinate file (xx.gro, N) does not match</title>
      <link>https://simuhome.cn/thread-61-1-1.html</link>
      <description><![CDATA[我在运行gromacs时候出现下面错误：Fatal error: number of coordinates in coordinate file (xx.gro, N)does not match topology (topol.top, M)。请问大家应该如何解决呢？]]></description>
      <category>模拟报错</category>
      <author>xiaopacai</author>
      <pubDate>Tue, 10 Mar 2026 06:23:51 +0000</pubDate>
    </item>
    <item>
      <title>运行gromacs时候出现下面错误：Atom index n in position_restraints out of bounds</title>
      <link>https://simuhome.cn/thread-56-1-1.html</link>
      <description><![CDATA[我在运行gromacs时候出现下面错误：Atom index n in position_restraints out of bounds。请问大家应该如何解决呢？]]></description>
      <category>模拟报错</category>
      <author>18380446913</author>
      <pubDate>Tue, 10 Mar 2026 06:19:38 +0000</pubDate>
    </item>
    <item>
      <title>错误：Only triclinic boxes with the first vector parallel to the x-axis and the</title>
      <link>https://simuhome.cn/thread-55-1-1.html</link>
      <description><![CDATA[我在运行gromacs时候出现下面错误：Only triclinic boxes with the first vector parallel to the x-axisand the second vector in the xy-plane are supported. Box: [ nan, nan, nan]。请问大家应该如何解决呢？]]></description>
      <category>模拟报错</category>
      <author>18380446913</author>
      <pubDate>Tue, 10 Mar 2026 06:19:11 +0000</pubDate>
    </item>
    <item>
      <title>运行gromacs时候出现下面错误：Cannot allocate memory</title>
      <link>https://simuhome.cn/thread-54-1-1.html</link>
      <description><![CDATA[我在运行gromacs时候出现下面错误：Cannot allocate memory。请问大家应该如何解决呢？]]></description>
      <category>模拟报错</category>
      <author>18380446913</author>
      <pubDate>Tue, 10 Mar 2026 06:18:53 +0000</pubDate>
    </item>
    <item>
      <title>错误：Fatal error: The total potential energy is nan/inf</title>
      <link>https://simuhome.cn/thread-50-1-1.html</link>
      <description><![CDATA[我在运行gromacs时候出现下面错误：Fatal error: The total potential energy is nan/inf。请问大家应该如何解决呢？]]></description>
      <category>模拟报错</category>
      <author>dongji</author>
      <pubDate>Tue, 10 Mar 2026 06:15:03 +0000</pubDate>
    </item>
    <item>
      <title>错误：Step X: Some atoms have moved too far 或 LINCS WARNING: relative coordinat</title>
      <link>https://simuhome.cn/thread-48-1-1.html</link>
      <description><![CDATA[我在运行gromacs时候出现下面错误：Step X: Some atoms have moved too far 或 LINCSWARNING: relative coordinate change。请问大家应该如何解决呢？]]></description>
      <category>模拟报错</category>
      <author>dongji</author>
      <pubDate>Tue, 10 Mar 2026 06:14:39 +0000</pubDate>
    </item>
    <item>
      <title>错误：Segmentation fault (core dumped)</title>
      <link>https://simuhome.cn/thread-47-1-1.html</link>
      <description><![CDATA[我在运行gromacs时候出现下面错误：Segmentation fault (core dumped)。请问大家应该如何解决呢？]]></description>
      <category>模拟报错</category>
      <author>dongji</author>
      <pubDate>Tue, 10 Mar 2026 06:13:53 +0000</pubDate>
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