牧生 发表于 2023-4-15 19:22
编译一次单精度，再编译一次双精度。这是两个独立的过程。不存在“在单精度版本的基础上编译双精度版本[/ ...

好的 谢谢老师解答

tiny 发表于 2023-4-15 18:42
您好，请教您一个问题，请问可以在单精度版本的基础上编译双精度版本吗

编译一次单精度，再编译一次双精度。这是两个独立的过程。不存在“在单精度版本的基础上编译双精度版本”

您好，请教您一个问题，请问可以在单精度版本的基础上编译双精度版本吗

sun666 发表于 2021-1-28 21:59
您好 我也有这个情况，请教您双精度是什么意思，该怎么操作呢

http://sobereva.com/457


注3：编译双精度版本     一般计算只需要按照前述编译单精度版本就够了，但如果模拟刚开始就崩溃，有时候用双精度版本可解决，但计算比单精度版慢将近一倍、trr/edr等文件体积大一倍。另外，做正则振动分析时在能量极小化和对角化Hessian矩阵的时候一般也需要用双精度版以确保数值精度。注意，编译双精度版本时不支持GPU加速。
    要编译双精度版本的话，先按照前文方式编译一遍单精度版本，毕竟这之后在研究中肯定也得用。然后再重复一遍编译过程，但是在编译FFTW时去掉--enable-float，并且在使用cmake3命令时额外加上-DGMX_DOUBLE=ON选项。双精度版本的GROMACS可执行文件是gmx_d，而单精度是gmx，因此单精度和双精度的可执行文件可以同时存在于同一目录，互不冲突。

牧生 发表于 2021-1-25 16:35
双精度解决了这个问题了。

您好 我也有这个情况，请教您双精度是什么意思，该怎么操作呢

wuzhiyi 发表于 2021-1-25 05:27
你试试用双精度版本的gmx来优化

双精度解决了这个问题了。

你试试用双精度版本的gmx来优化

重新来了一遍，引用的是amber99sb.ff力场，但是在预平衡的时候，仍然出错，仍然是由于能量太大。


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
PME tasks will do all aspects on the GPU

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.080675, max 3.668313 (between atoms 8436 and 8461)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
Wrote pdb files with previous and current coordinates
starting mdrun 'CTABMS in water'
50000 steps,     50.0 ps.

WARNING: Listed nonbonded interaction between particles 8314 and 8317
at distance 2.225 which is larger than the table limit 2.098 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.



WARNING: Listed nonbonded interaction between particles 6651 and 6654
at distance 2.126 which is larger than the table limit 2.098 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.



WARNING: Listed nonbonded interaction between particles 7999 and 8030
at distance 2.285 which is larger than the table limit 2.098 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.



-------------------------------------------------------
Program:     gmx mdrun, version 2019.6
Source file: src\gromacs\mdlib\sim_util.cpp (line 752)

Fatal error:
Step 0: The total potential energy is 3.86013e+17, which is extremely high.
The LJ and electrostatic contributions to the energy are 3.85815e+17 and
-448567, respectively. A very high potential energy can be caused by
overlapping interactions in bonded interactions or very large coordinate
values. Usually this is caused by a badly- or non-equilibrated initial
configuration, incorrect interactions or parameters in the topology.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

acpype也同时产生OPLS-AA力场的拓扑文件，不是光用于GAFF的。只不过用acpype的人通常都用其产生的GAFF的拓扑文件，产生OPLS-AA拓扑文件另有其它诸多选择
但如果CTAB_GMX.itp对应的是GAFF的，肯定不能引OPLS-AA的相关itp

acpype是专门服务于amber系力场的，你这top中都引用了opls力场属实一大失误。