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标题: 求助：能量最小化时突然终止，并且没有产生gro文件 [打印本页]

作者
Author: wwl 时间: 2021-6-1 16:08
标题: 求助：能量最小化时突然终止，并且没有产生gro文件
各位老师，各位大佬好，我是一个小菜鸟，问一个比较基础的问题，希望各位大佬不吝赐教，批评指正，非常感谢。
我在使用gromacs软件做模拟时，用packmol软件生成的盒子，在进行能量最小化时，跑了一下突然就终止掉了，也没有出现报错（刚开始生成tpr文件时确实出现了一些报错，但是都被我修改好了）。我查看了top文件，没有发现什么错误（也可能是我没看出来），计算机应该也没有问题，因为该计算机模拟类似的体系时没有出现过这种情况。我个人能力有限，也没遇到过这种情况，试了很久也没有解决，希望各位老师大佬们指点一二，非常感谢，感激不尽。
生成的log文件如下（最后几段）：
Using AVX2_256 4x8 non-bonded kernels

Using Lorentz-Berthelot Lennard-Jones combination rule

Removing pbc first time

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity

Linking all bonded interactions to atoms

The initial number of communication pulses is: X 2 Y 2 Z 2
The initial domain decomposition cell size is: X 2.71 nm Y 1.63 nm Z 2.71 nm

The maximum allowed distance for charge groups involved in interactions is:
               non-bonded interactions          3.000 nm
         two-body bonded interactions  (-rdd) 3.000 nm
      multi-body bonded interactions  (-rdd) 1.626 nm

top文件如下：
#include "amber03.ff/forcefield.itp"

[ atomtypes ]
; name  at.nr    mass charge  ptype  sigma       epsilon
CI2       8  14.0270 0.265    A  3.95000e-01  4.60000e-01
HI       9 1.0080 0.4350    A  0.00000e-01  0.00000e-01
OI       8  15.9990  -0.7000    A  3.02000e-01  9.30000e-01

#include "amber03.ff/ions.itp"

#include "EG.itp"

#include "1jkd.top"

[ system ]
; Name
LYSOZYME in water

[ molecules ]
; Compound       #mols
CL             8
EG             3700
1jkd             1

mdp文件如下：
integrator = cg ; Algorithm (steep = steepest descent minimization)
emtol = 1000    ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep       = 0.01       ; Energy step size
nsteps = 50000    ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 10 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)

作者
Author: sobereva 时间: 2021-6-1 16:16
换个版本，以确认是程序问题还是输入文件问题

作者
Author: wwl 时间: 2021-6-1 16:27

sobereva 发表于 2021-6-1 16:16
换个版本，以确认是程序问题还是输入文件问题

嗯嗯，好的，我再试试。非常感谢您

作者
Author: wwl 时间: 2021-6-1 16:50

wwl 发表于 2021-6-1 16:27
嗯嗯，好的，我再试试。非常感谢您

sob老师，我换了2019版本的以后发现跑出来gro文件了，但是速度特别快，这边输入命令，那边就出来了，不知道有没有问题。而且还给出了如下的提示，我不知道这个是哪里出问题了，请您帮忙看看。
WARNING: Listed nonbonded interaction between particles 18112 and 18116
at distance 2.721 which is larger than the table limit 2.260 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 6557 and 6559
at distance 2.376 which is larger than the table limit 2.260 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.

writing lowest energy coordinates.

Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 288 steps
Potential Energy  =  1.9931295e+05
Maximum force    =  7.3834521e+02 on atom 16441
Norm of force    =  7.6803987e+01
非常感谢

作者
Author: wwl 时间: 2021-6-1 20:04

wwl 发表于 2021-6-1 16:50
sob老师，我换了2019版本的以后发现跑出来gro文件了，但是速度特别快，这边输入命令，那边就出来了，不知 ...

已经解决了，发现是我体系里的一个分子的top文件的问题

作者
Author: zhangyingying 时间: 2022-7-4 16:22

wwl 发表于 2021-6-1 20:04
已经解决了，发现是我体系里的一个分子的top文件的问题

你好麻烦问一下你怎么改的呀

作者
Author: wwl 时间: 2022-7-4 20:22

zhangyingying 发表于 2022-7-4 16:22
你好麻烦问一下你怎么改的呀

已经过去很久，具体原因已经忘记了。不过一般出现问题的话，你检查一下自己的top文件和各分子的itp文件的书写顺序是否正确，如果这些信息没问题的话，力场参数也没有问题的话，一般不会出现这些报错。所以你还是再检查一下自己的输入文件最好

作者
Author: zhangyingying 时间: 2022-7-6 09:29

wwl 发表于 2022-7-4 20:22
已经过去很久，具体原因已经忘记了。不过一般出现问题的话，你检查一下自己的top文件和各分子的itp文件的 ...

谢谢哦

作者
Author: Prof.Huang 时间: 2023-4-3 21:21
我也是这个问题请问如何解决，一直提示报错，top文件看不出来

作者
Author: wwl 时间: 2023-4-12 17:05

Prof.Huang 发表于 2023-4-3 21:21
我也是这个问题请问如何解决，一直提示报错，top文件看不出来

已经过去很久了，我的原因是top文件有错误，改了之后就好了

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