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标题: A charge group moved too far between two domain decomposition steps [打印本页]

作者
Author: 王子璇 时间: 2022-7-18 15:17
标题: A charge group moved too far between two domain decomposition steps
本帖最后由王子璇于 2022-7-18 16:15 编辑

在进行能量最小化，平衡相模拟一下步骤时：gmx grompp -f eq.mdp -c em.gro -p topol.top -o eq.tpr -r em.gro -maxwarn 1下一步gmx mdrun -v -deffnm eq出现了一下错误。

Step 0:

The charge group starting at atom 33456 moved more than the distance allowed by the domain decomposition (3.438400) in direction X

distance out of cell -4.853197

Old coordinates: 3.679 4.974 8.550

New coordinates: -1.415 3.694 5.884

Old cell boundaries in direction X: 3.438 6.877

New cell boundaries in direction X: 3.438 6.877

Step 0:

The charge group starting at atom 108 moved more than the distance allowed by the domain decomposition (3.438400) in direction X

distance out of cell -5.772584

Old coordinates: 3.670 5.018 1.690

New coordinates: -2.334 3.552 8.994

Old cell boundaries in direction X: 3.438 6.877

New cell boundaries in direction X: 3.438 6.877

-------------------------------------------------------

Program: gmx mdrun, version 2018.8

Source file: src/gromacs/domdec/domdec.cpp (line 4077)

MPI rank: 3 (out of 4)

Fatal error:

A charge group moved too far between two domain decomposition steps

This usually means that your system is not well equilibrated

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

请问是盒子大小问题还是需要添加位置限制呢？
查询了top文件还有其他的，我认为可能是mdp文件设置不合理，以下是我的eq.mdp文件，需要怎么修改呢？

define = -DPOSRES
integrator = md
dt       = 0.002  ; ps
nsteps    = 100000 ; 200ps
comm-grps  = system
energygrps =
energygrp-excl =
;
nstxout = 0
nstvout = 0
nstfout = 0
nstlog  = 500
nstenergy = 500
nstxout-compressed = 1000
compressed-x-grps  = system
;
annealing = single
annealing_npoints = 2
annealing_time = 0 100 ;ps
annealing_temp = 0 298.15
;
periodic-molecules = yes
pbc          = xyz
cutoff-scheme = group
nstlist             = 10
rlist             = 1.2
coulombtype = PME
rcoulomb    = 1.2
vdwtype    = cut-off
rvdw       = 1.2
DispCorr    = EnerPres
;
Tcoupl  = V-rescale
tau_t = 0.2
tc_grps = system
ref_t = 298.15
;
Pcoupl    = Berendsen
pcoupltype = isotropic
tau_p = 0.5
ref_p = 1.0
compressibility = 4.5e-5
refcoord_scaling = all
;
gen_vel  = no
gen_temp = 298.15
gen_seed = -1
;
freezegrps  =
freezedim =
constraints = hbonds

作者
Author: sobereva 时间: 2022-7-19 15:01
http://sobereva.com/soft/Sobtop#FAQ8

作者
Author: 王子璇 时间: 2022-7-29 10:21
谢谢老师

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