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标题: 对四丁基溴化铵+甘油体系NPT模拟报错 [打印本页]

作者
Author:
二饼妹    时间: 2021-9-14 09:43
标题: 对四丁基溴化铵+甘油体系NPT模拟报错
本帖最后由 二饼妹 于 2021-9-14 09:50 编辑

想模拟一下四丁基溴化铵+甘油的密度,力场为GAFF,先对阳离子部分进行了优化(初始结构不优化也出现了报错),输入文件如下;然后用优化后的结构使用packmol构建盒子和拓扑文件,最小化时出现如下报错,请问应该怎么解决呢?(之前模拟的氯化胆碱+甘油体系是成功的,也计算了RESP电荷)
WARNING: Listed nonbonded interaction between particles 10805 and 10811
at distance 38628.598 which is larger than the table limit 2.000 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.

Segmentation fault (core dumped)
最小化mdp文件如下:integrator = cg
nsteps = 10000
emtol  = 1.0
emstep = 0.01
;
nstxout   = 20
nstlog    = 50
nstenergy = 50
;
pbc = xyz
cutoff-scheme            = Verlet
coulombtype              = PME
rcoulomb                 = 1.0
vdwtype                  = cut-off
rvdw                     = 1.0
DispCorr                 = EnerPres
;
constraints              = none




作者
Author:
sobereva    时间: 2021-9-15 02:02
mdp并没什么明显问题,gjf文件也没问题

只能反复测试。比如先不考虑甘油,只考虑一个四丁基溴化铵的情况进行能量极小化看看,如果没问题,再考虑多个四丁基溴化铵...逐渐还原成原本状态,不断测试,弄清楚哪里有问题。




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