为什么添加离子后体系电荷不为0而是小数（0.308640）

ShineZhu · 发表于 Post on 2023-6-15 20:11:34

想请教各位前辈一个问题，我用一下命令加离子之后为什么运行到能量最小化的时候，还会提醒我体系不是电中性的，此时带电0.308640.这种小数电荷应该怎么去中和呀。谢谢大家。
gmx genion -s em.tpr -p topol.top -o system.gro -neutral (SOL)

sobereva · 发表于 Post on 2023-6-16 00:21:25

ShineZhu · 发表于 Post on 2023-6-16 08:16:42

sobereva 发表于 2023-6-16 00:21

谢谢老师

ShineZhu · 发表于 Post on 2023-6-16 09:18:28

ShineZhu 发表于 2023-6-16 08:16
谢谢老师

老师还想打扰多请教一个问题，就是为什么用RESP.sh脚本计算的NADP+的电荷最后所有原子相加电荷都是不是整数呢？生成的NAP.chg文件如下
P    6.118499 2.081129 1.181281 1.2189458148
P    2.399427 -2.886301 0.745443 1.0780043845
P -0.083839 -4.442444 -0.019432 1.1283240760
C    3.290301 1.913102 -1.644634 0.2180940489
C -3.598545 0.192284 -0.391831 0.0578747853
N -1.039141 2.060358 1.261058  -0.5044475312
N -5.070103 0.186371 -0.591540 0.2481884698
O    3.670658 -3.295135 1.371461  -0.6353510258
O -1.091732 -4.423877 1.226272  -0.5819513572
O    7.387583 1.232388 0.562221  -0.7005801316
C    0.125497 1.419939 1.480964 0.2676946870
C    4.097775 1.426151 -0.422727 0.3851084149
C -3.203106 -0.326823 1.015691 0.1613109475
C -5.794989 1.017594 0.185834  -0.0693706656
O    1.595092 -1.793722 1.573430  -0.5664193543
O    5.201180 2.273914 -0.239118  -0.5960985425
O -3.195351 0.594051 2.037564  -0.6111933931
O -0.205703 -5.676006 -0.814280  -0.6331602933
O    5.296086 1.210310 2.101926  -0.8390787077
C    4.494947 -0.028343 -0.800511 0.1647743216
C -1.883844 -1.026316 0.695741 0.3409917311
C -7.176240 1.075844 0.071502  -0.0105183483
N    1.222528 1.468724 0.739962  -0.5058168093
O    1.385570 -4.172871 0.595644  -0.4286001552
O    5.813210 -0.102476 -1.321362  -0.6694566781
O -1.068262 -1.392682 1.516807  -0.4431667189
O    6.627195 3.438738 1.565523  -0.7890851350
C    1.107749 2.281045 -0.321993 0.3699507084
C    3.438571 -0.419992 -1.835274 0.0959085288
C -1.791573 -1.189367 -0.808369 0.1238881009
C -7.802008 0.241233 -0.864762  -0.0375419428
O    3.059318 0.799907 -2.482092  -0.4555561719
O -3.019142 -0.678964 -1.315824  -0.3728587830
C -0.026401 3.044835 -0.639585 0.2490797733
C    2.190282 -1.075739 -1.253724 0.0946955116
C -1.597367 -2.632992 -1.267301  -0.0650621649
C -7.029262 -0.614366 -1.650912  -0.1058638020
O    2.526999 -2.381677 -0.767922  -0.4553113202
O -0.313593 -3.034115 -0.787079  -0.3704736752
C -1.146379 2.907107 0.212898 0.4349976393
C -5.651852 -0.627802 -1.501077  -0.0243068816
N -2.313610 3.540270 -0.016123  -0.7868935277
C -7.867307 2.037384 1.018655 0.7153875358
N    0.179674 3.782355 -1.786034  -0.6376260238
N -9.174817 2.266193 0.798183  -0.8990829355
O -7.225707 2.553323 1.924593  -0.5984095066
C    1.395223 3.468079 -2.159003 0.2457261517
N    2.025675 2.567141 -1.314567  -0.2418280427
H    7.036595 0.496197 0.023127 0.4161303170
H -2.439654 1.235381 1.882050 0.3564926727
H    5.987589 0.706929 -1.827357 0.4439975504
H    0.628835 -1.667648 1.409910 0.4026053863
H    3.877188 2.658977 -2.199268 0.1003361552
H -3.270315 1.234965 -0.542776 0.1578365696
H    0.146011 0.765149 2.356711 0.1219306879
H    3.474254 1.391414 0.477114  -0.0192100628
H -3.898683 -1.149508 1.273182 0.1582569903
H    4.478308 -0.682852 0.079856 0.1131342285
H -5.263674 1.616706 0.925193 0.1686922221
H -1.051360 -3.633494 1.792655 0.4453347083
H    3.882062 -1.085219 -2.590431 0.1250791577
H -0.943065 -0.581159 -1.172135 0.1462220481
H -8.885906 0.232765 -0.985467 0.1710614527
H -7.489166 -1.277270 -2.383278 0.1846596094
H -4.983518 -1.263874 -2.076810 0.1882047135
H    1.909874 3.851440 -3.040646 0.1536166487
H    1.769627 -0.462818 -0.445377 0.1043519835
H    1.438049 -1.194468 -2.045223 0.1043519835
H -2.400601 -3.273126 -0.873002 0.1495807256
H -1.610210 -2.677735 -2.364725 0.1495807256
H -2.998996 3.609856 0.727740 0.4201485835
H -2.352130 4.233023 -0.754781 0.3985948823
H -9.658212 2.916818 1.408371 0.4467858340
H -9.681680 1.907917 -0.000191 0.4283882200

sobereva · 发表于 Post on 2023-6-16 11:24:59

ShineZhu 发表于 2023-6-16 09:18
老师还想打扰多请教一个问题，就是为什么用RESP.sh脚本计算的NADP+的电荷最后所有原子相加电荷都是不是整 ...

最后一列加和仅为-2E-10，明显是整数，记录精度足够实际使用

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[GROMACS] 为什么添加离子后体系电荷不为0而是小数（0.308640）

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