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标题: 求助Lammps-NEMD由于拟合RESP电荷不合理导致系统能量及平均温度上升的问题 [打印本页]

作者
Author: AngYi 时间: 2021-3-18 22:18
标题: 求助Lammps-NEMD由于拟合RESP电荷不合理导致系统能量及平均温度上升的问题
本人想计算一下C10-DNTT的热导率，建模周期性模型，NVT之后转NVE，在NVE下通过在冷区和热区减增相同热流的方式构建温度梯度求解热导率，力场参数采用gaff,电荷采用RESP进行拟合电荷。拟合电荷采用Multiwfn,根据Sob大神的教程：RESP拟合静电势电荷的原理以及在Multiwfn中的计算；计算RESP原子电荷的超级懒人脚本（一行命令就算出结果）。但是！！！NEMD过程整个系统的平均温度不断上升，能量也缓慢增加；当改用MS中COMPASS分配的电荷后，整个系统的温升就很小了。（附件中具有不同步数系统温度和能量对比结果）

RESP过程：1.取模型中的一个单体 2.Gaussion # B3LYP/def2SVP em=GD3BJ scrf(solvent=water) opt=loose 优化结构 3.在out文件中保存为优化结构后的gif文件，计算单点能# B3LYP/def2TZVP em=GD3BJ scrf(solvent=water) pop=MK IOp(6/33=2,6/42=6) 4.Multiwfn 7 18 1 得到电荷。
本人做过的尝试解决办法：1.在真空中计算热导率，是否应该去掉 scrf(solvent=water) ，无效。
2.改用HF/6-31G*其他采用相同，无效。
3.有考虑过是否为结构的原因，拿出一个单体，我的做法是不经opt，直接计算单点能，拟合电荷，无效。
RESP拟合电荷发现两个烷烃侧链上H带了负电荷？这是不是问题的所在呢？
个人感觉应该是拟合方法过程的问题，希望各位老师不吝赐教！详细过程及模型图在附件中 (, 下载次数 Times of downloads: 4)
(, 下载次数 Times of downloads: 47)

C10DNTT模型图，黄色为S原子。

作者
Author: sobereva 时间: 2021-3-19 06:46
求助帖标题别写那么多叹号，攻击性极强，给你去掉了，以后注意

作者
Author: sobereva 时间: 2021-3-19 08:01
COMPASS下模拟温度、能量照样有波动。波动是不可能避免的。
之所以COMPASS模拟时看起来总能量波动小，应当是因为对此体系，RESP电荷的数量级整体比COMPASS大一些，因此非键作用计算误差产生的影响也更大。恰当设定让静电作用计算得更精确、步长更小，应当能让能量保守性明显更好。

烃链部分用COMPASS电荷无所谓，反正电荷数量级非常小。但是中间含硫的pi共轭区域，明显很多COMPASS电荷不合理，有的简单地当成了0，因为根本没考虑实际电子结构。这种必须考虑电子结构而不能简单地根据连接关系做键电荷校正的情况用COMPASS电荷会导致静电作用描述不当。

作者
Author: AngYi 时间: 2021-3-19 10:24

sobereva 发表于 2021-3-19 08:01
COMPASS下模拟温度、能量照样有波动。波动是不可能避免的。
之所以COMPASS模拟时看起来总能量波动小，应当 ...

感谢sob老师的指导，我会注意的下次。对于这种lammps真空中计算某一分子有序排列周期性模型的热导率，RESP拟合电荷的时候计算单点能是否应该在气相中呢，或者是RESP2.0呢？

作者
Author: k64_cc 时间: 2021-3-19 16:04
本帖最后由 k64_cc 于 2021-3-19 16:13 编辑

总能量不守恒纯粹就是数值问题，不能在模型上找答案。
你确定你Lammps跑的是double precision吗，要不你先别管NEMD的事情，先减小步长做个平衡态NVE看看总能量波动会不会小一点。

作者
Author: sobereva 时间: 2021-3-19 18:07

AngYi 发表于 2021-3-19 10:24
感谢sob老师的指导，我会注意的下次。对于这种lammps真空中计算某一分子有序排列周期性模型的热导率，RES ...

看具体什么分子。比如水这种极性分子，凝聚相下产生的相互极化效应很显著，这就得让原子电荷能等效体现溶剂的极化效应。
而你当前的体系极性很低，就在真空下用B3LYP/def2-TZVP的波函数算RESP电荷即可。

作者
Author: AngYi 时间: 2021-3-19 18:07

k64_cc 发表于 2021-3-19 16:04
总能量不守恒纯粹就是数值问题，不能在模型上找答案。
你确定你Lammps跑的是double precision吗，要不你先 ...

老师您好，关于是否是双精度我不确定，用的是学校的服务器集群。数值问题具体指什么？是比如势函数或者截断距离一些参数的设置不合理吗？关于NVE，我的时间步长是0.5fs，运行100万步，这样的步长是否足够小了；目前来讲，采用COMPASS电荷的模型在NVE下温度在300+-2摄氏度范围下波动，能量也在基本稳定，在几百的范围内波动；采用RESP电荷后，可能是由于电荷数量级较大的原因，NVE下在100万的步数内系统平均温度上升了3K，能量也逐步上升。lammps真空中计算某一分子有序排列周期性模型的热导率，RESP拟合电荷的时候计算单点能是否应该在气相中呢，还是在水的环境中呢？下面是两种电荷的NVE过程。另外，RESP拟合电荷，H出现负的电荷值是否合理呢？#NVE RESP
fix             nve all nve
run             1000000
Per MPI rank memory allocation (min/avg/max) = 14.68 | 14.85 | 15.3 Mbytes
Step    Temp                E_pair       E_mol    TotEng       Press
  500009 298.68579    -10167.6 44033.218 72155.851 2342.0385
  510000 302.12845 -10336.468 43608.502 72003.601 2407.9355
  520000 301.66243 -10728.073 43684.798    71628.55 2533.7712
  530000 301.68158 -10727.88 43592.509    71538.91 2806.4157
  540000 300.82744 -10808.846 43801.363 71557.301 2565.9097
  550000 300.57263 -10123.592 43794.517 72203.043    3005.88
  560000 300.36605 -11037.583 43860.507    71328.56 2579.3259
  570000    301.1261 -10267.171 43819.601    72155.5 2250.9745
  580000 300.30806 -9808.5259 43827.665 72517.341 2639.3842
  590000 300.26756 -11018.715 43961.832 71436.126 2358.6274
  600000 300.48587 -10915.733 43867.938 71473.201 2753.0608
  610000 302.88018 -9667.5577 43609.839 72770.218 2795.3854
  620000 301.02626 -10177.53 43837.513 72250.255 2028.6244
  630000 300.52349 -10040.753 43913.115    72398.18 2333.1702
  640000 300.27693 -9793.2733 43929.939 72630.876 2471.8012
  650000 300.75174 -10767.722 43866.171 71653.528 2752.2466
  660000 300.56305 -11044.818 43943.273 71429.346 2835.4635
  670000 301.16513 -10338.42 43838.871 72108.524 2812.7368
  680000 299.83532 -10005.213 44026.055 72458.441 2606.8843
  690000 302.64825 -11062.655 43738.363 71473.911    2058.75
  700000 302.29645 -10331.801 43752.996 72174.299 2427.7965
  710000 302.09435 -10356.414    43783.57 72154.352 2647.7888
  720000 302.62162 -10721.024    43785.19 71858.957 1980.3826
  730000 300.96673 -10521.144 43842.973 71904.468    2776.048
  740000    301.1998 -11146.371 43828.008 71294.155 2712.2117
  750000 300.80763 -10447.385 43894.392 72009.251 2079.3998
  760000 300.30301 -11060.47 44004.902 71441.986 2616.5363
  770000 301.14724 -10920.965 43910.776 71595.591 2236.1605
  780000 300.34056 -11108.931 44048.038 71441.475 2532.7542
  790000    302.5625 -10886.531    43729.67 71630.349 2324.5234
  800000    299.0912 -10833.691    44171.2 71679.713 2441.2861
  810000 301.38771 -9628.6709 43911.649 72919.587 3119.2833
  820000 302.37526 -10319.07    43805.28 72249.418 2267.1842
  830000 300.78745 -10466.308 43995.491 72088.839 2506.9556
  840000 301.08141 -10888.42 43955.187 71664.108 2947.2625
  850000 301.04021 -10925.083 43915.509 71582.485 2617.0063
  860000 300.21359 -10484.438 44083.139 72084.792 2499.9521
  870000 303.18375 -10442.549 43765.312 72189.615 2687.1801
  880000 301.67097 -10336.687 43856.592 72192.825 2400.2132
  890000 300.93333 -11190.692 44010.428 71398.094 2451.7778
  900000 301.50417 -10499.624    43932.34 72084.254 2341.2999
  910000 301.06999 -11110.682 43905.537 71390.733 3096.3319
  920000 302.03929 -9825.2327 43900.466 72795.371 2519.5934
  930000 301.75815 -10523.122 43975.655 72136.629    2214.871
  940000 301.85594 -10257.335 43982.875 72422.173 2080.6175
  950000 301.51743 -10258.257 43979.558 72374.537 2711.8229
  960000 299.70251 -10067.95 44177.503 72530.125 2611.5269
  970000 302.94718 -11230.745 43790.303 71396.083 1905.8009
  980000 301.45768 -11585.189    44078.12 71138.508 2523.5782
  990000 303.22206 -10801.459 43841.824 71912.128 1955.6817
1000000 300.34853 -11012.203 44181.697 71672.882 2399.8607
1010000 300.79917 -9527.3956 44066.592 73100.357 2412.9959
1020000 302.76006 -10082.837    43796.32 72526.021 2479.4832
1030000 300.67771 -11039.733 44079.452 71585.308    2450.847
1040000 305.24254 -10612.441 43685.629 72203.968 2225.7598
1050000    301.4675 -10385.619 44012.494 72273.711 2655.1978
1060000 302.54971 -10466.646 43902.213 72221.138 3008.6677
1070000 301.83095 -10411.109 43974.747 72257.068 2862.6712
1080000 302.45083 -10025.582 43871.922 72619.236 2316.0209
1090000 301.71025 -11373.628 44098.132    71402.46 2586.8582
1100000    302.2981 -11241.004 44023.259    71535.57 1795.9471
1110000 301.58705 -10170.16 44076.936 72568.938 2446.0564
1120000 304.31818 -10967.76 43783.283 71827.804 2078.5085
1130000 301.41317 -10412.708 44077.787    72304.95 2588.7697
1140000    301.2752 -10655.679 44091.252 72057.757 2423.2655
1150000    301.6288 -10533.763 43955.431 72089.183 2718.1907
1160000 301.86907 -11339.997 44051.399 71409.719    2658.682
1170000 302.45859 -10704.216 43943.848 72013.522 2459.4792
1180000 301.41572 -10114.733 44022.282 72547.748 2767.9157
1190000 301.22523 -10599.521 44080.766 72097.023 3199.6938
1200000 303.13193 -11048.489 43899.964 71711.685 2578.0172
1210000 303.07856 -9922.1993    43993.55 72924.718 2173.3128
1220000 303.03386 -10251.766 43952.724 72548.595 2922.2561
1230000 304.78262 -10811.273 43767.767 72028.314 2714.5053
1240000 302.36762 -10008.127 43972.193 72726.294 2980.7962
1250000 302.68836 -10601.908 43960.044 72161.482 2677.1978
1260000 302.55538 -9939.0464 44062.153 72909.404 2874.1353
1270000 302.28745 -10211.091 44063.743 72604.603 2201.0688
1280000 302.80402 -10283.893 43965.966 72500.246 2956.1798
1290000 302.78509 -11184.916 43924.406 71555.237 2459.8767
1300000 301.75787 -10341.187 44132.169 72475.044 2721.2744
1310000 302.48391 -10581.724 44100.339 72295.751 2355.7948
1320000 302.49952 -10686.17 44068.241 72161.209 2589.3674
1330000 304.41344 -10180.36 43879.202 72723.335 2579.5449
1340000 303.41944 -10785.172 44011.056 72122.951 2071.9447
1350000 303.28968 -10371.327 44014.271 72523.376 1624.5058
1360000 303.13649 -10726.268    43960.37 72094.896 2132.0205
1370000 303.19956 -9901.1288 44057.651 73025.402 2466.9079
1380000 301.52702 -9984.5949    44301.48 72971.351 2581.1992
1390000 301.11336 -10427.221 44342.572 72516.788 2757.3936
1400000 301.48473 -10739.138 44223.325 72133.232 2658.3536
1410000 302.51568 -10444.434 44087.816 72424.591 2961.9412
1420000 304.08722 -10685.27 43944.248 72241.651 2448.4698
1430000 303.04606 -10394.756 44099.626 72554.072 2546.7075
1440000 303.26271 -9827.2946 44067.743 73117.422 1995.6916
1450000 302.62357 -11046.631 44138.215 71886.623 2123.5725
1460000 302.03154 -10492.624 44215.165 72441.685 2327.7714
1470000 303.52948 -10299.837 44038.977 72650.313 2956.2299
1480000 302.68829 -10145.736 44113.321 72770.921 2944.1574
1490000 302.60297 -9258.8436 44179.745    73713.3 2663.4186
1500000 303.19886 -10398.354 44107.864 72578.299 2168.5538
1500009 304.10531 -10137.103 44016.094 72863.983 2403.6226

#NVE COMPASS 电荷
fix             nve all nve
run             1000000
Per MPI rank memory allocation (min/avg/max) = 15.67 | 15.71 | 15.9 Mbytes
Step Temp E_pair E_mol TotEng Press
1000005 301.12025 -19372.424 43483.095    62712.99 2072.8897
1010000 301.05591 -19509.314 43495.278 62580.036 1875.6079
1020000 300.75821 -19605.245 43598.117 62548.781 1377.7422
1030000 301.50906 -19546.664 43529.292 62634.793 1187.2122
1040000 301.19414 -19450.297 43528.222 62689.718 2063.3331
1050000 301.36282 -19300.892 43445.171 62777.696 2304.3903
1060000 301.62174 -19387.271 43526.991 62806.329 1449.0643
1070000 301.55518 -19556.434 43473.168    62574.81 1083.4228
1080000 301.63466 -19467.18 43410.987 62612.072 2168.5872
1090000 300.53313 -19182.834 43492.416 62836.637 1943.9288
1100000 300.44136 -19362.304 43671.197 62824.182 1645.6681
1110000 301.53966 -19066.672 43452.903 63042.318    2309.371
1120000 299.84068 -19599.438 43721.608 62560.455 1537.7765
1130000 302.08054 -19718.987 43359.537 62365.976 1558.3674
1140000 301.09012 -19589.789 43491.472 62500.141 2243.0463
1150000 298.79262 -19519.725 43755.473 62539.677    1714.884
1160000    300.3381 -19615.148 43587.997 62474.902 1713.6501
1170000 300.06073 -19246.632 43611.692 62831.554 1732.0124
1180000 301.66225 -19291.631 43434.845 62815.017 2083.8872
1190000 300.25291 -19726.809    43624.48 62388.802 2102.7865
1200000 300.88227 -19547.562 43574.841 62599.092 1495.8538
1210000 301.14524 -19359.961    43524.78 62770.342    2168.813
1220000 300.59497 -19669.416 43638.864 62504.431 1104.5708
1230000 301.27457 -20046.739 43535.622 62110.987 1964.3663
1240000 300.20572    -19270.3 43585.542 62800.324 1972.7391
1250000 300.33793 -19498.565 43541.591 62545.057    1951.339
1260000 300.44646 -19518.884 43543.088 62540.148 1912.3481
1270000 300.21235 -19754.96 43574.896 62305.868 2048.7602
1280000 301.88558 -19617.294 43380.816 62463.954 1782.3136
1290000 302.08413 -19617.652 43398.914 62507.148    2494.309
1300000 301.71234 -19580.942 43439.754 62537.037    1635.583
1310000 300.22596 -19457.081 43659.722 62690.317 2458.9475
1320000 300.59414 -19451.422 43592.478 62675.932 1858.2029
1330000 301.15675 -19660.227 43453.588 62400.361 2284.5641
1340000 301.28828 -19787.766 43499.851 62335.947    1593.119
1350000 300.57396 -19575.391 43520.811 62477.708 1942.8081
1360000 299.82888 -19412.746 43694.325 62718.351 1897.8333
1370000 301.54327 -19744.306 43484.997 62397.241 1084.8454
1380000 301.22504 -19393.716 43447.532 62669.571 1467.3059
1390000 301.60166 -19941.616    43465.59    62188.01 2156.7784
1400000 301.56045 -19503.585 43426.292 62581.459    1930.128
1410000 300.65809 -19492.07 43600.506 62651.509 1091.4641
1420000 301.62733 -19436.485 43479.106 62709.947 2040.9157
1430000 300.27736 -19565.812 43603.381 62531.835 2110.1525
1440000 301.36891 -19536.38 43448.616 62546.434 1824.6908
1450000 299.91082 -19628.298 43676.376 62495.355 1474.1176
1460000 300.79766 -19829.422 43580.121 62311.665 1534.8501
1470000 300.29528 -19650.287    43621.44 62467.716 2474.0377
1480000 300.22308 -19570.961 43600.051 62516.397 2181.2413
1490000 302.52429 -19428.703 43354.157 62707.767 2095.2174
1500000 300.99428 -19488.457 43495.782 62593.497    1691.567
1510000 302.84022 -19700.832 43355.516 62477.497 1870.0782
1520000 301.76044 -19204.135 43435.371 62915.625 2136.3166
1530000 300.42721 -19711.923 43647.944 62449.497 1311.8604
1540000    301.5368 -19221.106    43543.06 62977.675 1851.6392
1550000 300.69527 -19689.509 43603.346 62461.676 1702.3529
1560000 302.41016 -19431.254 43340.388 62676.817 1793.1992
1570000 303.26296 -19822.34    43287.85 62342.516 1780.6382
1580000    301.874 -19079.904 43379.779 62998.822 2251.2567
1590000 300.13554 -19609.803 43675.419 62541.702 1694.8136
1600000 300.78535 -19272.669 43570.513 62857.231    1454.526
1610000 301.80564 -19354.717 43415.172    62750.64 2196.1224
1620000    299.9186 -19424.397 43669.796 62693.674 2417.2324
1630000 300.77484 -19270.494 43618.293 62905.839 1634.0225
1640000 301.17593 -19461.825 43578.643 62726.276 1816.5369
1650000 302.01592    -19467.5       43456 62705.642 2254.1756
1660000 301.03773 -19695.982 43512.405 62408.165 2243.7095
1670000 302.28572 -19557.832 43435.548 62629.445 1368.7898
1680000 301.08804 -19736.933 43517.623 62378.882 2098.3396
1690000 299.27871 -19762.138 43724.387 62328.492 2263.4403
1700000 301.36957 -19440.87 43586.369 62779.781 2253.1916
1710000 301.82788 -19470.007 43504.027 62727.056 1943.9095
1720000 300.67771 -19340.419 43618.389 62823.558 1875.3933
1730000 300.55653 -19384.049 43610.799 62756.804 1918.2181
1740000 301.00768 -19338.938 43572.849 62821.802 1639.6843
1750000 300.53508 -19735.793    43690.52 62482.031 1553.7031
1760000 301.56939 -19416.569    43527.55 62770.879 1684.9285
1770000 300.25083 -19365.403    43739.87 62865.331 1176.7435
1780000    300.8671 -19632.002 43660.609 62598.475 1528.2404
1790000 300.57218 -19636.937 43638.089 62533.213 1832.2064
1800000 302.78411 -19582.795    43442.5 62675.327 2298.1295
1810000    300.3834 -19322.943 43715.604    62900.52 1274.8442
1820000 300.75874 -19695.823 43690.581 62550.735 1443.8723
1830000 302.40075 -19241.843 43392.892 62917.524 1233.2432
1840000 300.67537 -19407.151 43608.995 62747.133    1712.68
1850000 300.87348 -19574.504 43638.227 62634.408 1778.9896
1860000 300.66097 -19439.672 43576.513 62680.284 1866.7982
1870000 302.11737 -19632.722 43530.143 62627.568 1927.1987
1880000 300.70486 -19498.205 43606.406 62657.271 2411.4865
1890000 299.92719 -19429.544 43705.298    62725.13 1835.3194
1900000 301.62254 -19494.236 43584.578 62757.054 1647.4245
1910000 300.78416 -19855.744 43692.969    62396.46 1875.5474
1920000 301.66124 -19443.21 43555.835 62784.297    1913.25
1930000 301.32018 -19633.939 43560.703 62554.715 2553.0613
1940000 300.63624 -19549.93 43716.353 62706.696 2162.8129
1950000 301.19203 -19386.811 43616.091 62840.802 1858.9419
1960000 301.08556 -19698.857 43628.523    62527.54 2049.7204
1970000 301.91689 -19486.813 43550.589 62768.222 1673.0744
1980000 300.46779 -19439.457 43680.716 62759.936 1886.2458
1990000 300.82631 -19183.821 43635.448 63016.266 1334.8165
2000000 299.92297 -19293.267    43793.65 62949.217 1808.1652
2000005    302.3887 -19322.129 43492.645 62935.447    1907.843

作者
Author: AngYi 时间: 2021-3-19 18:58

sobereva 发表于 2021-3-19 18:07
看具体什么分子。比如水这种极性分子，凝聚相下产生的相互极化效应很显著，这就得让原子电荷能等效体现溶 ...

好的，感谢老师的指导

作者
Author: k64_cc 时间: 2021-3-20 17:29

AngYi 发表于 2021-3-19 18:07
老师您好，关于是否是双精度我不确定，用的是学校的服务器集群。数值问题具体指什么？是比如势函数或者截 ...

emmmmmmmm

你知道NVE是指总能量守恒吧，那它现在能不能守恒呢？不能守恒的话不就是数值问题了吗？

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