{"id":69716,"date":"2026-11-14T21:42:19","date_gmt":"2026-11-14T13:42:19","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=69716"},"modified":"2026-11-14T21:42:19","modified_gmt":"2026-11-14T13:42:19","slug":"gromacs-water-box-temperature-windows-equilibration","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/gromacs-water-box-temperature-windows-equilibration\/","title":{"rendered":"GROMACS \u6c34\u76d2\u5b9e\u8dd1\uff0c\u6700\u540e\u4e00\u5e27\u63a5\u8fd1 300 K\uff0c\u5c31\u53ef\u4ee5\u5f00\u59cb\u751f\u4ea7\u6a21\u62df\u5417\uff1f"},"content":{"rendered":"
\n

\u6709\u4eba\u53d1\u6765\u4e00\u5f20\u6e29\u5ea6\u66f2\u7ebf\uff0c\u6700\u540e\u4e00\u4e2a\u70b9\u5728 295 K \u5de6\u53f3\uff0c\u76ee\u6807\u6e29\u5ea6\u662f 300 K\u3002\u53ea\u770b\u672b\u5e27\uff0c\u4f3c\u4e4e\u4f53\u7cfb\u5df2\u7ecf\u8db3\u591f\u63a5\u8fd1\u76ee\u6807\u3002\u6211\u4eec\u7528 GROMACS \u8dd1\u4e86\u4e00\u4e2a\u4ec5\u6709\u4e8c\u767e\u4e8c\u5341\u4e00\u679a\u6c34\u5206\u5b50\u7684\u76d2\u5b50\uff0c\u6700\u540e\u4e00\u5e27\u6b63\u597d\u7b26\u5408\u8fd9\u4e2a\u63cf\u8ff0\uff0c\u4f46\u7b2c\u4e00\u76ae\u79d2\u7684\u5e73\u5747\u6e29\u5ea6\u53ea\u6709\u7ea6 250 K\uff0c\u6574\u4e2a\u77ed\u7a97\u53e3\u8fd8\u7ecf\u5386\u4e86\u5f88\u5927\u7684\u538b\u529b\u53d8\u5316\u3002\u8fd9\u4e2a\u5c0f\u4f8b\u5b50\u53ef\u4ee5\u7ec3\u4e60\u4e09\u4e2a\u5e38\u88ab\u6df7\u5728\u4e00\u8d77\u7684\u5224\u65ad\u3002\u6700\u5c0f\u5316\u662f\u5426\u8fbe\u5230\u9884\u5148\u8bbe\u5b9a\u7684\u529b\u9608\u503c\uff0c\u63a7\u6e29\u662f\u5426\u7ecf\u8fc7\u660e\u663e\u7684\u521d\u59cb\u6682\u6001\uff0c\u4ee5\u53ca\u89c2\u6d4b\u957f\u5ea6\u662f\u5426\u8db3\u4ee5\u652f\u6301\u51c6\u5907\u56de\u7b54\u7684\u7269\u7406\u95ee\u9898\u3002<\/p>\n

\u4ece\u5750\u6807\u6570\u56de\u5230\u62d3\u6251\u4e2d\u7684\u5206\u5b50\u6570<\/h2>\n

\u51c6\u5907\u4f53\u7cfb\u65f6\uff0c\u5750\u6807\u6587\u4ef6\u7ed9\u51fa\u539f\u5b50\u7684\u4f4d\u7f6e\uff0c\u62d3\u6251\u63cf\u8ff0\u5206\u5b50\u7531\u54ea\u4e9b\u539f\u5b50\u7ec4\u6210\u3001\u600e\u6837\u76f8\u4e92\u4f5c\u7528\uff0c\u53c2\u6570\u6587\u4ef6\u51b3\u5b9a\u79ef\u5206\u3001\u8fb9\u754c\u6761\u4ef6\u548c\u8f93\u51fa\u9891\u7387\u3002\u8fd0\u884c\u9884\u5904\u7406\u65f6\uff0c\u4e09\u8005\u8981\u653e\u5728\u4e00\u8d77\u6838\u5bf9\u3002\u7528\u81ea\u5e26\u6c34\u76d2\u586b\u5145\u4e00\u4e2a\u8fb9\u957f\u4e8c\u7eb3\u7c73\u7684\u7acb\u65b9\u76d2\uff0c\u5e76\u8ba9\u6eb6\u5242\u5316\u5de5\u5177\u540c\u6b65\u66f4\u65b0\u62d3\u6251\u7684\u5206\u5b50\u6bb5\u3002\u5982\u679c\u624b\u5de5\u590d\u5236\u4e86\u6eb6\u5242\u5316\u524d\u7684\u62d3\u6251\uff0c\u5c31\u53ef\u80fd\u770b\u5230\u6c34\u5206\u5b50\u5df2\u7ecf\u6324\u6ee1\u76d2\u5b50\uff0c\u9884\u5904\u7406\u5374\u62a5\u544a\u5750\u6807\u4e0e\u62d3\u6251\u7684\u539f\u5b50\u603b\u6570\u4e0d\u7b26\u3002\u5904\u7406\u65f6\u5148\u67e5\u5206\u5b50\u8868\u548c\u6c34\u6a21\u578b\u7684\u539f\u5b50\u6570\uff0c\u518d\u68c0\u67e5\u662f\u5426\u5f15\u7528\u4e86\u65e7\u6587\u4ef6\u3002\u901a\u8fc7\u63d0\u9ad8\u5141\u8bb8\u8b66\u544a\u7684\u6570\u91cf\u6765\u7ee7\u7eed\uff0c\u4e0d\u4f1a\u7ea0\u6b63\u539f\u5b50\u6392\u5217\u6216\u76f8\u4e92\u4f5c\u7528\u7684\u9519\u914d\u3002GROMACS \u9884\u5904\u7406\u5668\u8bf4\u660e<\/a><\/p>\n

\u8fd9\u6b21\u7528\u968f\u8f6f\u4ef6\u5206\u53d1\u7684 SPC \u521a\u6027\u6c34\u62d3\u6251\u548c\u6c34\u76d2\u6a21\u677f\u3002\u586b\u5145\u540e\u6570\u5f97\u516d\u767e\u516d\u5341\u4e09\u4e2a\u539f\u5b50\uff0c\u6070\u597d\u7b49\u4e8e\u4e8c\u767e\u4e8c\u5341\u4e00\u679a\u4e09\u4f4d\u70b9\u6c34\u5206\u5b50\u3002\u4e09\u6761\u76d2\u8fb9\u90fd\u662f\u4e8c\u7eb3\u7c73\uff0c\u77ed\u7a0b\u622a\u65ad\u8bbe\u4e3a\u96f6\u70b9\u516b\u7eb3\u7c73\uff0c\u5c0f\u4e8e\u6700\u77ed\u76d2\u8fb9\u7684\u4e00\u534a\uff0c\u957f\u7a0b\u9759\u7535\u7528\u7c92\u5b50\u7f51\u683c Ewald \u6c42\u548c\u3002\u5c06\u6765\u66ff\u6362\u6210\u86cb\u767d\u3001\u914d\u4f53\u6216\u819c\u65f6\uff0c\u8fd8\u8981\u6838\u5bf9\u6eb6\u8d28\u4e0e\u6c34\u6a21\u578b\u7684\u53c2\u6570\u517c\u5bb9\u6027\u3001\u6eb6\u8d28\u4e0e\u5176\u5468\u671f\u955c\u50cf\u7684\u8ddd\u79bb\u3001\u79bb\u5b50\u6570\u53ca\u4f53\u7cfb\u7535\u8377\u3002\u4ec5\u51ed\u8f93\u51fa\u6587\u4ef6\u4e2d\u5199\u7740\u201c\u6c34\u76d2\u201d\uff0c\u8fd8\u65e0\u6cd5\u77e5\u9053\u662f\u5426\u4f7f\u7528\u4e86\u9884\u671f\u7684\u7ec4\u5408\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n
\u6587\u4ef6\u6216\u91cf<\/th>\n\u672c\u6b21\u5b9e\u9645\u8bfb\u5230\u4ec0\u4e48<\/th>\n\u53ef\u4ee5\u56de\u7b54\u4ec0\u4e48<\/th>\n<\/tr>\n<\/thead>\n
\u6700\u5c0f\u5316\u65e5\u5fd7<\/td>\n32 \u6b65\u8fbe\u5230\u6700\u5927\u529b\u9608\u503c<\/td>\n\u51e0\u4f55\u677e\u5f1b\u662f\u5426\u7b26\u5408\u672c\u6b21\u505c\u6b62\u6761\u4ef6<\/td>\n<\/tr>\n
\u80fd\u91cf\u6587\u4ef6\u4e2d\u7684\u6e29\u5ea6<\/td>\n101 \u4e2a\u5bfc\u51fa\u65f6\u70b9<\/td>\n\u4e0d\u540c\u65f6\u6bb5\u662f\u5426\u7ecf\u5386\u6e29\u5ea6\u6682\u6001<\/td>\n<\/tr>\n
\u6052\u5bb9\u9636\u6bb5\u7684\u538b\u529b<\/td>\n\u4ece\u7ea6 \u22125870 \u5230 142 bar<\/td>\n\u56fa\u5b9a\u4f53\u79ef\u4e0b\u8fd9\u6bb5\u77ed\u8f68\u8ff9\u7684\u6ce2\u52a8<\/td>\n<\/tr>\n
\u5bfc\u51fa\u7684\u672b\u5e27<\/td>\n\u7ea6 295.36 K<\/td>\n\u8be5\u65f6\u523b\u7684\u72b6\u6001\uff0c\u4ecd\u9700\u524d\u9762\u7684\u65f6\u95f4\u5e8f\u5217<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u672b\u5e27
221 \u679a\u6c34\u5206\u5b50\u7684\u77ed\u6a21\u62df\uff5c\u5148\u770b\u505c\u6b62\u6761\u4ef6\uff0c\u518d\u6bd4\u8f83\u65f6\u95f4\u7a97\u3002<\/figcaption><\/figure>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u540c\u4e00\u8f68\u8ff9\uff0c\u6362\u4e00\u4e2a\u65f6\u95f4\u7a97\u5c31\u6362\u4e86\u4e00\u4e2a\u7ed3\u8bba<\/h2>\n

\u6211\u4eec\u5728 Ubuntu \u5b89\u88c5 GROMACS 2023.3\uff0c\u7528\u4e00\u4e2a\u8fdb\u7a0b\u3001\u4e00\u4e2a\u7ebf\u7a0b\u5b8c\u6210\u6eb6\u5242\u5316\u3001\u80fd\u91cf\u6700\u5c0f\u5316\u548c\u6052\u7c92\u5b50\u6570\u3001\u6052\u4f53\u79ef\u3001\u6052\u6e29\u7684\u77ed\u52a8\u529b\u5b66\u8fd0\u884c\u3002\u6700\u5c0f\u5316\u91c7\u7528\u6700\u901f\u4e0b\u964d\u6cd5\uff0c\u5c06\u6700\u5927\u529b\u9608\u503c\u8bbe\u4e3a\u6bcf\u7eb3\u7c73\u6bcf\u6469\u5c14\u4e8c\u767e\u5343\u7126\u3002\u65e5\u5fd7\u8bb0\u5f55\u7b2c\u4e09\u5341\u4e8c\u6b65\u8fbe\u5230\u505c\u6b62\u6761\u4ef6\uff0c\u6700\u7ec8\u6700\u5927\u529b\u7ea6\u4e3a 159.8\uff0c\u843d\u5728\u7f16\u53f7\u4e09\u767e\u96f6\u56db\u7684\u539f\u5b50\u4e0a\u3002\u5bfc\u51fa\u7684\u9996\u672b\u52bf\u80fd\u7ea6\u4e3a\u6bcf\u6469\u5c14\u8d1f\u4e00\u5343\u4e5d\u767e\u4e94\u5341\u4e09\u548c\u8d1f\u4e5d\u5343\u516d\u767e\u4e94\u5341\u4e5d\u5343\u7126\u3002\u8fd9\u91cc\u5e94\u4e00\u5e76\u62a5\u544a\u505c\u6b62\u539f\u56e0\u548c\u6700\u5927\u529b\u3002\u5355\u770b\u52bf\u80fd\u660e\u663e\u4e0b\u964d\uff0c\u65e0\u6cd5\u533a\u5206\u8fbe\u5230\u9608\u503c\u4e0e\u7528\u5c3d\u5141\u8bb8\u6b65\u6570\u4e24\u79cd\u60c5\u5f62\u3002<\/p>\n

\u968f\u540e\u4ee5\u4e24\u98de\u79d2\u4e3a\u6b65\u957f\u79ef\u5206\u4e24\u5343\u6b65\uff0c\u5168\u7a0b\u56db\u76ae\u79d2\uff0c\u6e29\u5ea6\u8026\u5408\u4f7f\u7528\u901f\u5ea6\u91cd\u6807\u5b9a\uff0c\u76ee\u6807\u4e09\u767e\u5f00\u5c14\u6587\uff0c\u5173\u95ed\u538b\u529b\u8026\u5408\u3002\u6bcf\u4e8c\u5341\u6b65\u5199\u4e00\u6b21\u80fd\u91cf\uff0c\u5305\u542b\u96f6\u65f6\u523b\u5171\u5f97\u5230\u4e00\u767e\u96f6\u4e00\u4e2a\u6e29\u5ea6\u8bb0\u5f55\u3002\u4ece\u8fd9\u4e9b\u5bfc\u51fa\u8bb0\u5f55\u4f5c\u7b49\u6743\u7b97\u672f\u5e73\u5747\uff0c\u6574\u6bb5\u7ea6\u4e3a 281.29 K\u3002\u82e5\u628a\u524d\u56db\u76ae\u79d2\u4f9d\u6b21\u6309\u5de6\u95ed\u53f3\u5f00\u7684\u4e00\u76ae\u79d2\u7a97\u53e3\u5206\u6210\u56db\u6bb5\uff0c\u6bcf\u6bb5\u4e8c\u5341\u4e94\u4e2a\u65f6\u70b9\uff0c\u5747\u503c\u4f9d\u6b21\u7ea6\u4e3a 249.80\u3001295.21\u3001294.82 \u548c 284.76 K\u3002\u56db\u76ae\u79d2\u5904\u7684\u6700\u7ec8\u8bb0\u5f55\u5355\u72ec\u4e3a 295.36 K\uff0c\u672a\u8ba1\u5165\u4e0a\u8ff0\u56db\u4e2a\u5206\u6bb5\u3002\u8bf4\u660e\u7a97\u53e3\u7aef\u70b9\u548c\u91c7\u6837\u95f4\u9694\uff0c\u522b\u4eba\u624d\u80fd\u4ece\u540c\u4e00\u4efd\u6587\u4ef6\u5f97\u5230\u540c\u4e00\u7ec4\u6570\u5b57\u3002<\/p>\n

# md.edr \u662f\u52a8\u529b\u5b66\u8fd0\u884c\u7684\u80fd\u91cf\u6587\u4ef6\u3002\u6309\u540d\u79f0\u9009\u62e9\uff0c\u907f\u514d\u7167\u642c\u53e6\u4e00\u4f53\u7cfb\u7684\u83dc\u5355\u7f16\u53f7\u3002\r\nprintf 'Temperature\\n0\\n' | gmx energy -f md.edr -o temperature.xvg -xvg none\r\nprintf 'Pressure\\n0\\n' | gmx energy -f md.edr -o pressure.xvg -xvg none\r\n# \u8ba1\u7b97\u7b2c\u4e00\u4e2a\u5de6\u95ed\u53f3\u5f00\u7a97\u53e3\u7684\u5bfc\u51fa\u6837\u672c\u5747\u503c\uff0cxvg \u7b2c\u4e00\u5217\u4e3a ps\r\nawk '$1 >= 0 && $1 < 1 {sum += $2; n++} END {print n, sum\/n}' temperature.xvg\r\n<\/code><\/pre>\n
\u547d\u4ee4\u884c\u7684\u80fd\u91cf\u5de5\u5177\u8fd8\u80fd\u8bfb\u53d6\u50a8\u5b58\u5728\u80fd\u91cf\u6587\u4ef6\u91cc\u7684\u7d2f\u79ef\u7edf\u8ba1\u91cf\uff0c\u6253\u5370\u7684\u7edf\u8ba1\u503c\u672a\u5fc5\u7b49\u4e8e\u5c4f\u5e55\u4e0a\u6709\u9650\u4e2a\u5bfc\u51fa\u70b9\u7684\u624b\u7b97\u5e73\u5747\u3002\u672c\u6587\u7684\u6570\u5b57\u660e\u786e\u6765\u81ea\u5bfc\u51fa\u70b9\uff0c\u65b9\u4fbf\u8bfb\u8005\u76f4\u63a5\u590d\u67e5\u3002\u5982\u679c\u81ea\u5df1\u7684\u5747\u503c\u5bf9\u4e0d\u4e0a\uff0c\u5148\u6838\u5bf9\u4f7f\u7528\u7684\u662f\u7a0b\u5e8f\u6253\u5370\u7684\u5e73\u5747\u3001\u5bfc\u51fa\u8bb0\u5f55\u7684\u5e73\u5747\u8fd8\u662f\u9009\u5b9a\u533a\u95f4\u7684\u6570\u636e\uff0c\u540c\u65f6\u68c0\u67e5\u6709\u6ca1\u6709\u628a\u96f6\u65f6\u523b\u548c\u6700\u540e\u4e00\u5e27\u90fd\u7b97\u4e86\u4e24\u6b21\u3002\u80fd\u91cf\u5de5\u5177\u5bf9\u7edf\u8ba1\u91cf\u548c\u53ef\u5bfc\u51fa\u5e27\u7684\u8bf4\u660e<\/a><\/p>\n
\u8fd8\u53ef\u4ee5\u7528\u8fd9\u4efd\u6c34\u76d2\u7ec3\u4e60\u5ba1\u6838\u4ea4\u63a5\u8bb0\u5f55\u3002\u6700\u5c0f\u5316\u7684\u8f93\u51fa\u5750\u6807\u8981\u6210\u4e3a\u52a8\u529b\u5b66\u7684\u8f93\u5165\uff0c\u521d\u6b21\u8d4b\u4e88\u901f\u5ea6\u7684\u53c2\u6570\u5e94\u4e0e\u968f\u540e\u4ece\u68c0\u67e5\u70b9\u7eed\u8dd1\u7684\u53c2\u6570\u5206\u5f00\u4fdd\u5b58\u3002\u5ef6\u957f\u4e00\u6761\u5df2\u6709\u8f68\u8ff9\u65f6\uff0c\u5982\u679c\u53c8\u751f\u6210\u4e86\u4e00\u5957\u521d\u901f\u5ea6\uff0c\u4e4b\u524d\u8bb0\u5f55\u7684\u8f68\u8ff9\u548c\u65b0\u6bb5\u5c31\u4e0d\u80fd\u5f53\u6210\u540c\u4e00\u6761\u8fde\u7eed\u6f14\u5316\u6765\u89e3\u91ca\u3002\u628a\u6700\u5c0f\u5316\u8f93\u5165\u3001\u52a8\u529b\u5b66\u8f93\u5165\u548c\u76f8\u5e94\u68c0\u67e5\u70b9\u5206\u522b\u547d\u540d\uff0c\u518d\u6bd4\u8f83\u6700\u540e\u4e00\u4e2a\u65f6\u95f4\u6233\u4e0e\u4e0b\u4e00\u6bb5\u7b2c\u4e00\u4e2a\u65f6\u95f4\u6233\uff0c\u6bd4\u770b\u5230\u4e24\u4e2a\u540c\u540d\u6587\u4ef6\u540e\u51ed\u4fee\u6539\u65e5\u671f\u62fc\u63a5\u53ef\u9760\u3002<\/p>\n
\u538b\u529b\u5747\u503c\u4e3a\u4ec0\u4e48\u4e0d\u80fd\u62ff\u6765\u8bc1\u660e\u5df2\u7ecf\u5e73\u8861<\/h2>\n
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