| 查看: 1603 | 回复: 1 | |||
[交流]
【求助】gromacs下对大分子体系QM/MM计算的问题
|
|
我用的是gromacs4.0.3+MOPAC7.0 模拟对象是MHC/VIRAL PEPTIDE/T-CELL RECEPTOR三者复合体(1AO7)，五条链，一共11000个原子，加上水和离子后270000左右的原子。 主要是计算MHC和VIRAL PEPTIDE的结合能，在这两者上分别取若干氨基酸用QM计算，其余用MM计算。整个体系能量最小化到1000一下，开始模拟是有如下错误， RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 35 keywords are: PRECISE GEO-OK CHARGE=0 GRAD MMOK ANALYT AM1 Back Off! I just backed up qmmm.trr to ./#qmmm.trr.1# Back Off! I just backed up qmmm.xtc to ./#qmmm.xtc.1# Back Off! I just backed up qmmm.edr to ./#qmmm.edr.1# WARNING: This run will generate roughly 3863 Mb of data starting mdrun 'HLA-A 0201' 5000 steps, 5.0 ps. counting the number of NH-C=O groups step 0 Step 44, time 0.044 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000010, max 0.000487 (between atoms 2254 and 2257) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3941 3942 34.1 0.0945 0.0945 0.0945 Step 45, time 0.045 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000013, max 0.000668 (between atoms 2254 and 2257) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3941 3942 41.1 0.0945 0.0945 0.0945 Step 46, time 0.046 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000017, max 0.000853 (between atoms 2254 and 2256) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3941 3942 49.3 0.0945 0.0945 0.0945 Step 47, time 0.047 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000023, max 0.001332 (between atoms 2254 and 2256) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3941 3942 58.9 0.0945 0.0945 0.0945 ALL CONVERGERS ARE NOW FORCED ON SHIFT=10, PULAY ON, CAMP-KING ON AND ITERATION COUNTER RESET MAXIMUM SIZE: 9 EMAT 0.100000E+01-0.100000E+01 -0.100000E+01 0.000000E+00 EMAT Infinity 0.000000E+00 0.000000E+00 0.000000E+00 Step 48, time 0.048 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000034, max 0.001928 (between atoms 2254 and 2256) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3941 3942 70.1 0.0945 0.0945 0.0945 Step 49, time 0.049 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000059, max 0.002527 (between atoms 3941 and 3942) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3941 3942 90.0 0.0945 0.0947 0.0945 2254 2256 30.9 0.1012 0.1012 0.1010 t = 0.049 ps: Water molecule starting at atom 272720 can not be settled. Check for bad contacts and/or reduce the timestep. Back Off! I just backed up step49b.pdb to ./#step49b.pdb.1# Back Off! I just backed up step49c.pdb to ./#step49c.pdb.1# Wrote pdb files with previous and current coordinates Step 50, time 0.05 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000399, max 0.028944 (between atoms 3941 and 3942) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3941 3942 90.0 0.0947 0.0972 0.0945 2254 2256 34.1 0.1012 0.1012 0.1010 t = 0.050 ps: Water molecule starting at atom 272852 can not be settled. Check for bad contacts and/or reduce the timestep. Back Off! I just backed up step50b.pdb to ./#step50b.pdb.1# Back Off! I just backed up step50c.pdb to ./#step50c.pdb.1# Wrote pdb files with previous and current coordinates Step 51, time 0.051 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000548, max 0.039885 (between atoms 3941 and 3942) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3941 3942 90.0 0.0972 0.0983 0.0945 2254 2256 35.2 0.1012 0.1012 0.1010 t = 0.051 ps: Water molecule starting at atom 272720 can not be settled. Check for bad contacts and/or reduce the timestep. Back Off! I just backed up step51b.pdb to ./#step51b.pdb.1# Back Off! I just backed up step51c.pdb to ./#step51c.pdb.1# Wrote pdb files with previous and current coordinates Step 52, time 0.052 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000232, max 0.016477 (between atoms 3941 and 3942) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3941 3942 90.0 0.0983 0.0961 0.0945 2254 2256 33.8 0.1011 0.1010 0.1010 ALL CONVERGERS ARE NOW FORCED ON SHIFT=10, PULAY ON, CAMP-KING ON AND ITERATION COUNTER RESET MAXIMUM SIZE: 2 EMAT 0.100000E+01-0.100000E+01 -0.100000E+01 0.000000E+00 EMAT Infinity 0.000000E+00 0.000000E+00 0.000000E+00 Step 53, time 0.053 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000045, max 0.002539 (between atoms 2254 and 2257) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3941 3942 84.1 0.0960 0.0945 0.0945 2254 2256 30.3 0.1010 0.1009 0.1010 t = 0.053 ps: Water molecule starting at atom 272720 can not be settled. Check for bad contacts and/or reduce the timestep. Back Off! I just backed up step53b.pdb to ./#step53b.pdb.1# Back Off! I just backed up step53c.pdb to ./#step53c.pdb.1# Wrote pdb files with previous and current coordinates ALL CONVERGERS ARE NOW FORCED ON SHIFT=10, PULAY ON, CAMP-KING ON AND ITERATION COUNTER RESET """""""""""""UNABLE TO ACHIEVE SELF-CONSISTENCE DELTAE= -0.1994E-03 DELTAP= NaN ------------------------------------------------------------------------------- PRECISE GEO-OK CHARGE=0 GRAD MMOK ANALYT AM1 A FAILURE HAS OCCURRED, TREAT RESULTS WITH CAUTION!! ++++----**** FAILED TO ACHIEVE SCF. ****----++++ AM1 CALCULATION VERSION 7.00 Sun Mar 27 22:07:56 2011 FOR SOME REASON THE SCF CALCULATION FAILED. THE RESULTS WOULD BE MEANINGLESS, SO WILL NOT BE PRINTED. TRY TO FIND THE REASON FOR THE FAILURE BY USING "PL". CHECK YOUR GEOMETRY AND ALSO TRY USING SHIFT OR PULAY. ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES) (I) NA:I NB:NA:I NC:NB:NA:I NA NB NC 1 N 2 H 0.00000 0 3 C 0.00000 0.00000 0 0 4 H 0.00000 0.00000 0.00000 0 0 0 5 C 0.00000 0.00000 0.00000 0 0 0 6 H 0.00000 0.00000 0.00000 0 0 0 7 H 0.00000 0.00000 0.00000 0 0 0 8 H 0.00000 0.00000 0.00000 0 0 0 9 C 0.00000 0.00000 0.00000 0 0 0 10 O 0.00000 0.00000 0.00000 0 0 0 11 H 0.00000 0.00000 0.00000 0 0 0 12 H 0.00000 0.00000 0.00000 0 0 0 13 N 0.00000 0.00000 0.00000 0 0 0 14 C 0.00000 0.00000 0.00000 0 0 0 15 H 0.00000 0.00000 0.00000 0 0 0 16 C 0.00000 0.00000 0.00000 0 0 0 17 H 0.00000 0.00000 0.00000 0 0 0 18 H 0.00000 0.00000 0.00000 0 0 0 19 C 0.00000 0.00000 0.00000 0 0 0 20 H 0.00000 0.00000 0.00000 0 0 0 21 H 0.00000 0.00000 0.00000 0 0 0 22 C 0.00000 0.00000 0.00000 0 0 0 23 H 0.00000 0.00000 0.00000 0 0 0 24 H 0.00000 0.00000 0.00000 0 0 0 25 C 0.00000 0.00000 0.00000 0 0 0 26 O 0.00000 0.00000 0.00000 0 0 0 27 H 0.00000 0.00000 0.00000 0 0 0 28 H 0.00000 0.00000 0.00000 0 0 0 另外求教对大体系能量最小化应该怎么设置比较合理？emtol设到多少比较合适？constraints应该选用何种算法？ |
回复此楼» 猜你喜欢
什么是人一生最重要的？
已经有10人回复
-
面上可以超过30页吧？
已经有13人回复
-
网上报道青年教师午睡中猝死、熬夜猝死的越来越多，主要哪些原因引起的？
已经有10人回复
-
为什么中国大学工科教授们水了那么多所谓的顶会顶刊，但还是做不出宇树机器人？
已经有13人回复
-
版面费该交吗
已经有17人回复
-
【博士招生】太原理工大学2026化工博士
已经有8人回复
-
280求调剂
已经有4人回复
» 本主题相关商家推荐: (我也要在这里推广)
» 本主题相关价值贴推荐，对您同样有帮助:
- 氨基酸在线衍生测定过程中遇到的一些问题
已经有6人回复
- 本人查阅文献，遇到一个问题，请教哪位给我解答哈，在下将不胜感激！
已经有18人回复
- 陕西省榆林市大能源体系建设2008-2018年重大项目规划表
已经有34人回复
- 面试时应对跳槽原因问题的诀窍
已经有7人回复
- 关于熵变的计算，有人知道怎么计算大的体系的熵变吗？比如将近一千个残基的体系？
已经有11人回复
- 分子模拟时间越长越好吗？
已经有44人回复
- AMBER中qm/mm的问题
已经有5人回复
- 求助各位，关于初学分子模拟
已经有9人回复
- 【求助】gromacs的又一个问题
已经有22人回复
- 【求助】psf文件的生成
已经有19人回复
» 抢金币啦！回帖就可以得到:
-
单曲循环久了很多都会变
+1/399
-
招聘科研助理
+1/197
-
87 年东北人定居苏州，诚寻携手余生的你
+1/162
-
2026时光标本=已经注册了 5608 天，合计 16 年
+1/130
-
【最后机会】深圳大学2026级土木工程博士急招
+5/95
-
福建师范大学环境与资源学院刘斯宝课题组招聘青年教师（带编）
+1/79
-
吉林师范大学宽禁带半导体材料生长与器件实验室招收2026年入学申请考核制博士生4名
+2/52
-
【博士招生】北方工业大学招收机械工程方向申请考核制博士
+1/41
-
澳门理工大学人工智能智慧康养方向26 年9月入学博士招生有奖学金
+1/34
-
澳门理工大学人工智能智慧康养26 年9月入学 博士招生有奖学金
+1/32
-
南通大学生物医药方向国家级人才团队招收“申请-考核”制博士研究生20260222
+2/30
-
招聘启事（酶工程与发酵工程方向）
+2/30
-
211大学【2026学博】补招
+1/27
-
坐标南京，高校老师，诚征女友
+1/12
-
北京某研究院结构生物学相关专业申请考核制博士招生（春季）
+1/8
-
吉林师范大学宽禁带半导体材料生长与器件实验室招收2026年入学申请考核制博士生4名
+2/6
-
大连理工大学智能系统实验室优秀博士研究生招生
+1/4
-
斯德哥尔摩博士后基金申请 - 基于视频的三维人体运动学提取 / 姿态估计
+1/2
-
南京大学苏州校区环境与健康研究院招收博士、硕士研究生及科研助理
+1/2
-
攀钢研究院2026年招聘（央企，钒钛国家重点实验室）
+1/1
2楼2011-06-07 21:46:58