| 查看: 1628 | 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
2026年博士申请求捞
已经有3人回复
-
2026博士或科研助理转27年博士
已经有6人回复
-
26年博士申请自荐-电催化
已经有6人回复
-
国自科送审了吗
已经有11人回复
-
博士招生
已经有5人回复
-
夜，静悄悄的
已经有8人回复
-
研究生做的很差，你们会让毕业吗？
已经有6人回复
-
26年申博自荐-计算机视觉
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:
-
坐标南京，诚租女友
+5/9321
-
昆明理工大学交通载运车辆方向招收2026年秋季入学博士生2名
+3/174
-
东南大学废弃碳资源利用团队（杰青/海优团队）27级博士研究生和科研助理招生
+1/127
-
国自然申报交流祈福
+4/126
-
求认识靠谱妹纸@山西
+1/71
-
2026年江西师范大学流动化学与工程研究院陈芬儿院士团队化学博士招生
+3/68
-
生命学部的面地青本子开始分发了么？
+1/61
-
双一流高校-南京林业大学-化学工程学院-国家海外优青团队招2026级博士（5月15号截止）
+1/40
-
google ai pro 会员/gemini分享
+1/33
-
急招-华南理工大学-26秋季博士生-生物质材料及电池方向
+1/29
-
坐标北京，83年男征女友
+1/26
-
天津大学 合成生物技术全国重点实验室 国家级青年人才团队常年招收博士后
+1/22
-
南京邮电大学李巍教授招收2026博士生（5月12日前有效）
+1/16
-
类器官/器官芯片 有编制研究员
+1/11
-
吉林大学任雷课题组招机器人和触觉传感方向2026年入学博士生
+1/9
-
【期刊动态】Biofunctional Materials 已被 Scopus 收录，长期征稿（APC全免）
+1/7
-
招收2026年秋季入学博士生1名（河北工业大学/北京科技大学联合 增材制造/生物材料）
+1/3
-
重庆医科大学感染病教育部重点实验室唐开福课题组2026年拟招学术型博士研究生一名
+1/3
-
美国Vanderbilt University博士后招聘
+1/3
-
科研新人必看：立项/开题/报奖都绕不开科技查新
+1/2
2楼2011-06-07 21:46:58