 |
 |
 |
 |
 |
 |
||
 |
 |
 |
 |
 |
| 2 | 1/1 | 返回列表 |
| 查看: 1604 | 回復: 1 | |||
[交流]
【求助】gromacs下對大分子體系QM/MM計算的問題
|
|
我用的是gromacs4.0.3+MOPAC7.0 模擬對象是MHC/VIRAL PEPTIDE/T-CELL RECEPTOR三者復合體(1AO7)，五條鏈，一共11000個原子，加上水和離子后270000左右的原子。 主要是計算MHC和VIRAL PEPTIDE的結(jié)合能，在這兩者上分別取若干氨基酸用QM計算，其余用MM計算。整個體系能量最小化到1000一下，開始模擬是有如下錯誤， 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 另外求教對大體系能量最小化應該怎么設置比較合理？emtol設到多少比較合適？constraints應該選用何種算法？ |
回復此樓» 猜你喜歡
求b區(qū)院校調(diào)劑
已經(jīng)有4人回復
-
材料與化工考研調(diào)劑
已經(jīng)有9人回復
-
求調(diào)劑
已經(jīng)有3人回復
-
347求調(diào)劑
已經(jīng)有3人回復
-
總分293求調(diào)劑
已經(jīng)有4人回復
-
284求調(diào)劑
已經(jīng)有15人回復
-
359求調(diào)劑
已經(jīng)有3人回復
-
各位老師您好：本人初試372分
已經(jīng)有5人回復
-
285求調(diào)劑
已經(jīng)有3人回復
-
282求調(diào)劑
已經(jīng)有3人回復
» 本主題相關商家推薦: (我也要在這里推廣)
» 本主題相關價值貼推薦，對您同樣有幫助:
- 氨基酸在線衍生測定過程中遇到的一些問題
已經(jīng)有6人回復
- 本人查閱文獻，遇到一個問題，請教哪位給我解答哈，在下將不勝感激！
已經(jīng)有18人回復
- 陜西省榆林市大能源體系建設2008-2018年重大項目規(guī)劃表
已經(jīng)有34人回復
- 面試時應對跳槽原因問題的訣竅
已經(jīng)有7人回復
- 關于熵變的計算，有人知道怎么計算大的體系的熵變嗎？比如將近一千個殘基的體系？
已經(jīng)有11人回復
- 分子模擬時間越長越好嗎？
已經(jīng)有44人回復
- AMBER中qm/mm的問題
已經(jīng)有5人回復
- 求助各位，關于初學分子模擬
已經(jīng)有9人回復
- 【求助】gromacs的又一個問題
已經(jīng)有22人回復
- 【求助】psf文件的生成
已經(jīng)有19人回復
» 搶金幣啦！回帖就可以得到:
-
中國散裂中子源誠聘“AI材料計算”方向博士后/職工
+1/426
-
祈福中標
+1/228
-
西南交通大學醫(yī)學院招收生物醫(yī)學工程和材料與化工專業(yè)碩士研究生
+1/183
-
太原科技大學材料科學與工程學院招收金屬材料類博士一名
+1/86
-
招收調(diào)劑生，動物醫(yī)學專業(yè)
+1/84
-
招收材料、化學類調(diào)劑生，專碩學碩均可
+1/33
-
【實戰(zhàn)型】【生物醫(yī)藥】2026青島大學招博士生 含少數(shù)民族骨干計劃2名！
+1/20
-
同濟大學環(huán)境學院 肖倩特聘研究員課題組 招聘碩士/博士（長期有效）
+1/17
-
贛南師范大學智能制造與未來能源學院2026年碩士調(diào)劑信息
+1/16
-
招聘科研助理——儲能方向（儲能、流體傳熱、CFD模擬）
+1/14
-
中科院物理所二維材料方向招收推免研究生
+1/13
-
雙一流湘潭大學化工學院招收化工、能源動力、工程熱物理相關研究生調(diào)劑
+1/12
-
中南大學喻桂朋教授團隊新增2026年博士研究生
+1/12
-
電子信息求調(diào)劑
+1/10
-
中國民航飛行學院先進連接團隊招收航空宇航、航空機械專業(yè)碩士研究生（學碩專碩均可）
+1/7
-
211/雙一流---石河子大學---有機化學方向招調(diào)劑生
+1/5
-
上海師范大學有機化學專業(yè)研究生招生
+1/5
-
上海交通大學化學化工學院張智濤課題組誠聘博士后
+1/3
-
上海交通大學招聘：新型X射線管設計仿真計算工程師/博士后/助理研究員
+1/2
-
11自命題 294分求調(diào)劑
+1/1
2樓2011-06-07 21:46:58
相關版塊跳轉(zhuǎn)
我要訂閱樓主 come4c 的主題更新
| 2 | 1/1 | 返回列表 |
| 最具人氣熱帖推薦 [查看全部] | 作者 | 回/看 | 最后發(fā)表 | |
|---|---|---|---|---|
|
[考研] 347求調(diào)劑 +3 | L when 2026-03-25 | 3/150 |
|
|---|---|---|---|---|
|
|
[考研] 求調(diào)劑 一志愿 本科 北科大 化學 343 +4 | 13831862839 2026-03-24 | 5/250 |
|
|
|
[考研] 318求調(diào)劑 +5 | plum李子 2026-03-21 | 8/400 |
|
|
[考研] 289材料與化工（085600）B區(qū)求調(diào)劑 +4 | 這么名字咋樣 2026-03-22 | 5/250 |
|
|
|
[考研] 0856材料專碩353求調(diào)劑 +6 | NIFFFfff 2026-03-20 | 6/300 |
|
|
|
[考研] 調(diào)劑 +4 | 13853210211 2026-03-24 | 4/200 |
|
|
|
[考研] 求調(diào)劑 +5 | 林之夕 2026-03-24 | 5/250 |
|
|
|
[考研] 材料292調(diào)劑 +8 | 橘頌思美人 2026-03-23 | 8/400 |
|
|
|
[考研] 求調(diào)劑一志愿武漢理工大學材料工程（085601） +5 | WW.' 2026-03-23 | 7/350 |
|
|
|
[考研] 305分求調(diào)劑（食品工程） +5 | Sxy112 2026-03-21 | 7/350 |
|
|
|
[考研] 一志愿吉大化學322求調(diào)劑 +4 | 17501029541 2026-03-23 | 6/300 |
|
|
|
[考研] 材料/農(nóng)業(yè)專業(yè)，07/08開頭均可，過線就行 +3 | 呵唔哦豁 2026-03-23 | 4/200 |
|
|
|
[考研] 材料求調(diào)劑 +5 | @taotao 2026-03-21 | 5/250 |
|
|
|
[考研] 考研調(diào)劑 +3 | 呼呼？~+123456 2026-03-21 | 3/150 |
|
|
|
[考研] 求助 +5 | 夢里的無言 2026-03-21 | 6/300 |
|
|
|
[考研] 296求調(diào)劑 +4 | www_q 2026-03-20 | 4/200 |
|
|
|
[基金申請]
學校已經(jīng)提交到NSFC，還能修改嗎？
40+4
|
babangida 2026-03-19 | 9/450 |
|
|
|
[考研] 南昌大學材料專碩311分求調(diào)劑 +6 | 77chaselx 2026-03-20 | 6/300 |
|
|
|
[考研] 一志愿 西北大學 ，070300化學學碩，總分287，雙非一本，求調(diào)劑。 +4 | 晨昏線與星海 2026-03-19 | 4/200 |
|
|
|
[考研] 材料學碩318求調(diào)劑 +5 | February_Feb 2026-03-19 | 5/250 |
|