版块导航: 正在加载中...

登录注册

应《网络安全法》要求，自2017年10月1日起，未进行实名认证将不得使用互联网跟帖服务。为保障您的帐号能够正常使用，请尽快对帐号进行手机号验证，感谢您的理解与支持！

24小时热门版块排行榜

北京石油化工学院2026年研究生招生接收调剂公告

返回列表

come4c

铁虫 (初入文坛)

应助: 0 (幼儿园)
金币: 96.4
帖子: 9
在线: 4.8小时
虫号: 1182015

[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

318求调剂已经有8人回复
求调剂已经有7人回复
0703化学已经有13人回复
307分材料专业求调剂已经有4人回复
0855求调剂材料已经有8人回复
332求调剂已经有9人回复
甲醇/二氯 1:15过柱子已经有3人回复
272求调剂已经有4人回复
一志愿西北农林畜牧专硕336分求调剂已经有3人回复
求调剂已经有10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:

查看全部散金贴

1楼 2011-03-29 10:58:06

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

sijifengsd

银虫 (小有名气)

应助: 0 (幼儿园)
金币: 273.7
帖子: 94
在线: 12.1小时
虫号: 794988

★
come4c(金币+1):谢谢参与

呵呵，请问您用Gromacs设置qmmm连接原子的时候虚原子怎么写入gro文件的？这个问题我很感兴趣，但不知道怎么处理，谢谢赐教

赞一下(1人)