我在做namd最后一步的时候，出现如下错误：
TCL: Running for 2500 steps
ERROR: Constraint failure in RATTLE algorithm for atom 4401!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4360!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4995!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1870!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4847!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2983!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2752!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2296!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4541!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 495!
ERROR: Constraint failure in RATTLE algorithm for atom 4208!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4132!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 984!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.

是怎么回事？怎么解决呢
请高手帮助！！！

[ 本帖最后由 chenjung0825 于 2008-7-22 22:06 编辑 ]

Try minimizing for at least 10,000 steps before running a simulation.

我在minimize这一步做了20000步，还是同样的错误

do not apply any constraints in em

那就是说将minimize 和 run分开两次跑,前者不限制，后者限制？

引用:

原帖由 yutian 于 2007-9-29 14:36 发表
那就是说将minimize 和 run分开两次跑,前者不限制，后者限制？

certainly, u can also use no constraints in md run

那这两者对体系的模拟有什么影响呢

又发现了一个问题，在minimize的第一步，体系的能量就指数般的增长，按照manual我改了pairlistdist的数值，还是没有变化,请高手指点

minimize能量还增长,不可思议,贴上来看看

引用:

原帖由 yutian 于 2007-9-29 17:12 发表
又发现了一个问题，在minimize的第一步，体系的能量就指数般的增长，按照manual我改了pairlistdist的数值，还是没有变化,请高手指点

注意负号

TCL: Minimizing for 10000 steps
PRESSURE: 0 4.09204e+15 -5.82067e+14 1.71875e+14 -5.82067e+14 4.28541e+15 9.63163e+13 1.71875e+14 9.63163e+13 4.27389e+15
GPRESSURE: 0 4.09204e+15 -5.82067e+14 1.71875e+14 -5.82067e+14 4.28541e+15 9.63163e+13 1.71875e+14 9.63163e+13 4.27389e+15
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP         TOTAL2         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG

ENERGY:       0     18348.3413      4099.1894      1464.1644         0.3455        -105698.1311  99999999.9999         0.0000         0.0000         0.0000       99999999.9999         0.0000  99999999.9999  99999999.9999         0.0000       99999999.9999  99999999.9999     71705.0880  99999999.9999  99999999.9999

OPENING EXTENDED SYSTEM TRAJECTORY FILE
INITIAL STEP: 1e-06
GRADIENT TOLERANCE: 1.25941e+11
PRESSURE: 1 1.77757e+13 -7.37304e+12 -6.37803e+12 -7.37304e+12 3.25092e+13 2.4799e+13 -6.37803e+12 2.4799e+13 2.91611e+13
GPRESSURE: 1 1.77757e+13 -7.37304e+12 -6.37803e+12 -7.37303e+12 3.25092e+13 2.4799e+13 -6.37803e+12 2.4799e+13 2.91611e+13
ENERGY:       1    378642.8816     57248.2897      2881.5910      1876.0135          81104.7955  99999999.9999         0.0000         0.0000         0.0000       99999999.9999         0.0000  99999999.9999  99999999.9999         0.0000       99999999.9999  99999999.9999     71705.0880  99999999.9999  99999999.9999

再往下基本上处于振荡状态

有点乱，还是贴个log附件上来吧

minimize长的文件太大了，所以做了一个短点的，出错问题是一样的，请帮忙看看

http://simulation.5d6d.com/thread-198-1-1.html

What about the box size and the system size?