NAMD复合物分子动力学菜鸟求助~~！！

jamesxue

请教各位大侠！
小弟正在学习NAMD做复合物分子动力学，水球和水盒子结果如下，跪求大侠指导~！
水球结果如下:
TCL: Running for 2500 steps
ERROR: Constraint failure in RATTLE algorithm for atom 1202!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 480!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 763!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 471!
ERROR: Constraint failure; simulation has become unstable.
水盒子结果如下:MINIMIZER SLOWLY MOVING 20075 ATOMS WITH BAD CONTACTS DOWNHILL
听了几个大牛建议，把受体断的地方修补了loop，conf中加入了margin=3，但还是跑散了，不知各位大侠有何建议？
小弟发帖不多，银子有限，先谢过各位大侠了！！

leos

看看这个链接对你有帮助吧：http://www.ks.uiuc.edu/Research/ ... 2009-2010/3992.html

jamesxue

leos 发表于 2013-3-28 18:46

                               
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看看这个链接对你有帮助吧：http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2009-2010/3992.ht ...

抱歉回复晚了，谢谢leos~~~~~！！！

alicelu

把你的文件贴出来啊？不然怎么帮你解决。

whl2dxl

周期性边界条件给的对吗？wrapall这个选项开了？