AMBER Archive (2009)

Subject: [AMBER] Why the calculation ofen stop with the calculation process not end?

From: xuemeiwang1103 (
Date: Wed Oct 21 2009 - 09:04:57 CDT

    I have sucessfully heated my protein system to 300K in 45ps .Then production of 5000ps were carried out at physilogical conditions (300k 1atm) in the NPT ensemble.But the odd thing is that the calculation often stopped with nothing seems wrong .So I have to use the sander command again and again to let the computer continue the calculation.But when I use the sander command the 4th ,my system began to change after few caiculation steps , one residue which should form the coordination bond with the Znic atom run far away ,I am rather puzzeled with this phenomenon.As a newer ,this is the first time I run the MD ,could someone kind enough to tell me the reaon why the calculation often stop,and is it the reason which may lead to the system change?Thank you very much!
   hear is my inputfile which I used again and again:
Stage equilibration of qqup



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