AMBER: check COM velocity

From: Pankaj R. Daga <>
Date: Fri, 4 Jan 2008 10:06:26 -0600

Dear Amber community,


I am running one equilibration using NTP conditions. During simulation, I am
observing one message repetitively, mentioning


"check COM velocity, temp: 0.002756 0.01(Removed)

 check COM velocity, temp: 0.002198 0.01(Removed)"


The simulation runs for few thousand cycles (almost half the way) and then
stops with no message. Could anyone suggest where am I going wrong?


I tried to run simulation using keyword "nscm =100", However this keyword
didn't help. I will like to know if this keyword will make any difference in
the simulation or not? I also searched in the archives, I could not get the
solution for the problem. Here is the input file.


Equilibration Run





     ntb = 2,

     ntp = 1








     nstlim = 200000, dt= 0.002,

     ntpr =2000,

     ntwx = 5000,

     ntwr = 5000,

     cut = 10




I will be thankful to you if you could suggest me the way out from this


Thanks and Regards




If your ship doesn't come in, swim out to it...Jonathan Winters
Pankaj R. Daga |
Dept. of Medicinal Chemistry | e-mail:
417 Faser Hall, | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |


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Received on Sat Jan 05 2008 - 00:03:40 PST
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