AMBER Archive (2008)

Subject: AMBER: check COM velocity

From: Pankaj R. Daga (pdaga_at_olemiss.edu)
Date: Fri Jan 04 2008 - 10:06:26 CST

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

 &cntrl

     imin=0,

     irest=1,

     ntx=7,

     ntb = 2,

     ntp = 1

     ntr=0,

     ntc=2,

     ntf=2,

     tempi=300.00,

     temp0=300.00,

     ntt=3,

     gamma_ln=1.0,

     nstlim = 200000, dt= 0.002,

     ntpr =2000,

     ntwx = 5000,

     ntwr = 5000,

     cut = 10

/

END

 

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

 

Thanks and Regards

 

Pankaj

 

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

 

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