AMBER Archive (2009)

Subject: [AMBER] md simulation on parallel PMEMD

From: oguz gurbulak (gurbulakoguz_at_gmail.com)
Date: Mon Feb 02 2009 - 07:32:31 CST

Dear All,

I'm trying to run a md simulation on parallel PMEMD. I have 6 equilibration
file with rising the temperature for 50 K ( 0-273 K ). My first
equilibration file is in below. I used ntc=3, ntf=3, and I got this error in
output file :

3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 0
 this parallel version only works for ntc < 3

Isn't it possible to use ntc=3, ntf=3, on parallel PMEMD ? Or I should just
use ntc=2, ntf=2, on parallel PMEMD . or I can only use sander with ntc=3,
ntf=3, ? Could you help me to slove this problem ?

Thanks in advance.

MD equilibration
 &cntrl
  imin=0, irest=0, nstlim=5000000, dt=0.002, ntx=1,
  ntc=3, ntf=3, ntpr=2000, ntwx=2000, ntwr=2000, ntwe=2000, ntwv=2000,
  cut=9.825, ntb=1, ntp=0, ntr=0, ntt=1,tautp=2.0,
  tempi=0.0, temp0=50.0,
 /
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