AMBER Archive (2003)

Subject: water box distortion

From: GUILLERMINA L ESTIU (gle10_at_psu.edu)
Date: Fri May 23 2003 - 15:36:17 CDT

Hi,
I am running simulations (amber 7) for a sistem of 2500 residuos (50000 after
building the water box)
I am trying to equilibrate the system. As a way of starting, I am heating only
the solvent, but the water box is not kept "cubic"

Can someone tell me waht is wrong in this input file?

molecular dynamics run
 &cntrl
 imin=0, irest=1,
 ntx=5, ntr=1,
  lastist=9000000,
  lastrst=12000000,
 tempi= 300.,
 ntt=1, temp0=300.0, tautp=0.5,
 ig=71277, heat=0.0,
 ntb=1, ntc=2, tol= 0.00001, ntf=2,
 scee=1.2, dt=0.0005,
 cut=9.0, nsnb=25,
 nstlim=100000,
 vlimit= 20
 ntwe=50, ntwx=50, ntpr=10, ntwr=100,
 &end
Group input for restrained atoms
 10000.0
RES 1 2479
END
END

Dr Guillermina Estiu
Chemistry Department
Pennsylvania State University
PA 16802