water box distortion

From: GUILLERMINA L ESTIU <gle10.psu.edu>
Date: Fri, 23 May 2003 16:36:17 -0400 (EDT)

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
Received on Fri May 23 2003 - 21:53:01 PDT
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