Hi
Have you crossed check your structure after minimization?
Kindly make sure that structure you obtained from minimization is correct.
If it is correct then you can follow my script.
I think you are heating up system.
#Heating up the system at equilibration stage
&cntrl
nstlim=50000, dt=0.001, ntx=1, irest=0, ntpr=1000, ntwr=10000, ntwx=5000,
tempi=000.0, temp0=300.0, ntt=1, tautp=2.8, ig=-1,
ntb=1, ntp=0,
ntc=2, ntf=2,
cut=10.0, iwrap=1,
&end
EOF
-AT
________________________________
From: esther nehu <estherchem12.gmail.com>
Sent: Tuesday, June 28, 2016 6:40:59 PM
To: AMBER Mailing List
Subject: [AMBER] equilibration problem
Dear Amber users,
I am simulating a polyamide duplex, which is buit from gaussian09. The
charges are derived from RED Server using amber99sb force field. When I
view the mdcrd file in vmd, some of the bonds have really elongated, the
structure has distorted totally.
This is my input file
&cntrl
imin=0, irest=0, ntx=1,
nstlim=10000, dt=0.0005,
ntc=2, ntf=2,
ntb=0, igb=1,
ntpr=50, ntwx=50,
ntt=3, gamma_ln=2.0
tempi=0.0, temp0=300.0,
cut=999, rgbmax=999,
/
I am enclosing the prmtop and mdcrd file
Thanks
Esther
NEHU
India
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Received on Wed Jun 29 2016 - 07:30:07 PDT
