Dear Amber Users,
As a fairly new user of AMBER I have been trying to build an interface
between water molecules and a "vacuum" or air in order to study the
effects of the long and medium range interactions it has on some molecules
of interest.
I have started by using the ff03 force field and Also included the pol3
parameters to make the .prmtop and .inpcrd files from tLeap . After this I
run a minimization, a heating, an equilibration at NVT and then an
equilibration at NPT for about 10ps applying surface tension on the xy
plane, then the idea was to increase the dimensions of the box in the Z
direction after the NPT equilibration but I'm having problems with this
step, as the density decreases very fast during the NPT process and when I
try increasing the box z-direction I get an error saying the "*system must
be very inhomogenious"* . If you guys have any insight into how to get
these air-water interface any help will be appreciated. Below are all the
commands used for every step:
Minimization (imin=1, irest=0, maxcyc=9700, ncyc=4000, cut=3.0, igb=0,
ntc=1, ntf=1, ntb=1, ntp=0, ntpr=1 ).
Heating (imin=0,irest=0,ntx=1, nstlim=150000,dt=0.001, cut=3.0, ntf=1,
ntc=1, ntt=3, gamma_ln=2.0, ig=-1, ntb=1,ntp=0,taup=1.0,
tempi=0.0,temp0=270.0,tautp=2.0, ntpr=50, ntwx=50, vlimit=20)
Equilibration NVT (imin=0,irest=1,ntx=5, nstlim=90000, dt=0.001, cut=8.0,
ntf=1,ntc=1, ntt=3, gamma_ln=5.0, ig=-1, ntb=1,ntp=0,taup=1.0 ,
tempi=270.0,temp0=270.0,tautp=2.0, ntpr=50, ntwx=50, vlimit=20, iwrap=1)
Equilibration NPT (imin=0,irest=1,ntx=5, nstlim=10000,dt=0.001,
ntf=1,ntc=1,tol=0.0000001 cut=8.0,ntb=2,ntp=2,taup=1.0,pres0=1.1, ntpr=50,
ntwx=50,ntwe=50, ntt=3,gamma_ln=5.0,
tempi=270,temp0=270.0,tautp=5.0,ig=-1, csurften = 3,gamma_ten =
10.0,ninterface = 2, iwrap=1,)
Thank you in advance, Jesus Berlanga.
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Received on Tue Sep 26 2017 - 23:00:02 PDT
