Constant pressure (NPT) will attempt to scale the box to achieve
pressure. Try NVT? A droplet model should work, without issues, I think.
Bill
On 9/26/17 10:58 PM, jesus berlanga wrote:
> 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 - 23:30:02 PDT
