Are there Any tutorials Dealing with Droplet Models available on the AMBER
site?
Thanks for the input.
Jesus Berlanga
On Wed, Sep 27, 2017 at 1:03 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> 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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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed Sep 27 2017 - 10:00:02 PDT
