> Any tutorials Dealing with Droplet Models
I don't think so. Leap's 'solvateshell' is the command for it - set
sander params for running in vacuum.
Bill
On 9/27/17 9:44 AM, jesus berlanga wrote:
> 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.
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Wed Sep 27 2017 - 10:00:03 PDT
