Just to add to the comment, the total electrostatic force = qE force + DB
force ...
Ray
On Sat, May 26, 2012 at 10:25 PM, Qin Cai <qcai.uci.edu> wrote:
> There are four kinds of forces printed in force.dat.
>
> qE force, contact force, reentry force and dielectric boundary (DB) force,
> where DB force = contact force + reentry force
>
> If the system has 1667 atoms, there supposed to be (1667+1) *4 = 6672
> lines. The extra four lines are titles.
>
> If your file has 13343 (or 13344) lines, I guess you were using sander
> which runs minimization twice even though the number of steps is set to 1.
>
> Best,
> Qin
>
> On May 25, 2012, at 12:11 PM, Ray Luo, Ph.D. wrote:
>
> Qin,
>
> Can you comment on this?
>
> Ray
>
> ---------- Forwarded message ----------
> From: <tommaso.casalini.mail.polimi.it>
> Date: Fri, May 25, 2012 at 8:20 AM
> Subject: Re: [AMBER] Electrostatic potential and forces computation
> To: amber.ambermd.org
>
>
> Thank you for the answer.
> However, in my system I have 1667 atoms, while the "force.dat" file
> has 13343 rows, and this is not in agreement with the output
> convention that you mentioned.
> Can these be force components on every point of the grid? Can periodic
> boundary conditions affect the file "force.dat" ?
>
> Thank you again for your help and collaboration,
>
> Tommaso Casalini
>
> Def. Quota Qin Cai <qcai.uci.edu>:
>
> >
> > On May 24, 2012, at 11:35 AM, Ray Luo, Ph.D. wrote:
> >
> >> The force output file lists the total electrostatic force (x,y,z)
> >> components (in kcal/mol-A) on each atom in the order of the
> >> prmtop/inpcrd file. I'm also CC'ing Qin on this to confirm the
> >> output convention ...
> >>
> > Yes, each row represents the force on an atom and the three columns
> > are x,y,z components of the force.
> >
> >> So far I don't think any modeling software can visualize force
> >> vectors, at least in the standard releases. I may be wrong though
> >> ... Of course this is not impossible to do.
> >>
> >> All the best,
> >> Ray
> >>
> >> On Thu, May 24, 2012 at 6:52 AM, <tommaso.casalini.mail.polimi.it>
> wrote:
> >> Dear Amber users and developers,
> >> I am using pbsa module from AmberTools 12, in order to compute the
> >> electrostatic potential due to a polyelectrolyte network.
> >> Moreover, I also need to compute electrostatic forces in order to make
> >> a proper analysis of the system.
> >> Choosing forceopt = 2 in the pbsa input file, I obtain a "force.dat"
> >> file as output, which is constituted by the force values in three
> >> columns.
> >> I would like to ask you what exactly these numbers represent, and if I
> >> can visualize these values with a proper software like VMD or pymol.
> >> Thank you for your help and collaboration.
> >>
> >> Tommaso Casalini
> >>
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Received on Sun May 27 2012 - 06:30:02 PDT
