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 Thu May 24 2012 - 15:00:03 PDT
