Now everything is clear.
Thank you very much for your help!
Tommaso Casalini
Def. Quota "Ray Luo, Ph.D." <ray.luo.uci.edu>:
> 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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