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 Fri May 25 2012 - 08:30:03 PDT
