[AMBER] »Ø¸´: »Ø¸´: Issue about atomic forces acting on each atom

From: Huang ZiJian via AMBER <amber.ambermd.org>
Date: Wed, 28 Jun 2023 02:13:29 +0000

Hi Kelvin,

I guess the command ¡°vector forces .1-18516 @1-18516 out forces.dat¡± adds all the vectors up. Perhaps using a loop to obtain the force of each atom would be fine.

e.g.
¡®¡¯¡®
vector forces .1 .1 out forces_1.dat
vector forces .2 .2 out forces_2.dat
....
¡®¡¯¡® (I'm unfamiliar with using a loop in cpptraj...)

Hope this helps.

Regards,
Zijian
________________________________
·¢¼þÈË: º†ôËŸ¨ via AMBER <amber.ambermd.org>
·¢ËÍʱ¼ä: 2023Äê6ÔÂ27ÈÕ 19:36
ÊÕ¼þÈË: Huang ZiJian <Hzj-0820.outlook.com>
³­ËÍ: AMBER Mailing List <amber.ambermd.org>
Ö÷Ìâ: Re: [AMBER] »Ø¸´: Issue about atomic forces acting on each atom

Hi Zijian,




Thank you for your reply. I have tried the "vector" command in cpptraj




parm com_solv.prmtop
trajin prod.mdcrd 1 2000 1
reference com_solv.pdb
autoimage
vector forces .1-18516 @1-18516 out forces.dat


cpptraj <trajin.in> trajout.out




But it just shows me the atomic forces acting on the origin, but what I want will be the atomic forces acting on each atom.

#Frame forces
       1 0.0000 0.0000 0.0000 28.6162 28.7392 28.5792
       2 0.0000 0.0000 0.0000 28.7330 28.6781 28.6547
       3 0.0000 0.0000 0.0000 28.7460 28.7278 28.6430
       4 0.0000 0.0000 0.0000 28.7193 28.7508 28.6700
       5 0.0000 0.0000 0.0000 28.6784 28.7103 28.6934
       6 0.0000 0.0000 0.0000 28.7448 28.6899 28.6626
       7 0.0000 0.0000 0.0000 28.7498 28.6882 28.5991
       8 0.0000 0.0000 0.0000 28.7274 28.6950 28.7269
       9 0.0000 0.0000 0.0000 28.6549 28.7850 28.5620
      10 0.0000 0.0000 0.0000 28.7422 28.7688 28.6493
~
Do you have any ideas about how to get the atomic forces on each atoms ?




Thanks,

Kelvin



-----ԭʼà]¼þ-----
°l¼þÈË:"Huang ZiJian" <Hzj-0820.outlook.com>
°lËÍ•rég:2023-06-24 11:46:04 (ÐÇÆÚÁù)
ÊÕ¼þÈË: "º†ôËŸ¨" <xh.jian.siat.ac.cn>, "AMBER Mailing List" <amber.ambermd.org>
³­ËÍ:
Ö÷î}: »Ø¸´: [AMBER] Issue about atomic forces acting on each atom


Hi,


It is obvious a pdb file does not contain the forces information. I guess the 'vector' command in cpptraj would help.


Regards,
Zijian
·¢¼þÈË: º†ôËŸ¨ via AMBER <amber.ambermd.org>
·¢ËÍʱ¼ä: 2023Äê6ÔÂ23ÈÕ 18:35
ÊÕ¼þÈË: amber.ambermd.org <amber.ambermd.org>
Ö÷Ìâ: [AMBER] Issue about atomic forces acting on each atom

Hi all,




I encountered a problem when using the keyword ntwf = -1, as I would like to compute the forces acting on each atom, I then followed the instruction from the manual..

However, when I would like to convert the mdcrd file to the .pdb format using cpptraj with the .in file (as shown below), it is not possible to obtain the forces acting on each atom.


Also, I have also tried to set ntwf = 500 intended to obtain the mdfrc file with using ioutfm = 0 to get the ACSII format (as shown below), but I have difficulty in finding what is the meaning of the corresponding column. Could you please also give me some instructions ?






Thank you very much for your time, and please let me know if I can provide you more information to have your instructions.




Regards,

Kelvin



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 27 2023 - 19:30:02 PDT