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Re: [ESPResSo-devel] Dihedral force calculation


From: Axel Arnold
Subject: Re: [ESPResSo-devel] Dihedral force calculation
Date: Fri, 31 Aug 2012 16:03:17 +0200
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:15.0) Gecko/20120827 Thunderbird/15.0

Dear Muhammad,

please find attached two scripts that verify that the implementation is correct.

- compare_potential_and_forces checks that minus the derivate of a given potential is indeed the force central difference up to 3rd order.

- check_dihedral makes a table of the dihedral energy, which to me looks exactly as described in the User's Guide.

There are however different definitions of dihedrals around, not to mention improper dihedrals. Therefore, you might want to compare the formula you expect with the one in the User's guide. Also carefully compare the command syntax and the provided sketch on how the particles are located. For cutoff reasons, the particle you define the bond on is one of the central particles. To me it looks like you just change the order of particles in the part p2 bond p1 p3 p4.

@all: as this is not the first time we have this discussion, the scripts are now in the samples folder, in case some other potential is challenged.

Axel

On 08/27/2012 10:28 AM, Muhammad Anwar wrote:
Hi dear Developers,
I am using dihedral bond potential for my simulations. I found there is a mistake in force calculation. Forces are shuffled. The force which should be on Particle 1, it is on part 2. The force which should be on Part 3 it is on Part 1.

You can change this
MDINLINE int calc_dihedral_force(Particle *p2, Particle *p1, Particle *p3, Particle *p4,
                 Bonded_ia_parameters *iaparams, double force2[3],
                 double force1[2], double force3[2])

Change this like
MDINLINE int calc_dihedral_force(Particle *p2, Particle *p1, Particle *p3, Particle *p4,
                 Bonded_ia_parameters *iaparams, double force1[3],
                 double force2[3], double force3[3])

Then change

/* store dihedral forces */
  for(i=0;i<3;i++) {
      force1[i] = fac*v23Xf1[i];
      force2[i] = fac*(v34Xf4[i] - v12Xf1[i] - v23Xf1[i]);
      force3[i] = fac*(v12Xf1[i] - v23Xf4[i] - v34Xf4[i]);
}
with

 for(i=0;i<3;i++) {
      force1[i] = fac*v23Xf1[i];
      force2[i] = fac*(v12Xf1[i] - v23Xf4[i] - v34Xf4[i]);
      force3[i] = fac*(v34Xf4[i] - v12Xf1[i] - v23Xf1[i]);
}
I have tested this and the way it is available in espresso it increase the stiffness of chain instead of decreasing. And after changing i compared the Rg and Re with published results.


One more efficient can be:
Compute all forces and multiply with force fac like
/* calculate force components (directions) */

 for(i=0;i<3;i++)  {
    f1[i] =  (v23Xv34[i] - cosphi*v12Xv23[i])/(l_v12Xv23);
    f4[i] =  (v12Xv23[i] - cosphi*v23Xv34[i])/(l_v23Xv34);
f2[i] = (-f1[i] + (scalar(v12,v23)/sqrlen(v23)) * f1[i] - (scalar(v34,v23)/sqrlen(v23)) * f4[i]); f3[i] = (-f4[i] - (scalar(v12,v23)/sqrlen(v23)) * f1[i] + (scalar(v34,v23)/sqrlen(v23))* f4[i]);
}

 /* store dihedral forces */
   for(i=0;i<3;i++) {
      force1[i] = fac * f1[i];
      force2[i] = fac * f2[i];
      force3[i] = fac * f3[i];
      force4[i] = fac * f4[i];
}
I did not test this second method, just gone through literature and found this in "Molecular Dynamics Simulation Methods Revised by H. Bekker" in Chapter 5. They claim in this method floating point operations are reduced by 40%.
Please have a look on this.
Thanks and have a nice day.





--
JP Dr. Axel Arnold           Tel: +49 711 685 67609
ICP, Universit├Ąt Stuttgart   Email: address@hidden
Pfaffenwaldring 27
70569 Stuttgart, Germany

Attachment: check_dihedral.tcl
Description: Text Data

Attachment: compare_potential_and_forces.tcl
Description: Text Data


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