Hi all
I looked into the file named bondfree.c of Gromacs-4.0
for bond, angle and dihedral force contribution to the virial.
And I have one problem that I can't understand. When the
periodicity has been taken into account for the virial
why do you put one atom's contribution to virial in the
central image? Just like the code int the file bondfree.c
of line 346 and 347
fshift[ki][m]+=fij;
fshift[CENTRAL][m]-=fij;
int the "real bonds" function.
And line 681 682 683
rvec_inc(fshift[t1],f_i);
rvec_inc(fshift[CENTRAL],f_j);
rvec_inc(fshift[t2],f_k);
int the "real angles" function.
The fshift array is used to calculate the PBC contribution
part of the virial in the formula (B.11) in the manual
Appendix B. It seems that the CENTRAL element of shift_vec
array is "0". The direct product of fshift[CENTRAL] and
shift_vec[CENTRAL] should be "0". So why should we accumulate
the CENTRAL element of the fshift array? Or I misunderstand
the shift_vec?
Second, in appendix B.1.4 the formula of virial from covalent
bonds is given. Can someone tell me the formulae of the angle
and dihedral contribution to virial?
Appreciate any help in advance!
xuji
[EMAIL PROTECTED]
2008-12-05
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