Re: [gmx-users] calculating com-com distances.

Tsjerk, your good reference helped me to understand the set_pbc and pbc_dx functions from g_dist... I changed few lines of it and my problem was solved. Thank you. Cheers. Fernando. 2009/4/14 Tsjerk Wassenaar > Hi Fernando, > > Just bear in mind that these lattice vectors are just translation

Re: [gmx-users] calculating com-com distances.

Hi Fernando, Just bear in mind that these lattice vectors are just translation vectors. You can add them to or subtract them from the positional vectors of the com. That way you'll get a number of points which you can use to calculate the distances the regular way. To see where you went wrong, con

Re: [gmx-users] calculating com-com distances.

Hi Tsjerk and all list! > You have to use the three vectors from the tricilinic representation > to obtain the correct distance in the periodic system. Check PBC in > Chapter 3 of the manual. I used the length values from rectangular box because I'd want believe that my problem would be solved e

Re: [gmx-users] calculating com-com distances.

Hi Fernando, > I've obtained the vectors for the rectangular box in g_energy, > using Box_XX, Box_YY and Box_ZZ options; I didn't use the vectors of the > skewed box.) You have to use the three vectors from the tricilinic representation to obtain the correct distance in the periodic system. Check

[gmx-users] calculating com-com distances.

Hi list! Is there the possibility of the g_dist program don't provide the correct com-com distances for molecules simulated in triclinic cells under anisotropic pressure? (I've been calculating com-com distances in order to study the clustering of lipids self-assembled. For it, I've written a sim