[gmx-users] fixing split molecules in trajectory file

Paula Andrea Delgado Pinzon pa-delga at uniandes.edu.co
Fri Aug 10 01:02:17 CEST 2012

Good afternoon,
I run a molecular dynamics simulation of two protein complex with periodic boundaries, when i check the trajectory file i realized that the molecules were split so i decided to use the trjconv command with the option -pbc, i tried with -pbc atom, -pbc res and they didn't seem to work or i am not very sure what they do, but whet i used -pbc whole i achieved complete molecules but they are supposed to be in contact but it seem that this option (whole), besides fixing the problem of split molecules they put the in different positions (before i run trjconv the complex was bind, after the proteins are unbound).  Another question is that after MD simulation i calculate distances between the two proteins along through with the command g_dist, i want to know if this calculation is correct even if don't fix the trajectory

Thank you for your time


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