[gmx-users] Diffusion/PBC

[Debashis Sahu]

Dear All,
              I have an problem related to jumping trajectory. In my MD
run, there is a receptor molecule which is binding with an halogen anion in
water solvent. In the original trajectory, the binding between them looks
fine but jumping present. To remove the jumping of the system from
trajectory, I have used 'nojump' as discussed in the forum. Now I got a
jump-free trajectory, but due to the diffusion here, I have observed that
the anion and the receptor are far away from each other. I could not fix
the problem. can any one suggest me?
Thanks in advance.
with regards,
*Debashis Sahu*
*Central Salt and Marine Chemical Research Institute*
*Bhavnagar, Gujarat*
*India, 364002.*