[gmx-users] Reduce the frequency to apply distance restrain

[Li, Hualin]

Dear GMX users,

           I am using pull code to make a distance restrain to my proteins and membrane,which looks like this:



 pull             =   umbrella
 pull_geometry    =   cylinder
 pull_vec1         =   0 0 1
 pull_r1          =   2.5
 pull_r0          =   2.5
 pull_dim         =   N N Y ;# 3D

pull_start       =   yes ;# add COM distance to initial value (initial value = equilibrium value)
pull_ngroups     =   32 ;# excluding the reference
pull_group0      =   membrane ;# the reference group - the membrane
pull_pbcatom0    =   -1 ;# or -1 - important for PBC of groups larger than half box,
                      ;# as here for membrane (see manual)
pull_group1      =   protein ;# the protein
pull_pbcatom1    =   0 ;# here is no issue since protein is smaller than half the box
pull_rate1       =   0 ;# do not pull, just maintain distance!
pull_k1          =   800 ;# kJ mol^(-1) nm^(-2)

However, I have 32 protein to keep this local dynamic distance restrain (   pull_geometry    =   cylinder ), making the calculation goes very slowly. Is there any method to reduce the frequency to update the dynamic distance check and restrain please?

Thank you very much in advance.

Thanks,
Hualin --