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

[Justin A. Lemkul]

Li, Hualin wrote:
> 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?
> 

If you are maintaining 32 pull groups, your calculations will be horrendously 
slow, there's no real way around that without re-writing the code.  If you can 
do that and maintain accuracy, then the developers are likely to be interested 
in it.  Otherwise, accept the performance hit.

-Justin

> Thank you very much in advance.
> 
> Thanks,
> Hualin ---- 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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