[gmx-users] questions about steer molecular dynamics by using gromacs4

[Justin A. Lemkul]

mircial at sjtu.edu.cn wrote:
> Dear All:
> 
> I am trying to use steer molecular dynamics simulations to pull a ligand 
> along a channel pore (along the Z axis) by constant rate. I know how to 
> realize this by GROMACS3, however, it seemed that in gromacs4, there are 
> some changes regarding this issues, so I am pasting my pull code 
> parameters and some of my questions here, Could any one be so kind to 
> answer my questions? Thanks in advance.
> 
> 
> My pull code parameters
> ---------------------------------------
> pull    =    umbrella
> pull_dim    =    N N Y
> pull_start    =    yes
> 
> ####### if the pull_start is set to "yes", it means that, the distance 
> between the pull group and the reference group of the starting structure 
> will be calculated and the value will be added to the pull_init1 and the 
> final result will be used a the inital distance between the pull group 
> and the reference group in the simulations, am i right?###########
> 
> pull_nstxout    =    500
> 
> #######  if the pull_nstxout is set to 500, the COM of the pull group 
> will be write every 500 steps (i.e. 1ps,if the time step is 
> 2fs)?############
> 
> pull_nstfout    =    500
> pull_group0        =    Protein
> pull_group1        =    Ligand
> pull_vec1        =    0 0 1
> pull_init1        =    0
> pull_rate1        =         0.025
> pull_k1        =     1000
> 
> ############how can I make sure the pull_rate1 and the pull_k1 I used is 
> appropriate?###############3
> __________________
> 
> ############  what is the out put of the pulling code?  #############
> 
> Does the above parameters can pull the ligand along the Z axis with a 
> constant rate successfully? Are there any problem the my pull code 
> parameters?
> 
> Thanks very much for your time and your kind!
> 

Please try the steered MD/umbrella sampling tutorial.  Your questions should be 
largely answered.

http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

-Justin

-- 
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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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