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normal a concern on MD production spped

  • albumns
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6 years 11 months ago #7240 by albumns
a concern on MD production spped was created by albumns
Hello,

I found that my equilibration speed and MD production speed various a lot. The only difference between these two .mdp file is that: in the equilibration step it has the following option which is absent in the production .mdp file:
define= -DPOSRES -DPOSRES_FC=50 -DBILAYER_LIPIDHEAD_FC=10

Other options are the same as followings:
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.4
cutoff-scheme            = group
epsilon_r                = 15
coulombtype              = Shift
rcoulomb                 = 1.2
vdw_type                 = Shift
rvdw_switch              = 0.9
rvdw                     = 1.2
DispCorr                 = No



The equilibration step gives me 10 us/day. However, the MD production step only give me 2 us/day.....

I am just wondering why such huge differences?

Thank you very much.

Albert

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6 years 11 months ago #7251 by riccardo
Replied by riccardo on topic a concern on MD production spped
I haven't really used position restraints myself but seems a pretty larger difference in performance. Are you sure you aren't doing anything else different? Can you check --
or link/post here -- that the mdout.mdp files (the mdp which gmx grompp spits out anytime you grompp) you get in both cases are really equal?

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  • albumns
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6 years 11 months ago #7253 by albumns
Replied by albumns on topic a concern on MD production spped
Now it seems to be all right.

I obtained the .mdp file from Charmm-GUI. To be honest, I didn't find the definition for the position restrain:

-DPOSRES_FC=50 -DBILAYER_LIPIDHEAD_FC=10

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