[gmx-users] umbrella-drug

[Justin A. Lemkul]

parto haghighi wrote:
> Dear gmx-users
> I am working on lipid membrane+drug system.I should do umbrella
> sampling in this procedure:
> 1.cat drug and lipid
> 2.energy minimization
> 3.run npt
> 4.run md_pull
> I want to pull drug into the membrane but gromacs pushes the drug to
> the sides of box.and this result is independent of drug location
> Also I have used 500 ps for my simulation time but when I use ngmx to
> see the process,it runs only 56 ps.why?

Perhaps the system crashed?

> What can I do when I want to move drug to the bilayer?

Set the .mdp options correctly.  You haven't supplied any relevant information 
as to how you are attempting to pull, but clearly something is wrong with your 
settings.

-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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