[gmx-users] DPOSRES not working

Hermann, Johannes J.Hermann at lrz.tu-muenchen.de
Thu Sep 7 11:18:37 CEST 2017


Dear Sergio,

how did you define the position restrain in your topology? Check your 
topology and position restrain file.

All the best

Johannes


On 07.09.2017 11:07, Sergio Manzetti wrote:
> Hello, I am running 5 simulations with the given mdp:
>
> title = DNA in water stabilization
> cpp = /lib/cpp
> include = -I../top
> define = -DPOSRES
> integrator = md
> dt = 0.002
> nsteps = 10000000
> nstxout = 5000
> nstvout = 5000
> nstlog = 5000
> nstenergy = 300
> nstxout-compressed = 300
> compressed-x-grps = PRB SOL NA CL DNA
> energygrps = PRB SOL NA CL DNA
> nstlist = 10
> ns-type = grid
> rlist = 0.8
> coulombtype = PME
> rcoulomb = 0.8
> rvdw = 0.8
> tcoupl = V-Rescale
> tc-grps = System
> tau-t = 0.1
> ref-t = 310
> Pcoupl = No
> tau-p = 1.0
> compressibility = 4.5e-5
> ref-p = 1.0
> gen-vel = yes
> gen-temp = 310
> gen-seed = 17527
> constraints = all-bonds
>
>
> and still, the DNA splits into two....
>
> Any ideas what could be wrong?
>
> Thanks
>
> Sergio Manzetti
>
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-- 
______________________________________
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
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Email: j.hermann at lrz.tum.de
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