[gmx-users] DNA splitting in simulations

[João Henriques]

Hi!

Your mdp file doesn't tell the engine to apply the restraints during the
simulation... You need to specify:
define = -DPOSRES

Also, didn't Justin already warn you about using separate temperature
couplings for every component of your system?

Please check the "What Not To Do" section under:
http://www.gromacs.org/Documentation/Terminology/Thermostats

Best regards,
João

On Tue, Jun 27, 2017 at 11:22 AM, Sergio Manzetti <
sergio.manzetti at fjordforsk.no> wrote:

> Hi, I Have run a DNA piece in a box of 7 7 7 , with NaCl ions
> neutralizing, as discussed earlier. The simulation went fine without any
> errors, however it turns out the DNA strands separate. The position
> restraints made by pdb2gmx using the AMBERDB ISTN ff are not working ?
>
> This is the posres file:
> In this topology include file, you will find position restraint
> ; entries for all the heavy atoms in your original pdb file.
> ; This means that all the protons which were added by pdb2gmx are
> ; not restrained.
>
> [ position_restraints ]
> ; atom type fx fy fz
> 1 1 1000 1000 1000
> 3 1 1000 1000 1000
> 6 1 1000 1000 1000
> 8 1 1000 1000 1000
> 9 1 1000 1000 1000
> 11 1 1000 1000 1000
> 12 1 1000 1000 1000
> 14 1 1000 1000 1000
> 15 1 1000 1.....................
>
>
> and here is the simulation mdp.
>
>
>
>
> itle = DNA in water stabilization
> cpp = /lib/cpp
> include = -I../top
> define =
> integrator = md
> dt = 0.002
> nsteps = 5000000
> nstxout = 5000
> nstvout = 5000
> nstlog = 5000
> nstenergy = 300
> nstxout-compressed = 300
> compressed-x-grps = DNA SOL NA CL
> energygrps = DNA SOL NA CL
> nstlist = 20
> ns-type = grid
> rlist = 0.8
> coulombtype = PME
> rcoulomb = 0.8
> rvdw = 0.8
> tcoupl = V-Rescale
> tc-grps = SOL DNA NA CL
> tau-t = 0.1 0.1 0.1 0.1
>
>
>
> Note that GMX gromp wanted 4 groups at tc_grps and tau_t, otherwise it
> wouldn't proceed.
>
>
> Thanks!
>
>
> Sergio Manzetti
>
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