[gmx-users] DNA splitting in simulations

[Sergio Manzetti]

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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