GMX bar in choosing molecule type for DNA simulation

User discussions
1

GROMACS version: 2018.8
GROMACS modification: Yes

Hello,

I want to run gmx bar for my free energy analysis. My molecule that I need to analyze is a 12-bp DNA. Below is the topology file.
###############################################################################
Include forcefield parameters
#include “amber99bsc1.ff/forcefield.itp”

; Include chain topologies
#include “1bna_DNA_chain_A.itp”
#include “1bna_DNA_chain_B.itp”

; Include water topology
#include “amber99bsc1.ff/tip3p.itp”

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include “amber99bsc1.ff/ions.itp”

#include “DEG_GMX.itp”

[ system ]
; Name
DNA (5’-D(CPGPCPGPAPAPTPTPCPGPCPG)-; 3 3’) in water

[ molecules ]
; Compound #mols
DNA_chain_A 1
DNA_chain_B 1
DEG 35
SOL 3619
NA 34
CL 12
#############################################################################

As far as I can understand, you can only analyze one molecule type for gmx bar analysis. (An example is shown below)
###########################################################################
free_energy = yes
init_lambda_state = 0
delta_lambda = 0
calc_lambda_neighbors = 1 ; only immediate neighboring windows
couple-moltype = DNA_chain_A ; name of moleculetype to decouple
couple-lambda0 = vdw ; only van der Waals interactions
couple-lambda1 = none ; turn off everything, in this case only vdW
couple-intramol = no
##########################################################################

I want to analyze the whole DNA itself, not the A-chain or B-chain alone. What should I do in order to run gmx bar analysis using both DNA chains?

2

Hi,
In the pre-processing phase, you can define DNA strands as one molecule using the
pdb2gmx with the option -merge interactive

Best regards
Alessandra

3

Thank you. I was thinking to analyze each chain but using the pdbgmx -merge option, I can instantly analyze my DNA structure.

Again, a big thanks for your help.