GROMACS version:GROMACS 2021.7-plumed-2.9.0
GROMACS modification: No
Hello, I want to find out the free energy of turning on a charge in my polymer. The polymer is a simple 32 bead polymer with one charged monomer.
When I am running my simulation for different values of lambda which scales only the charged interactions, I am getting the error:
tal error:
There are 2 perturbed non-bonded pair interactions beyond the pair-list cutoff
of 1.098 nm, which is not supported. This can happen because the system is
unstable, or because intra-molecular interactions are excluded. The latter
case is usually triggered by the use of couple-intramol=no. The issue can be
either due to a too small box, which can cause a molecule and its periodic
image to end up in the pairlist. In this case increase the box size. Or it can
happen because interactions at distances longer than rlist are excluded, in
which case you can try to increase nstlist or rlist to avoid this.
I think what I gather from this is that there are two monomers in my polymer which are too far as per the cut-off, but I dont know how to fix this.
How can I transform charge of only one atom in a molecule? I think this is one possible solution.
Any help will be appreciated.
Here is how I am running my simulation:
$exe grompp -f EM_noFEP.mdp -c system.gro -p correct.top -o 6_min.tpr -n index.ndx -maxwarn 1
$exe mdrun -nt 16 -deffnm 6_min
$exe grompp -f EM.mdp -c system.gro -p correct.top -o 6_min.tpr -n index.ndx -maxwarn 1
$exe mdrun -nt 16 -deffnm 6_min
$exe grompp -f NVT.mdp -c 6_min.gro -p correct.top -o 7_nvt.tpr -n index.ndx -maxwarn 1
$exe mdrun -nt 16 -deffnm 7_nvt
$exe grompp -f NPT.mdp -c 7_nvt.gro -p correct.top -o 8_npt.tpr -n index.ndx -maxwarn 1
$exe mdrun -nt 16 -deffnm 8_npt
$exe grompp -f MD.mdp -c 8_npt.gro -n index.ndx -p correct.top -maxwarn 1 -o
$exe mdrun -nt 16 -plumed plumed.dat -s topol.tpr -deffnm traj_radg
I am including the relevant forcefield details here:
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
P C 6 14.0270 0.00 A 0.400 1.0
PX C 6 14.0270 0.00 A 0.400 1.0
PA C 6 14.0270 -0.7 A 0.400 1.0
PB C 6 14.0270 +0.7 A 0.400 1.0
BUF 11 12.000000 0.000 A -0.250000000000 4.00000
[ moleculetype ]
; molname nrexcl
BUF 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 BUF 1 BUF BUF 1 0
I am attatching all my input files in this post.
Thank you.
correct.top (5.9 KB)
EM.mdp (3.2 KB)
EM_noFEP.mdp (3.2 KB)
MD.mdp (4.0 KB)
NPT.mdp (4.1 KB)
NVT.mdp (3.6 KB)