GROMACS version:2018
GROMACS modification: NO
Hello!
I am currently trying to run an MD simulation of 1 small drug molecule with a DOPC lipid bilayer using the united-atom Berger lipid FF. I generated the topology using PRODRG server using the GROMOS 53a6 forcefield and corrected the charges by restrained electrostatic potential fit (RESP).
I was able to run Energy Minimization with the energy converging just fine but I get the following error when I try to run NVT eqilibration
WARNING 1 [file topol.top, line 42]:
There are atoms at both ends of an angle, connected by constraints and
with masses that differ by more than a factor of 13. This means that
there are likely dynamic modes that are only very weakly coupled. To
ensure good equipartitioning, you need to either not use constraints on
all bonds (but, if possible, only on bonds involving hydrogens) or use
integrator = sd or decrease one or more tolerances:
verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >=
4 or SHAKE tolerance <= 1e-05
I know the issue is in the nvt.mdp file due to setting the constraints to constraints= all-bonds which is required for gromos force field.
I also believe the issue might be with this certain angle
[ angles ]
; ai aj ak fu c0, c1, …
1 2 3 2 109.5 425.0 109.5 425.0 ; CAK NAJ HAQ
where 1 ,2 ,3 are
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 MOL CAK 1 0.139860 15.0350
2 NL 1 MOL NAJ 1 -0.607922 14.0067
3 H 1 MOL HAQ 1 0.306988 1.0080
where the mass of 3 and 1 differs by a factor greater than 13.
Could anyone give me any tips on how I can resolve this issue? I have changed the constraints = h-bonds and I stopped getting that error but i know GROMOS forcefield requires all bonds to be constrained.
Any help would be greatly appreciated! Thank you!