[gmx-users] amber force field in Gromacs

[Mark Abraham]

servaas wrote:
> Hello,
> 
> I tried using the amber force field in GROMACS. I proceeded as follows:
> Determined my parameters with RED/ANTECHAMBER/tleap converted them with amb2gmx.pl 
> (or with acpypi, problem is the same) to gromacs coordinate and topology files. It concerns a modified nucleotide. I minimized with steepest descent, everything was fine. 
> When I tried running a simulation in single precision with this .mdp file (only nucleotide without solvent):
> 
> integrator       = md
> 
> dt               = 0.002
> nsteps           = 250000
> nstcomm  = 1
> 
> ;output
> nstxout   = 1
> nstvout   = 1
> nstfout   = 0
> nstlog    = 500
> nstenergy = 1
> 
> nstlist          = 10
> ns_type          = grid
> rlist            = 1.2
> coulombtype      = PME
> rcoulomb         = 1.2
> vdwtype          = cut-off
> rvdw             = 1.2
> 
> fourierspacing   = 0.12
> pme_order        = 4
> ewald_rtol       = 1e-5
> 
> ;constraints
> constraints      = all-bonds
> 
> 
> ;  temperature coupling is on
> Tcoupl              = v-rescale
> tau_t               = 0.1
> tc-grps             = system
> ref_t               = 300
> 
> pcoupl              = no
> 
> I get LINCS errors and eventually a crash. Now I tried running the same simulation with the same force field parameters in amber and everything was fine. 
> I also ran the calculation in GROMACS with double precision here again everything was fine... I also tried running a small nucleic acid fragment (so no modified parameters here) 
> that I created in  tleap and converted to GROMACS again this crashes with lincs errors in GROMACS. When I look at the trajectories it is the O4' of the ribose who clashes with the O3'. 
> 
> The fact that I still get this problem with non modified amber parameters makes me thing there is something wrong with my .mdp file to run with amber FF, any suggestions?
>  Strange also that double precision seems to work just fine....

When switching precision, are the starting configurations different? 
What are the actual command lines in your procedures?

Mark