[gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion

[Justin Lemkul]

On 4/23/20 5:42 AM, ABEL Stephane wrote:
> Deal all,
>
> I am using acpype to convert a set of glycolipids modeled with the GLYCAM06 force fiedl  into the GROMACS format. acpype works well for this task. But I would like to check if the conversion is correctly done by performing single point energy (SPE) calculations with Amber and GROMACS codes and thus computes the energy differences  for the bonded and non bonded terms
>
> For the former test I using the prmtop and inpcrd files generated with tleap and sander with the minimal commands below
>
> | mdin Single point
> &cntrl
> imin=0,
> maxcyc=0,
> ntmin=2,
> ntb=0,
> igb=0,
> cut=999
> /
>
> But For GROMACS vers > 5.0 and 2018.x , I did not find the equivalent mdp parameters that can be used for doing the same task. I I used  the minimal file below The bonded energy terms are very similar between the two codes but not the non bonded terms
>
> integrator  = steep         ; Algorithm (steep = steepest descent minimization)
> emtol       = 1000.0        ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
> emstep      = 0.01          ; Minimization step size
> nsteps      = 0           ; Maximum number of (minimization) steps to perform (should be 50000)
>
> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
> nstlist         = 1         ; Frequency to update the neighbor list and long range forces
> cutoff-scheme   = Group   ; Buffered neighbor searching
> ns_type         = grid      ; Method to determine neighbor list (simple, grid)
> coulombtype     = Cut-off   ; Treatment of long range electrostatic interactions
> rcoulomb        = 0       ; Short-range electrostatic cut-off
> rvdw            = 0       ; Short-range Van der Waals cut-off
> rlist           = 0
> pbc             = no       ; P
> continuation = yes
>
> I also also notice that a tpr generated with this mdp can not be used with -rerun argument so how I can compute a SPE equivalent to Sander

Why is it incompatible with mdrun -rerun? Do you get an error?

You also shouldn't use a minimizer when doing a zero-point energy. Use 
the md integrator.

-Justin

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Justin A. Lemkul, Ph.D.
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