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

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 
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 A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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