Hi Justin

I obtained the following error with the following command and the mdp mentioned 
below 

gmx mdrun -s 1_OGNG_GLYCAM_SPE_GMX.tpr -rerun 1_OGNG_Amber.pdb

Thank you 

St├ęphane

------------------------------------------------------------------
Program:     gmx mdrun, version 2018.1
Source file: src/programs/mdrun/runner.cpp (line 736)

Fatal error:
The .mdp file specified an energy mininization or normal mode algorithm, and
these are not compatible with mdrun -rerun

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

>> You also shouldn't use a minimizer when doing a zero-point energy. Use the 
>> md integrator.
OK I try your suggestion

----------------------------------------------------------------------

And the mdp 

Message: 1
Date: Thu, 23 Apr 2020 06:18:33 -0400
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GROMACS mdp file for doing a single point
        energy after acpype conversion
Message-ID: <28a2dc8e-20e9-abee-4b10-0f3cceb4f...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



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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