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

[ABEL Stephane]

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 

Stéphane

------------------------------------------------------------------
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 <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] GROMACS mdp file for doing a single point
        energy after acpype conversion
Message-ID: <28a2dc8e-20e9-abee-4b10-0f3cceb4fdcc at 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