GROMACS version: 2021.2
GROMACS modification: No
Here post your question
This is the continuation of my previous post on Freeze group: potential energy increasing.
As you suggested (and you are completely right) the issue I have with increasing the potential energy during the simulation is related to not excluding the interaction of the frozen group.
But, the main reason for not excluding the energy groups is that when I do it as:
freezegrps = IAUM freezedim = Y Y Y energygrps =W IAUM energygrp-excl = IAUM IAUM
which I guess is the correct way of doing it, I get an interesting error:
ERROR 1 [file martini_md.mdp]: Energy group exclusions are currently not supported
This is why I had not put the Energy group exclusions in my map file as apparently they are not supported despite being mentioned in the mdp options.
I have also put the whole output of grompp here:
gmx grompp -f martini_md.mdp -c run-short.gro -p topol.top -o run.tpr -r run-short.gro -maxwarn 1 :-) GROMACS - gmx grompp, 2021.2 (-: GROMACS is written by: Andrey Alekseenko Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Gilles Gouaillardet Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2021.2 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/mkhatami/uoft/gromacs/Au-C6-1ao6-1hzh-1d3k/all-elastic/full-structures/80nmbox/006-run-water-freeze Command line: gmx grompp -f martini_md.mdp -c run-short.gro -p topol.top -o run.tpr -r run-short.gro -maxwarn 1 Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'ns_type' Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' Replacing old mdp entry 'xtc_precision' by 'compressed-x-precision' WARNING 1 [file martini_md.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. Setting the LD random seed to -184715285 Generated 844 of the 356590 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'IAUM' Excluding 1 bonded neighbours molecule type 'W' Velocities were taken from a Maxwell distribution at 310 K Analysing residue names: There are: 88663 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... NOTE 1 [file martini_md.mdp]: There are 18642 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) Number of degrees of freedom in T-Coupling group IAUM is 0.00 Number of degrees of freedom in T-Coupling group W is 210060.00 ERROR 1 [file martini_md.mdp]: Energy group exclusions are currently not supported Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K Calculated rlist for 1x1 atom pair-list as 1.286 nm, buffer size 0.186 nm Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.100 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file martini_md.mdp]: This run will generate roughly 4275 Mb of data There were 2 notes There was 1 warning ------------------------------------------------------- Program: gmx grompp, version 2021.2 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2389) Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------