So the command I want execute is in this short little document:
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy,
being $ gmx mdrun -s input.tpr -rerun configuration.pdb
The issue is that while I able to use a special forcefield, create a topology file, and a .gro file with $gmx pdb2gmx ... -water none", I am not able to create the .tpr file.
I had high hopes that by using grompp with this .mdp file, I could create the .tpr file, and then do an mdrun. But I'm getting a lot of errors which I don't understand with respect to Verlet Lists and incompatibility with the latest version of Gromacs 5.1.3.
http://www.shourjya.thinkbiosolution.com/md-simulation-in-gas-phasevacuum-with-gromacs/
It would be easy if I was doing a solvation. But I need to do this vacuum, and I'm surprised why that's so difficult. Is it possible to create a .tpr file without an .mdp file? My superior would like me to figure out a sequence of commands that works and then we can loop through several files, and do some energy statistics.
Please. Would someone please help me?
Thank you.
Looks like you're using a version of our CHARMM36 port that has a typo. Get the latest:
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
I figured it out. I changed the cutoff scheme from Verlet to group, and I modified any implicit referencing of solvent as SOL in the mpi template files. That was literally all I had to do. Wow!
Justin Lemkul, you are one of the writers of Gromacs. Nice to meet you! What are the main differences between group and Verlet as cutoff-schemes? Verlet is the default cutoff-scheme in the latest version of Gromacs. The error message seems to tell me that in Verlet nstlist has to be larger than zero which makes me realize that on page 197 of the Gromacs manual nstlist = 0 for vacuum simulations. Are there exceptions to this?
Citation: M.J. Abraham, D. van der Spoel, E. Lindahl, B. Hess, and the GROMACS
development team,
GROMACS User Manual version 5.0.7
, www.gromacs.org
(2015)
Vacuum simulations are a special case, in which neighbor lists and cutoffs are basically thrown out. All interactions are considered (rlist = rcoulomb = rvdw = 0) and the neighbor list is fixed (nstlist = 0). This is of course very different from a condensed-phase simulation.
For more on group vs. Verlet, see manual section 3.4.2 and http://www.sciencedirect.com/science/article/pii/S0010465513001975
Justin, I would like to add a perl script to a Gromacs repository of scripts to
perform a single calculation on multiple proteins. The script is a loop and if you look at the documentation, you can see that it's easy to make slight changes to the script to fit a user's needs.
I think that this would help a lot of users: https://github.com/AAdragon/Biological_Scripts/blob/master/point_energy_calc_of_multiple_proteins.pl
How can I add it to the gromacs repository of scripts?
You can upload a user contribution on gromacs.org or publicize the availability of your github link on the gmx-users mailing list.
Thankyou Justin for the information.
I have a very basic question of doing vacuum md simulation of my polymer molecule. Shall I put the position restraint on my polymer (solute) molecule while doing vacuum MD simulation ? Is the pbc set to no with all cut-off's set to zero during vacuum simulation of a solute ?
In my case solute is polymer chains.
While removing position restraint on my molecule with no pbc condition in vacuum simulations, I am observing my solute flying out somewhere after starting of nvt run. Why ? Please calrify
When I set nstlist=0 (and rlist=rcoulomb=rvdw=0.0) I get an error saying:
"Domain decomposition does not work with nstlist=0"
Is there a way to turn off DD?
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