Hello I just performed the ´pulling/window generation over again´after correcting the WARNING 1 being set off during my preparing of my umbrella sampling (please see-thread) and ran a new:
gmx trjconv -s pull.tpr -f pull.xtc -o conf.gro -sep but did not generate a new summary_distances.dat?
In order I ran:
gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -r npt.gro -n index.ndx -t npt.cpt -o pull.tpr
gmx mdrun -deffnm pull -pf pullf.xvg -px pullx.xvg
and then saved the Bash Script in my working directory as:
get_distances.sh
and then ran:
gmx trjconv -s pull.tpr -f pull.xtc -o conf.gro -sep
but do not have a new summary_distances.dat in my working directory after this sequence of commands, suggestions please?
I am not sure if my final input of:
gmx trjconv -s pull.tpr -f pull.xtc -o conf.gro -sep
is calling the saved Bash Script setting in the working directory, I know that I had inquired about this response earlier and my understanding is that via the above gmx trjconv the bash script should be automatically executed but can not see this.
Much Thanks:)
Joel
You have to run the get_distances.sh script to compute distances. trjconv generates coordinate files, it doesn’t calculate distances. That’s done in later steps. The content of get_distances.sh shows you everything that is done to generate the text file with the distances.
Hi Justin and thank you for your kind update, may I respectfully ask specifically what is the line of code to execute get_distances.sh (i.e. how do I run get_distances.sh)?
-
gmx trjconv -s pull.tpr -f pull.xtc -o conf.gro -sep
-
what would be what next line of coding to execute get_distances.sh? This is what is not clear to me, sorry for the inconvenience.
Thanks:)
Just like I told you how to run the bash script in another topic: Tutorial2 (Membrane) Bash Script Inquiry?
Hi ah ok I remember, ok will do thanks a bunch:)
Hello after fixing my past WARNING with the -D prefix and the topology POSRES_B files I started over and after running the preparation for the umbrella sampling a third time I got the same error that I originally had for the below command:
gmx grompp -f npt_umbrella.mdp -c conf195.gro -p topol.top -r conf195.gro -n index.ndx -o npt3.tpr
ERROR 1 [file npt_umbrella.mdp]:
When the maximum distance from a pull group reference atom to other atoms
in the group is larger than 0.5 times half the box size a centrally
placed atom should be chosen as pbcatom. Pull group 1 is larger than that
and does not have a specific atom selected as reference atom.
Accordingly would you now recommend that I re-install a clean version of the Gromacs 2020.3 to try and resolve this problem? Or would you recommend a clean version of the 2018 version since you had mentioned that this is the version that this tutorial was based on?
i.e. my third run had precipitated the below warning indicating the install of a different gromacs version indicated above.
WARNING 1 [file topol.top, line 56]:
The GROMOS force fields have been parametrized with a physically
incorrect multiple-time-stepping scheme for a twin-range cut-off. When
used with a single-range cut-off (or a correct Trotter
multiple-time-stepping scheme), physical properties, such as the density,
might differ from the intended values. Since there are researchers
actively working on validating GROMOS with modern integrators we have not
yet removed the GROMOS force fields, but you should be aware of these
issues and check if molecules in your system are affected before
proceeding. Further information is available at
https://redmine.gromacs.org/issues/2884 , and a longer explanation of our
decision to remove physically incorrect algorithms can be found at
https://doi.org/10.26434/chemrxiv.11474583.v1 .
- my box vectors for conf195.gro were 6.59015 4.38204 12.05514
Much Thanks:)
I suppose new checks are in place in the 2020 version and you will have to choose a PBC reference atom that is closer to the geometric center of each group to carry this out. I haven’t tried any of that and will again remind you that if you are doing my tutorials, the expectation is that you are using version 2018, for which they work cleanly. It is advisable to use the specified version to understand the process and then use that knowledge to troubleshoot anything else you run into.
Hello Justin thank you for your kind update and ok will do:)
@jalemkul I had US files that I tested with GROMACS 2020.4 version. The same MDP file which worked on the 2018 version was used.
This gives the following error:
When the maximum distance from a pull group reference atom to other atoms in the group Is larger than 0.5 times half the box size a centrally placed atom should be chosen as pbcatom. Pull group 1 is larger than that and does not have a specific atom selected as reference atoms.
The same error is not coming when I use GROMACS 5.1.4 version.
This is just an update.