GROMACS version: 2020
GROMACS modification: No
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Hi,
I am getting this fatal error whenever I try to generate my tpr file to run energy minimization.
From my understanding, it’s telling me it can’t read/find the forcefield directory? So I tried moving it to a different folder but I still can’t get past it.
Appreciate any suggestions/advice.
Thank you.
Cynthia
for oplssa, the forcefield file is usually in the oplsaa folder in the shared library. see the below the format for calling in the .top file.
#include “oplsaa.ff/forcefield.itp”
PS: if you generate your .top file using gmx pdb2gmx command, that shouldnt be a problem
Please provide the exact error message you received.
The message reads:
Fatal error:
Topology include file “/home/cynthia/Documents/Graphene sheet/gromos54a7.ff/forcefield.itp”
My working directory is ‘Graphene sheet’ where the ‘gromos54a7.ff’ forcefield folder is located which contains the ‘forcefield.itp’ file.
My GROMACS is located in /usr/bin/gmx…could this be why? Does the forcefield have to read from the gmx directory?
The message reads:
Fatal error:
Topology include file “/home/cynthia/Documents/Graphene sheet/gromos54a7.ff/forcefield.itp”
My working directory is ‘Graphene sheet’ where the ‘gromos54a7.ff’ forcefield folder is located which contains the ‘forcefield.itp’ file.
My GROMACS is located in /usr/bin/gmx…could this be why? Does the forcefield have to read from the gmx directory?
I suspect there is more to the error message. A file location is not a fatal error. Please provide the whole error. It could be there is a problem reading the file because you’re using spaces in your directory name, but that shouldn’t be an issue, I don’t think.
No, force field directories can be anywhere.
In case anyone else comes across this looking for a solution, here is what worked for me.
I’m new to Gromacs, but I ran into a similar issue. I resolved it by removed the first “/” in the include statement.
ie. Having the line
#include “/toppar/martini_v2.2.itp”
in my .top file resulted in the same fatal error you described, and this was fixed by replacing this include statement with
#include “toppar/martini_v2.2.itp”
It seems like the file path in your include statement began with “/” as well. Your fatal error shows the file path as “/home/…”.
If you have the file martini_v2.2.itp in folder toppar, there won’t be any error. Your current command will work if toppar is a folder that’s available in your pwd. / means steps into the following while …/ means take a step backward from this pwd.
If you copy the file (martini_v2.2.itp) to your pwd, you can replace the path with just #include “martini_v2.2.itp” or go to where you have the file, type pwd and modify it as follows: #include “put-path-here/martini_v2.2.itp”
Hello sir ,
I am new for molecular dynamics simulation. so, i have some doubt about running simulation using gromacs. whats is the optimum timestep for NVT and NPT running. if, 100ps running is enough for equilibration (100ps given in the gromacs tutorial).
Thanking you
“Time step” is the value of dt (the integration time step in the simulation), so that refers to something very specific. Be careful with terminology!
As far as the time required to equilibrate, there is no real answer to this. You need to equilibrate for sufficient time that all the relevant thermodynamic properties have stabilized. For reasonably small, simple systems, this may be very quick, but for large, heterogeneous systems, it can take somewhat longer.