I am running an MD simulation on DNA structure with DEG molecules as co-solvent. My forcefields for DNA and DEG are amberbsc1 and GAFF respectively. I generated my DEG topology files using acpype and I modify it to run in GROMACS. During the NVT run, I generate a fatal error.
Program: gmx grompp, version 2018.8
Source file: src/gromacs/gmxpreprocess/readir.cpp (line 2749)
Fatal error:
Atom 759 in multiple T-Coupling groups (2 and 3)
What are the possible problem/s during the NVT run?
Your groups are incorrectly set up, but without an actual description of what you did to create the index groups and what is in the .mdp file, it’s not possible to say exactly where the problem is. Something in the selection overlapped, that much is clear.
What is OGS? What is in your .mdp file? Please provide significantly more detail about what you’ve done, what your groups contain, how you generated them, etc.
The “OGS” residue is a residue that I’ve added in the residuetypes.dat. This will represent the organosolvents. The organosolvent coordinate and topology files were created by using antechamber and acpype tools.
Here is my intial temperature coupling on my nvt.mdp file:
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = DNA Water_and_ions ; three coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 323.15 323.15 ; reference temperature, one for each group, in K
As you can see, I did not include the OGS at the tc-grps. OGS is present on my coordinate file so I need to add OGS on the .mdp file. This will be like this:
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = DNA Water_and_ions OGS ; three coupling groups - more accurate
tau_t = 0.1 0.1 0.1 ; time constant, in ps
ref_t = 323.15 323.15 323.15 ; reference temperature, one for each group, in K
Note: I modified my residuetyes.dat on my Gromacs. That’s why I can run topology files with OGS residue.
Hello, may I know if you get a solution for this error? if yes, can you please let me know what you did, because I am facing the same issue I have peptide water and cyclohexane. So nvt.mdp file
tc-grps=peptide_chx and_water; three coupling groups-more accurate
tau_t=0.1 0.1 0.1
ref_t=300 300
fatal error showing what can i do i tried different ways but it is not working.
You already see the error as suggested in the error message:
tc-grps=eptide_chx and_water ; 2 groups
tau_t=0.1 0.1 0.1 ; 3 groups
ref_t=300 300 ; 2 groups
take away a value of tau_t so you are having two groups per line and you are defining correctly the thermostat. Also please don’t ask the same question multiple times in multiple threads!
