GROMACS version: 2021.4-Ubuntu-2021.4-2
GROMACS modification: No
Hi to everyone,
I’m really new to gromacs and I have a question about the constraint-algorithm.
So I want to simulate this polymer that I made up from the monomer paramters. I made the .itp and .gro files carefully paying attention to all. I assign to all the atom an opls_XXX code (that was not alredy occupied) and ad unique serial number (from 1 to let’s say 368)
Using those two input files I manege to solvate and putting ions to equilibrate the charge. I also manage to run a minimization.
After this I want to run a small nvt equilibration where I want to use constraint-algorithm for the h-bonds.
And now comes my questions:
If I use LINCS I have to use a very small timestep (0.1fs or 0.5fs) otherwise I obtain this warning
"
Step 5608, time 5.608 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000004, max 0.000044 (between atoms 46 and 11)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
18 17 77.1 0.1090 0.1090 0.1090
22 21 33.0 0.1090 0.1090 0.1090
"
That correspont to a C-H bond. I can understand this since it’s a complicated and long polymer so it make sense that it need a small timestep.
So in this case with small timestet the simulations goes on without any particula problem.
In another case I tried to use the SHAKE algorithm
and I keep running into the same error
"
Fatal error:
Double entries in block structure. Item 368 is in blocks 10 and 9
Cannot make an unambiguous inverse block.
"
I dind’t fully understand what that menas but I undestand that was something wrong with topology.
I checked the topology miltiple times and all seems fine to me.
In the .gro file every atom ha a unique number. The only thing is that I buil the topology in order to have atom of the backbone and that belongs to the same monomer to have the same name (of course element-wise like all the backbone oxygen ar called OB etc…)
Can somenone please help me ?
sorry if it’s a silly question I’m new to this software.
Many thanks in advance