Dear GMX-Users,


I am running some simulations of unsolvated DNA base pair dimers, with a 
topology generated from a structure previously optimised with quantum 
mechanical models. Because these structures have been highly-optimised it is 
important that Gromacs begins the MD with these atom positions.


After generating the topology with pdb2gmx I get the structure file (gc.gro) 
with the configuration seen below (after_pdb2gmx.jpg):



This configuration matches the optimised input structure. However, when I 
examine the trajectory (.trr) produced by running my NVT simulation (the MDP 
file for which is attached), the first timestep is very different from the 
input gc.gro structure, as seen below (first_nvt_frame.jpg):



The discrepancy is largest with the hydrogen atoms (which are not constrained 
of course), but all the atoms have been slightly shifted from the input 
configuration. Please could someone fill me in on the source of these position 
changes, and how I can modify my methods to avoid these.


Thank you and best regards,


Max Winokan


PhD Candidate in Theoretical Physics

Leverhulme Quantum Biology Doctoral Training Centre University of Surrey

GU2 7XH Guildford

United Kingdom

Office: 03AZ04



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