Hi Max,
In the .mdp file that you uploaded you are using
constraints = h-bonds ; bonds involving H are constrained
Is that the right file? Otherwise running without these constraints
might help.
On the off-chance that happened: not using -ignh in grompp avoids
re-placement of hydrogens.
Best,
Christian
On 2020-04-29 13:49, Max Winokan wrote:
My apologies for the missing images. Hopefully they are available along with
the MDP in the following link:
https://www.dropbox.com/sh/dnqz7c049f4tvw3/AAAGGZ8AF-ddQpBjD-QVf0OAa?dl=0
If anyone knows what could be going on, please let me know. Essentially the
atom positions in the first NVT step are very different to the input topology,
see my original email below.
Best,
Max
From: <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Max Winokan
<mwino...@me.com>
Reply to: <gmx-us...@gromacs.org>
Date: Wednesday, 29 April 2020 at 1:36 PM
To: <gmx-us...@gromacs.org>
Subject: [gmx-users] Atom positions change between topology generation and NVT
equilibration
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
Email: m.wino...@surrey.ac.uk
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