[gmx-users] Atom positions change between topology generation and NVT equilibration

[Christian Blau]

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
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> 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.
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> Best,
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> Max
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> From: <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Max Winokan <mwinokan at me.com>
> Reply to: <gmx-users at gromacs.org>
> Date: Wednesday, 29 April 2020 at 1:36 PM
> To: <gmx-users at gromacs.org>
> Subject: [gmx-users] Atom positions change between topology generation and NVT equilibration
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> Dear GMX-Users,
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> 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.
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> After generating the topology with pdb2gmx I get the structure file (gc.gro) with the configuration seen below (after_pdb2gmx.jpg):
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> 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):
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> 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.
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> Thank you and best regards,
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> Max Winokan
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> PhD Candidate in Theoretical Physics
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> Leverhulme Quantum Biology Doctoral Training Centre University of Surrey
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> GU2 7XH Guildford
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> United Kingdom
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> Office: 03AZ04
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> Email: m.winokan at surrey.ac.uk
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