From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Tue Sep 15 2015 - 18:58:52 CDT
In case of graphene sheet you can turn ON these terms in configuration file during NVT run.
useGroupPressure yes
useFlexibleCell yes
useConstantArea yes
Thanks
Abhi
Abhishek Tyagi
PhD Student
Chemical and Biomolecular Engineering
Hong Kong University of Science and Technology
Clear Water Bay, Hong Kong
________________________________
From: upayan baul <margheritan22_at_gmail.com>
Sent: Tuesday, September 15, 2015 7:57 PM
To: Abhishek TYAGI
Cc: Namd Mailing List
Subject: Re: namd-l: simulating graphene sheets (with bonds across boundaries) with water
Dear Abhishek,
Thank you for your response.
Using larger PBC did not cure the issue. Increasing PBC by 2A along X and Y directions resulted in
patch grid error (Periodic cell has become too small for original patch grid). The PME grid sizes were
also set up in accordance with system dimensions (60 along all axes with system dimensions < 55 along
each of the axes).
I had tried holding the graphene atoms fixed but that had resulted in the following errors:
Fixed atoms without constant area : simulations crashed (owing to fixed atoms at boundaries?)
Fixed atoms with constant area and flexible cell : system expands unusually along Z.
I tried restraining the graphene atoms (along Z) as suggested by you using
constraints on
consexp 2
consref fixed_GRA_beta_50.pdb
conskfile fixed_GRA_beta_50.pdb
conskcol B
selectConstraints on
selectConstrZ on
and this seems to be working. Further, the sheets are uniformly flat without impropers, but slightly rough
with the same. So I shall be simulating without improper interactions.
Regards,
Upayan
On Tue, Sep 15, 2015 at 5:58 AM, Abhishek TYAGI <atyagiaa_at_connect.ust.hk<mailto:atyagiaa_at_connect.ust.hk>> wrote:
Dear Upayan,
In your work you may try fixing the graphene sheet i hope you know how to do it or you may restrain them, and for the error, it seems like that your box is small, try to use bigger pbc than your original dimensions, have a look on PME too.
Thanks
Abhi
Abhishek Tyagi
PhD Student
Chemical and Biomolecular Engineering
Hong Kong University of Science and Technology
Clear Water Bay, Hong Kong
________________________________
From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> <owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> on behalf of upayan baul <margheritan22_at_gmail.com<mailto:margheritan22_at_gmail.com>>
Sent: Monday, September 14, 2015 7:59 PM
To: Namd Mailing List
Subject: namd-l: simulating graphene sheets (with bonds across boundaries) with water
Dear NAMD users,
Sorry for the long mail. I wished to let you know the things I have already tried.
I wish to simulate a system with stacked graphene sheets (with bonds across
boundaries in XY) in water in an NPT ensemble. The initial configuration of the
system is shown in.
https://www.imsc.res.in/~upayanb/graphene_namd/no_improper/graphene_wat_init.jpg
As an ideal test case, I wish to retain the planarity of the graphene sheets to as great a
degree as possible.
I am using atom type CA and corresponding parameters for bond, angle, dihedral
and nonbonded interactions from CHARMM protein parameters (par_all22_prot). I
have tried small simulations
without impropers : (based on Kenno's suggestion that impropers only over-rigidify 6
membered ring structures
http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=33962 )
which resulted in a configuration as shown (periodic) in:
https://www.imsc.res.in/~upayanb/graphene_namd/no_improper/graphene_wat_fin.jpg
with impropers: (based on Axel's suggestion (though this might be for the finite-sheet case,
I might have misunderstood) to include impropers for planarity
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19410.html )
which resulted in a configuration as shown in:
https://www.imsc.res.in/~upayanb/graphene_namd/with_improper/graphene_wat_fin_impropers.jpg
in which I have used an additional improper interaction of
!atom types Kpsi psi0
CA CA CA CA 10.0 0 0.00
Neither of the two cases are resulting in highly planar structures. Increasing Kpsi is resulting
in more puckered structures (for Kpsi > 20, the simulations are crashing with statements like
ERROR: Atoms moving too fast; simulation has become unstable (3 atoms on patch 1 pe 0).
How can I obtain a more planar configuration for graphene? I have tried fixed atom simulations.
In NPT, without constant area such simulations crash owing to fixed atom at boundaries. With
constant area, the system expands in the Z- direction, causing the water to move away from the
surface.
Thanking you,
Upayan
S.R.F., Physics
IMSc
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