[gmx-users] weird output from simultions of a protein between two sheets

[Zuzana Benkova]

Dear Justin,

thank you for your prompt response. I will answer your questions step by step.

Is this just in the final coordinate file? Are coordinates in the 
trajectory correct when visualized?

No, I converted all compressed trajectories to gro format and this outputs are identical in all trajectories. When I visualize the trajectory, I can see it as well. The atoms are placed in apices of boxes (1x1x1).


Are you sure you don't want to remove artificial contributions to COM 
motion? This is unusual for a periodic system.

I am not sure. If I leave the Linear option does the correction apply to all system even though I freeze the coordinates of graphene sheets? Anyway, I have just performed the same simulation with comm-mode = Linear and the problem persists. 

Saving output every step is unnecessary (because you will be skewing 
your statistics with completely correlated frames) and also will 
severely degrade the performance of your simulation.

Thank you for this notification. I reduce the frequency when I do equilibration and production run. I do block averages. I have saved the data every step because I tried to trace the problem.

Greetings

Zuzana
 



----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: "gmx-users" <gmx-users at gromacs.org>
Sent: Friday, April 17, 2020 1:48:28 PM
Subject: Re: [gmx-users] weird output from simultions of a protein between two sheets

On 4/17/20 7:14 AM, Zuzana Benkova wrote:
> Dear Gromacs users,
>
> I want to simulate a protein between two graphene sheets separated by 21 nm. The system is solvated and placed in the cell of dimensions 17.09360  17.18200  25.00000.
> The energy minimzation of this system with position restrain applied to protein and frozen carbon atoms ran OK.
> I continued with short simulations in an NVT ensemble with position restrains applied to protein. My output coordinates for all atoms of the systems were integers. Small fragment of a selected frame of the output is as follows
>
>      1GRA     C1    1    0    0    0
>      1GRA     C2    2    0    0    0
>      1GRA     C3    3    0    0    0
>      1GRA     C4    4    0    0    0
>      2GRA     C1    5    0    0    0
>      2GRA     C2    6    0    1    0
>      2GRA     C3    7    0    1    0
>      2GRA     C4    8    0    1    0
>      3GRA     C1    9    0    1    0
>      3GRA     C2   10    0    1    0
>      3GRA     C3   11    0    1    0
>      3GRA     C4   12    0    1    0

Is this just in the final coordinate file? Are coordinates in the 
trajectory correct when visualized?

> my mdp parameters are as follows
>
> integrator               = md
> tinit                    = 0
> dt                       = 0.001
> nsteps                   = 100
> comm-mode                = None

Are you sure you don't want to remove artificial contributions to COM 
motion? This is unusual for a periodic system.

> nstcomm                  = 0
> comm-grps                =
> freezegrps               = Gra1 Gra2
> freezedim                = Y Y Y Y Y Y
> energygrps               = Gra1 Gra2 Protein SOL NA
> ;energygrp-excl           = Gra1 Gra1 Gra2 Gra2 Gra1 Gra2
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> nstlog                   = 1
> nstcalcenergy            = 1
> nstenergy                = 1
> nstxout-compressed       = 1
> compressed-x-precision   = 1

Saving output every step is unnecessary (because you will be skewing 
your statistics with completely correlated frames) and also will 
severely degrade the performance of your simulation.

-Justin

> pbc                      = xyz
> periodic_molecules       = yes
> cutoff-scheme            = Verlet
> nstlist                  = 10
> ns_type                  = grid
> verlet-buffer-tolerance  = 0.005
> rlist                    = 1.4   ;ignored with Verlet
> coulombtype              = PME
> coulomb-modifier         = None
> rcoulomb-switch          = 1.1
> rcoulomb                 = 1.3
> vdw-type                 = Cut-off
> vdw-modifier             = Force-switch
> rvdw_switch              = 1.0
> rvdw                     = 1.3
> DispCorr                 = EnerPres
> fourierspacing           = 0.12
> pme-order                = 4
> ewald-rtol               = 1e-05
> ewald-geometry           = 3d
> Tcoupl                   = V-rescale
> nsttcouple               = -1
> tc-grps                  = Protein  SOL_NA  Gra1_Gra2
> tau-t                    = 0.1  0.1  0.1
> ref-t                    = 310  310  310
> Pcoupl                   = no
>
>
> I have to note that I got the same output with no position restraints on protein.
>
> Do you have any idea what the problem is?
>
> Thank you in advance.
>
> Greetings
>
> Zuzana
>
>
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================

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