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

[Justin Lemkul]

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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