[gmx-users] Re: Protein in vacum

[Shima Arasteh]

Am I supposed to skip this step?


Thanks for your reply.

Sincerely,
Shima
_______________________________
From: Dr. Vitaly Chaban <vvchaban at gmail.com>
To: gmx-users at gromuracs.org 
Sent: Monday, January 28, 2013 3:17 PM
Subject: [gmx-users] Re: Protein in vacum

>
> Dear users,
>
> I have done simulation with my protein in water earlier successfully using CHARMM36 FF. Now, I am trying to simulate protein in vacum similar to the last simulation of protein-water. When I go to the NPT equilibration, I get a fatal error.
> The commands I ran:
>
> The npt.mdp file settings are:
> ; Parameters describing neighbors searching and details about interaction calculations
> ns_type        = grid        ; Neighbor list search method (simple, grid)
> nstlist        = 5        ; Neighbor list update frequency (after every given number of steps)
> rlist        = 1.2        ; Neighbor list search cut-off distance (nm)
> rlistlong       = 1.4
> rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
> vdwtype         = switch
> rvdw_switch     = 0.8
> ; Parameters for treating bonded interactions
> continuation    = no        ; Whether a fresh start or a continuation from a previous run (yes/no)
> constraint_algorithm = LINCS    ; Constraint algorithm (LINCS / SHAKE)
> constraints    = all-bonds    ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles)
> lincs_iter    = 1        ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy)
> lincs_order    = 4        ; Highest order in the expansion of the constraint coupling matrix (related to accuracy)
>
> ; Parameters for treating electrostatic interactions
> coulombtype    = PME        ; Long range electrostatic interactions treatment (cut-off, Ewald, PME)
> pme_order    = 4        ; Interpolation order for PME (cubic interpolation is represented by 4)
> fourierspacing    = 0.16        ; Maximum grid spacing for FFT grid using PME (nm)
>
> ; Temperature coupling parameters
> tcoupl        = Nose-Hoover            ; Modified Berendsen thermostat using velocity rescaling
> tc-grps        = Protein     ; Define groups to be coupled separately to temperature bath
> tau_t        = 0.5            ; Group-wise coupling time constant (ps)
> ref_t        = 310             ; Group-wise reference temperature (K)
>
> ; Pressure coupling parameters
> pcoupl        = Parrinello-Rahman        ; Pressure coupler used under NPT conditions
> pcoupltype    = isotropic            ; Isotropic scaling in the x-y direction, independent of the z direction
> tau_p        = 5.0                ; Coupling time constant (ps)
> ref_p        = 1.0                ; Reference pressure for coupling, x-y, z directions (bar)
> compressibility = 4.5e-5    4.5e-5        ; Isothermal compressibility (bar^-1)
> refcoord_scaling = com



Vacuum is incompatible with pressure coupling.


Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark
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