[gmx-users] Re: Protein in vacum

[Dr. Vitaly Chaban]

YES.




On Mon, Jan 28, 2013 at 12:51 PM, Shima Arasteh
<shima_arasteh2001 at yahoo.com> wrote:
>
>
> 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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-- 
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