[gmx-users] Re: Protein in vacum
jalemkul at vt.edu
Mon Jan 28 12:53:04 CET 2013
On 1/28/13 6:51 AM, Shima Arasteh wrote:
> Am I supposed to skip this step?
Do not be tempted to think that there is a "standard" or "required" workflow.
The ensembles and environments you choose are dependent upon the task at hand.
There may be common workflows for proteins in water, but even those are not set
> Thanks for your reply.
> 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
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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