[gmx-users] In-Vacuo ligand only equilibration (Iris Nira Smith)
Iris Nira Smith
irisnsmith at comcast.net
Mon Apr 13 16:40:09 CEST 2015
Thank you Justin for your insight to your previous response.
I made adjustments to my equilibration .mdp file (below) to run as NVT in vacuo.
Can you review and advise on corrections?
eqb-nvt-invacuo.mdp
;Title = equilibration nvt (invacuo)
;
define = -DFLEXIBLE
;
;Run parameters
integrator = md ;Algorithm options
dt = 0.002 ; timestep for integration
nsteps = 50000 ; Maximum number of steps to perform 100 ps
comm_mode = angular ; remove center of mass translation and rotation around the center of mass
comm-grps = system
;
;Bond parameters
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
constraint_algorithm = lincs ; holonomic constraints
linc_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
;
;Output control
nstxout = 1000 ; frequency to write coordinates to output trajectory 2 ps
nstfout = 1000 ; frequency to write forces to output trajectory 2 ps
nstvout = 1000 ; frequency to write velocities to output trajectory 2 ps
nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps
nstlog = 1000 ; frequency to write energies to log 2 ps
nstenergy = 1000 ; frequency to write energies to edr 2ps
;
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 0 ; Frequency to update the neighbor list and long range forces
ns_type = simple
rlist = 0 ; Cut-off for making neighbor list (short range forces)
coulombtype = cut-off ; Treatment of long range electrostatic interactions
vdwtype = cut-off
rcoulomb = 0 ; long range electrostatic cut-off
rvdw = 0 ; long range Van der Waals cut-off
pbc = no ; Periodic Boundary Conditions (yes/no)
epsilon_rf = 0
;
; V-rescale temperature coupling is on
tcoupl = v-rescale
tc-grps = system
tau-t = 0.1
ref-t = 300
;
; Pressure coupling is off
Pcoupl = no
;
; Generate velocites is on
gen_vel = yes
gen_temp = 300
gen_seed = 952967
-Iris
On Apr 13, 2015, at 8:09 AM, gromacs.org_gmx-users-request at maillist.sys.kth.se wrote:
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> 1. Re: How to add a repulsive harmonic potential (Justin Lemkul)
> 2. Re: In-Vacuo ligand only equilibration (Justin Lemkul)
> 3. Re: A simple question (Justin Lemkul)
> 4. Re: How to add a repulsive harmonic potential (Mark Abraham)
> 5. Re: A query (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> On 4/13/15 12:38 AM, Iris Nira Smith wrote:
>> Hello,
>>
>> I'm utilizing gromacs 4.6.3 to set up my md simulation to run a ligand-only invacuo (no water) system for 500 ps prior to running my protein-ligand complex to determine the stability of the ligand. I have successfully run an energy minimization with the em-invaco.mdp file below (in absence of periodicity and infinite cut-offs).
>>
>> When running the equilibration should it be broken up into 2 phases: phase 1-nvt, phase 2-npt or is nvt sufficient?
>
> You can't do NPT in vacuo with an infinite system.
>
>> If so, should it also be done utilizing an implicit solvent model such as GBSA for both equilibration and production run (see also eqb-invacuo.mdp below)?
>>
>
> Implicit solvent and vacuum are physically different. If your in vacuo run is
> only to assess topological stability, don't bother with implicit solvent,
> because that adds a layer of complexity that will make it hard to tell if there
> are any problems. Implicit models are very approximate.
>
> -Justin
>
>>
>>
>> em-invacuo.mdp
>> ; Parameters describing what to do, when to stop and what to save
>> integrator = steep ; Algorithm options
>> ; steep = steepest descent minimization
>> ; MD = Leap Frog algorith for integrating Newton? equations of motion )
>> emtol = 10.0 ; Stop minimization when the Fmax < 10 kJ/mol/nm.
>> emstep = 0.01 ; Energy step size
>> nsteps = 10000 ; Maximum number of (minimization) steps to perform
>> nstenergy = 10 ; Write energies to disk every nstenergy steps
>> ;
>> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
>> nstlist = 0 ; Frequency to update the neighbor list and long range forces
>> ns_type = simple ; Method to determine neighbor list (simple, grid)
>> rlist = 0 ; Cut-off for making neighbor list (short range forces)
>> coulombtype = cut-off ; Treatment of long range electrostatic interactions
>> rcoulomb = 0 ; long range electrostatic cut-off
>> rvdw = 0 ; long range Van der Waals cut-off
>> constraints = none ; Bond types to replace by constraints
>> pbc = no ; Periodic Boundary Conditions (yes/no)
>>
>> eqb-invacuo.mdp
>>
>>
>> define = -DFLEXIBLE
>> constraints = none ; Bond types to replace by constraints
>> integrator = md ;Algorithm options
>> dt = 0.002 ; timestep for integration
>> nsteps = 50000 ; Maximum number of steps to perform 100 ps
>>
>> nstxout = 1000 ; frequency to write coordinates to output trajectory 2 ps
>> nstfout = 1000 ; frequency to write forces to output trajectory 2 ps
>> nstvout = 1000 ; frequency to write velocities to output trajectory 2 ps
>> nstxtcout = 1000
>> nstlog = 1000 ; frequency to write energies to log 2 ps
>> nstenergy = 1000 ; frequency to write energies to edr
>>
>> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
>>
>> nstlist = 0 ; Frequency to update the neighbor list and long range forces
>> ns_type = simple
>> rlist = 0 ; Cut-off for making neighbor list (short range forces)
>> coulombtype = cut-off ; Treatment of long range electrostatic interactions
>> vdwtype = cut-off
>> rcoulomb = 0 ; long range electrostatic cut-off
>> rvdw = 0 ; long range Van der Waals cut-off
>> pbc = no ; Periodic Boundary Conditions (yes/no)
>> epsilon_rf = 0
>> rgbradii = 0
>> comm_mode = angular
>> comm-grps = system
>> optimize_fft = yes
>> ;
>> ; V-rescale temperature coupling is on
>> tcoupl = v-rescale
>> tc-grps = system
>> tau-t = 0.1
>> ref-t = 300
>> ;
>> ; Pressure coupling is off
>> Pcoupl = no
>> ;
>> ; Generate velocites is on
>> gen_vel = yes
>> gen_temp = 300
>> gen_seed = -1
>> ;
>> ; Implicit solvent
>>
>> implicit_solvent = GBSA
>> gb_algorithm = Still
>> gb_epsilon_solvent = 80
>> sa_surface_tension = 2.25936
>>
>> nstgbradii = 1
>> rgbradii = 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist
>>
>> sa_algorithm = Ace-approximation
>> sa_surface_tension = -1
>>
>>
>>
>>
>>
>>
>>
>>
>> Best,
>>
>> Iris Nira Smith, Ph.D. Candidate
>> Briggs Computational Biochemistry/Biophysics Laboratory
>> University of Houston
>> 402E Health Science Center
>> Houston, TX 77204
>>
>> A Carnegie-designated Tier One public research university
>> Phone:281-726-0341
>> Email: irisnsmith at comcast.net
>> connormichaellogsdon.blogspot.com
>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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