[gmx-users] In-Vacuo ligand only equilibration (Iris Nira Smith)

Justin Lemkul jalemkul at vt.edu
Mon Apr 13 16:42:37 CEST 2015 


On 4/13/15 10:38 AM, Iris Nira Smith wrote:
> 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?
>

Looks fine (don't use -DFLEXIBLE for MD in general, but it only affects water so 
likely isn't relevant here).  Try it and report back if there are any actual 
problems.

-Justin

>
> 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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>> Today's Topics:
>>
>>    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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>>
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>> End of gromacs.org_gmx-users Digest, Vol 132, Issue 48
>> ******************************************************
>

-- 
==================================================

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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