[gmx-users] Doubt about g_lie

[Justin Lemkul]

On 6/13/17 9:02 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> I have used PME in the production runs of my systems for finding Delta G_Binding using g_lie. But many threads on Gromacs forum warn against it and advise to rerun the whole trajectory using Reaction field Zero, but the cutoff for this rerun is not clearly given. Some threads say a cutoff with large cutoff using RF-0 is necessary. Can you please uggest as to what cutoff(Relative to the system) should be given while re-running the trajectory and what all changes have to be done in the original mdp file(which uses PME). Also, a brief explanation for the whole process for the need of the re-run would be beneficial. Following are the changes I made after studying the past threads:
> 

You'll have to use much larger cutoffs such that the interaction energies 
converge (or at least close to it), which may or may not be possible.  I'm not 
sure if there's a real "rule" here and I have never relied on a LIE estimate for 
a free energy.

-Justin

------------------------------------------------------------------------------------------------------------------------
> ;; With PME  ;;;                                     | ;; Re-Run without PME ;;
> -------------------------------------------------------------------------------------------------------------------------
>   ; Neighborsearching                                 |  ; Neighborsearching
>    ns_type     = grid      ; search neighboring grid  |  ns_type     = grid      ; search neighboring grid cells
>    nstlist     = 5         ; 10 fs                    |  nstlist     = 5         ; 10 fs
>    rlist       = 0.9       ; short-range neighborlist |  rlist       = 1.2       ; short-range neighborlist cutoff (nm)
>    rcoulomb    = 0.9       ; short-range electrostatic|  rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
>    rvdw        = 1.4       ; short-range van der Waals|  rvdw        = 1.4       ; short-range van der Waals cutoff (in nm)
>                                                       |
> ; Electrostatics                                     | ; Electrostatics
> coulombtype     = PME                                | coulombtype  =  Reaction-Field-zero
>                                                       | epsilon_rf      =  0
> ---------------------------------------------------------------------------------------------------------------------------
> 
> Best Regards,
> 
> Bhagyesh
> 

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

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

==================================================