[gmx-users] rlist for implicit water

[Justin Lemkul]

On 6/3/14, 12:21 PM, Urszula Uciechowska wrote:
> Dear Justin,
>
> How could I change the cut-offs  to make the MD more faster in my case?
>

Well, there are plenty of things one can do to improve performance, but the 
better question is whether or not one can maintain something physically sensible 
at the same time :)  For implicit solvent, at least in my own experience, the 
only way I get stable trajectories is with the infinite cutoff approach.  Some 
advocate a "long cutoff" scheme with all cutoffs set to something like 2.0 or 
4.0 nm, but that's never worked for me, either.

You also should never judge performance from EM alone.

-Justin

> /Urszula
>>
>>
>> On 6/3/14, 4:15 AM, Urszula Uciechowska wrote:
>>> Dear Gromacs users,
>>>
>>> I would like to run simulations with implicit water. My protein system
>>> is
>>> quite big it contains 784AA. I prepared eM.mdp file (see below) however
>>> I
>>> am not sure if its ok especially the rlist what should I use there in
>>> case
>>> of such big system.
>>>
>>> define                  = -DFLEXIBLE
>>> constraints             = none
>>> integrator              = steep         ; steepest descents energy
>>> minimization
>>> dt                      = 0.001         ; ps
>>> nsteps                  = 3000          ; maximum number of steps to
>>> integrate
>>> implicit_solvent        = GBSA
>>> gb_algorithm            = Still
>>> nstgbradii              = 1
>>> gb_epsilon_solvent      = 80
>>> gb_saltconc             = 0
>>> sa_algorithm            = Ace-approximation
>>> sa_surface_tension      = -1
>>> pbc                     = no
>>> rgbradii                = 0
>>> ns_type                 = simple        ; method of updating neighbor
>>> list
>>> nstlist                 = 0
>>> rlist                   = 0             ; this means all-vs-all (no
>>> cut-off)
>>> coulombtype             = cut-off
>>> rcoulomb                = 0             ; [nm] distance for Coulomb
>>> cut-off
>>> vdwtype                 = cut-off       ; twin-range cut-off with rlist
>>> where rvdw >= rlist
>>> rvdw                    = 0             ; [nm] distance for LJ cut-off
>>> nstenergy               = 100
>>> emtol                   = 5.0
>>> emstep                  = 0.01
>>> comm-grps               = Protein
>>> optimize_fft            = yes
>>>
>>> Thank you in advance for any comments and suggestions.
>>>
>>
>> If you're using infinite cutoffs, the only acceptable value for rlist is
>> 0.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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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>
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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