[gmx-users] Simple gas-phase minimization help

[Justin Lemkul]

On 6/15/16 4:46 PM, Tarick E wrote:
> Thanks for the help!
>
> I am following the Lysozyme tutorial except I am not solvating with water
> or balancing the charge with counter ions. When generating my .tpr with
> grompp, I am receiving the error:
>
> ERROR 1 [file minim_nick_edit1.mdp]:
>   With Verlet lists only full pbc or pbc=xy with walls is supported
>

Then you need cutoff-scheme = group.

-Justin

> I have removed periodic boundary conditions. See my mdp below for a simple
> minimization:
>
> title           = Energy Minimization   ; Title of run
>
> ; The following line tell the program the standard locations where to find
> certain files
> cpp             = /lib/cpp      ; Preprocessor
>
> ; Define can be used to control processes
> define          = -DFLEXIBLE
>
> ; Parameters describing what to do, when to stop and what to save
> integrator      = cg            ; Algorithm (cg = conjugate gradient, steep
> = steepest descent minimization)
> emtol           = 10.0          ; Stop minimization when the maximum force
> < 1.0 kJ/mol
> nstcgsteep      = 10                    ; ; Frequency of steepest descents
> steps when doing CG
> nsteps          = 5000          ; Maximum number of (minimization) steps to
> perform
> nstenergy       = 1             ; Write energies to disk every nstenergy
> steps
> energygrps      = System        ; Which energy group(s) to write to disk
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist         = 0             ; Frequency to update the neighbor list
> ns_type         = simple        ; Method to determine neighbor list
> (simple, grid)
> rlist           = 0
> coulombtype     = cut-off ; Treatment of long range electrostatic
> interactions
> epsilon_rf      = 78
> 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)
>
>
> On Tue, Jun 14, 2016 at 1:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/14/16 1:02 PM, Tarick E wrote:
>>
>>> Hey everyone,
>>>
>>> I am new to this, so please forgive me if this has been asked before.
>>>
>>> I am trying to conduct an energy minimization in vacuum on individual
>>> proteins and small peptides at a constant temperature, but I am having
>>>
>>
>> There is no temperature during energy minimization.
>>
>> trouble with this. Is there any documentation someone can lead me to for
>>> producing a vacuum-phase minimization .mdp file? I have been trying to
>>> edit
>>> the various .mdp files provided in the Lysozyme tutorial written by Justin
>>> Lemkul, but I haven't had any luck and I can't seem to locate any info in
>>> the Gromacs users manual.
>>>
>>>
>> Set all cutoffs to zero and do not use PBC.  Then you're in vacuum.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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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-- 
==================================================

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

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