[gmx-users] Simple gas-phase minimization help

[Tarick E]

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

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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