[gmx-users] Simple gas-phase minimization help
Tarick E
telbaba1 at gmail.com
Thu Jun 16 19:01:00 CEST 2016
I have tried a number of edits to my minim.mdp file for minimization with
no luck. I can generate a tpr without any errors and initiate a simulation
via mdrun, but no matter what resources I allocate to it (on a
supercomputer), I cannot produce an output.
Here's my mdp file. I am trying to minimize the structure that I will then
feed into an md simulation in vacuum:
; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0 ; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep = 0.001 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to
perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list
and long range forces
rlist = 0
cutoff-scheme = group
ns_type = grid ; Method to determine neighbor list
(simple, grid)
coulombtype = cut-off ; Treat all long-range
electrostatics
rcoulomb = 0 ; Short-range electrostatic cut-off
rvdw = 0 ; Short-range Van der Waals cut-off
pbc = no ; Periodic Boundary Conditions
(yes/no)
Any help is greatly appreciated!
On Wed, Jun 15, 2016 at 4:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
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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
>
> ==================================================
> --
> Gromacs Users mailing list
>
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