[gmx-users] Simple gas-phase minimization help

Justin Lemkul jalemkul at vt.edu
Thu Jun 16 22:36:48 CEST 2016



On 6/16/16 4:25 PM, Tarick E wrote:
> Hi Mark,
>
> Thanks for the reply. I have attempted to run this on Gromacs installed on
> a local machine as well as on a cluster. In either case, the simulations
> would not complete after being run for ~12 hours. I feel that there is an
> error in my mdp file but I am not sure what it could be.
>

Either it runs or doesn't.  The .mdp options won't prevent a run from going.  It 
may simply be a very expensive (and thus slow) calculation.  "Not complete after 
12 hours" is different from not running at all.  Do you get any output?

> I'm trying to minimize the structure with a net charge of +8 in vacuum and
> then conduct simulated annealing in vacuum to determine the low energy
> gas-phase equilibrium structures to compare with collisional activation
> studies by ion mobility spectrometry.
>
> Thanks again for taking time to help me out.
>

You're still not giving us much to go on.  What is your system?  How many atoms? 
  What is your *exact* mdrun command?  How many cores are you trying to use? 
What does adding -v to your mdrun command tell you about the expected completion 
time?

-Justin

> Sincerely,
> Tarick
>
> On Thu, Jun 16, 2016 at 4:08 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> We can't help if all we have is  the information "does not produce an
>> output." I suggest doing tutorial material locally before you get involved
>> with the complexity of a cluster.
>>
>> Mark
>>
>> On Thu, 16 Jun 2016 19:01 Tarick E <telbaba1 at gmail.com> wrote:
>>
>>> 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
>>>>>>
>>>>>> ==================================================
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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
>>>>
>>>> ==================================================
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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

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


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