[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

[Justin Lemkul]

On 5/14/16 2:34 PM, Mark Abraham wrote:
> Hi,
>
> Please keep the discussion on the mailing list, so others can help and
> learn.
>
>> Antara said:
>> I have pasted the mdrun command i used to run it in parallel with the
> number of processors i used which was 16. The command is :
>>
>>
>> /app/setups/gromacs-5.1.1/build/bin -deffnm MD -pin on -rdd 1.8
>
> That still isn't a command you've copied and pasted from a terminal or a
> script. You needed a call that might include mpirun -np 16 gmx_mpi mdrun,
> etc.
>
>> In the pbs script, i used 16 in the number of processors option.
>
> What happens when you run on one rank?
>
>> For the production tpr, i used the gro file from the last equilibration
> step(step6.6) The command used was :
>>
>> gmx grompp -c step6.6equilibration.gro -p system.top -n new_index.ndx -f
> MD.mdp -o MD.tpr
>
> That looks like it could be reasonable, but as with any equilibration you
> need to look at observables to judge that it's equilibrated. Their builder
> should provide reasonable defaults, but you can't assume they're perfect,
> either. In particular, if the last equilibration ensemble doesn't match the
> production ensemble, that could be the problem.
>

Failing to pass the .cpt file to grompp -t after equilibration is a great way to 
do that.  The production simulation is starting from some unpredictable 
ensemble, without velocities, etc..

-Justin

> Mark
>
> On Sat, May 14, 2016 at 5:10 PM Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> On Sat, May 14, 2016 at 4:34 PM Antara mazumdar <antara.mazumdar at igib.in>
>> wrote:
>>
>>> Dear users,
>>>
>>> I am trying to run a coarse grained simulation of a membrane protein in a
>>> mixed lipid billayer using martini model 2.2. I have already performed all
>>> the equilibration steps successfully on my desktop with GROMACS 5.1.0.
>>> However, when i try to execute its production run in parallel(having
>>> gromacs 5.1 version installed)  it complains of LINCS warning and
>>> terminates at step 0. The lincs warning error is coming from BB and SC1
>>> atoms of one of the protein residues.
>>>
>>
>> There are lots of possible places to go wrong, including not making your
>> production .tpr based on the outputs of your equilibration. This seems
>> quite a likely possibility.
>>
>> You should also consider further equilibration - whether using Martini or
>> not, it is sometimes necessary to use a small time step when relaxing
>> problem configurations.
>>
>>
>>>  But on the contrary, it runs on the desktop successfully. *My production
>>> run mdp file details are below :*
>>>
>>>
>>> .
>>>
>>> This is the MD.mdp file :ntegrator               = md
>>> tinit                    = 0.0
>>> dt                       = 0.020
>>> nsteps                   = 2500000000
>>>
>>> nstxout                  = 2000
>>> nstvout                  = 2000
>>> nstfout                  = 2000
>>> nstlog                   = 2000
>>> nstenergy                = 2000
>>> nstxtcout                = 2000
>>> xtc_precision            = 100
>>>
>>> ns_type                  = grid
>>> pbc                      = xyz
>>> nstlist                 = 10
>>> cutoff-scheme           = Verlet
>>> rlist                   = 1.2
>>> vdwtype                 = Cut-off
>>> vdw-modifier            = none
>>> rvdw_switch             = 1.0
>>> rvdw                    = 1.2
>>> coulombtype             = pme
>>> rcoulomb                = 1.2
>>>
>>> tcoupl                   = v-rescale
>>> tc-grps                  = protein CHOL_POPC_DPSM_DPCE W_ION
>>>
>>> tau_t                    = 1.0 1.0  1.0
>>> ref_t                    = 303.15 303.15 303.15
>>>
>>> ; Pressure coupling:
>>> Pcoupl                   = berendsen
>>> Pcoupltype               = semiisotropic
>>> tau_p                    = 5.0  5.0
>>> compressibility          = 3e-4 3e-4
>>> ref_p                    = 1.0  1.0
>>> ; GENERATE VELOCITIES FOR STARTUP RUN:
>>> gen_vel                  = no
>>> refcoord_scaling         = all
>>>
>>> *the command used for mdrun :*
>>>
>>> -deffnm MD -pin on -rdd 1.8 -np 16
>>>
>>
>> mdrun 5.1 won't accept -np, so I don't know what you are actually doing.
>> Please don't edit and filture things, copy and paste whole actual things.
>> :-)
>>
>> Mark
>>
>> I would also like to mention that i generated the initial structure of the
>>> system using CHARMM GUI MARTINI MAKER protein-membrane system option. I
>>> have followed the exact builder protocol for the equilibration and
>>> minimisation.
>>>
>>> Kindly suggest something!
>>>
>>> Thanks,
>>> Antara
>>>
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>>> New Delhi -  110020
>>> M : +91-9717970040
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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

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