[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL
jalemkul at vt.edu
Sun May 15 00:33:21 CEST 2016
On 5/14/16 2:34 PM, Mark Abraham wrote:
> Please keep the discussion on the mailing list, so others can help and
>> 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,
>> 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..
> On Sat, May 14, 2016 at 5:10 PM Mark Abraham <mark.j.abraham at gmail.com>
>> On Sat, May 14, 2016 at 4:34 PM Antara mazumdar <antara.mazumdar at igib.in>
>>> 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.
>> 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
>>> Kindly suggest something!
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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
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Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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