[gmx-users] Protein-POPC-water

[Justin Lemkul]

On 12/11/12 8:45 AM, Shima Arasteh wrote:
>
>
>   Dears,
>
> I am trying to simulate a system of water, POPC and protein using charmm36 ff.
> I follow the protocol suggested in KALP15-DPPC tutorial.
> I follow the tutorial step by step up to NVT equilibration without any bond or any  other type warnings.
> Then I run the grompp :
>    # grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
>
> My nvt.mdp file is as :
> define        = -DPOSRES
> ; Parameters describing the details of the NVT simulation protocol
> integrator    = md
> dt        = 0.002
> nsteps        = 50000
> ; Parameters controlling output writing
> nstxout        = 1000
> nstvout        = 1000
> nstenergy    = 1000
> nstlog        = 1000
>
> ; Parameters describing neighbors searching and details about interaction calculations
> ns_type        = grid
> nstlist        = 5
> rlist        = 1.2
> rlistlong       = 1.4
> rcoulomb    = 1.2
> rvdw        = 1.2
> pbc        = xyz
>

Note that you should be using a switch potential for vdW interactions:

http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html

> ; Parameters for treating bonded interactions
> continuation    = no
> constraint_algorithm = LINCS
> constraints    = all-bonds
> lincs_iter    = 1
> lincs_order    = 4
>
> ; Parameters for treating electrostatic interactions
> coulombtype    = PME
> pme_order    = 4
> fourierspacing    = 0.16
>
> ; Temperature coupling parameters
> tcoupl        = v-rescale
> tc-grps        = Protein POPC    SOL_CL    ; Define groups to be coupled separately to temperature bath
> tau_t        = 0.1    0.1    0.1
> ref_t        = 310     310    310
>
> ; Pressure coupling parameters
> pcoupl        = no
>
> ; Miscellaneous control parameters
> ; Dispersion correction
> DispCorr    = EnerPres
> ; Initial Velocity Generation
> gen_vel        = yes
> gen_temp    = 310
> gen_seed    = -1
> ; Centre of mass (COM) motion removal relative to the specified groups
> nstcomm        = 1
> comm_mode    = Linear
> comm_grps    = Protein_POPC SOL_CL
>
>
>
>    # mdrun -deffnm nvt -v
>
> In this step, the nvt is not done and what I get is as :
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> step 0Warning: 1-4 interaction between 4707 and 4716 at distance 3.491 which is larger than the 1-4 table size 2.200 nm

The fact that NVT fails immediately (i.e. at step zero) indicates that energy 
minimization did not reach a sufficiently low value of Fmax.  You probably have 
unresolved clashes in the system.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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