[gmx-users] output - em.gro looks very strange

Fri Dec 8 14:37:06 CET 2017

Thank you Justin.
I actually did a control simulation with another protein that has the same
modified residue and that simulation went through with no errors or
warnings. Can I have a conclusion that the parameters of my modified
residue in charmm is ok? I made the new residue consistent in merged.rtp,
merged.hdb, residuetypes.dat, and adopted dihedral angles, bond angles from
similar pairs in ffbonded.itp.
If that's the case, does it mean it is my protein's pdb which is causing
all the issue?
Ming

On Fri, Dec 8, 2017 at 7:49 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/6/17 4:57 PM, MD wrote:
>
>> Hi Gromacs folks,
>>
>> After fixing the non-even charge issues I met new problems when running
>> em.mdp.
>> The grompp worked and mdrun em worked as well with warning, but I found
>> the
>> output em.gro looks very strange with several amino acids stretched to the
>> other side of the box. I had the command followed with log file. Any help
>> would be greatly appreciated.
>>
>> I looked at the distance between 4641 and 4657 in solv_ions.gro and it is
>> actually 11.354A. I am not quite sure about the warning message.
>>
>
> Make sure it's not just the structure being split across PBC. If it's not,
> then your topology is unstable and you need to revisit your parametrization
> to make sure everything about your new residue is sensible.
>
> -Justin
>
> Thanks,
>>
>> Ming
>>
>>
>>
>>
>> *gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr*
>>
>> GROMACS:      gmx grompp, VERSION 5.1.2
>> Executable:   /usr/bin/gmx
>> Data prefix:  /usr
>> Command line:
>>    gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr
>>
>> Ignoring obsolete mdp entry 'title'
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
>>
>> NOTE 1 [file em_real.mdp]:
>>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>>    that with the Verlet scheme, nstlist has no effect on the accuracy of
>>    your simulation.
>>
>> Setting the LD random seed to 2763204595 <(276)%20320-4595>
>>
>> Generated 97877 of the 97903 non-bonded parameter combinations
>> Generating 1-4 interactions: fudge = 1
>> Generated 64492 of the 97903 1-4 parameter combinations
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
>> Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
>> Excluding 3 bonded neighbours molecule type 'Other_chain_B'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
>> Excluding 2 bonded neighbours molecule type 'SOL'
>> Excluding 1 bonded neighbours molecule type 'NA'
>> Removing all charge groups because cutoff-scheme=Verlet
>> Analysing residue names:
>> There are:   345    Protein residues
>> There are:    11        Ion residues
>> There are:     1      Other residues
>> There are: 18021      Water residues
>> Analysing Protein...
>> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
>> into groups...
>> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
>> into groups...
>> Number of degrees of freedom in T-Coupling group rest is 179214.00
>> Calculating fourier grid dimensions for X Y Z
>> Using a fourier grid of 80x80x80, spacing 0.119 0.119 0.119
>> Estimate for the relative computational load of the PME mesh part: 0.20
>> This run will generate roughly 5 Mb of data
>>
>> There was 1 note
>>
>> Back Off! I just backed up em.tpr to ./#em.tpr.3#
>>
>>
>>
>> *gmx mdrun -v -deffnm em*
>>
>> Reading file em.tpr, VERSION 5.1.2 (single precision)
>> Using 1 MPI thread
>> Using 6 OpenMP threads
>>
>>
>> Back Off! I just backed up em.trr to ./#em.trr.2#
>>
>> Back Off! I just backed up em.edr to ./#em.edr.2#
>>
>> Steepest Descents:
>>     Tolerance (Fmax)   =  1.00000e+03
>>     Number of steps    =        50000
>>
>> WARNING: Listed nonbonded interaction between particles 4641 and 4657
>> at distance 2.141 which is larger than the table limit 2.000 nm.
>>
>> This is likely either a 1,4 interaction, or a listed interaction inside
>> a smaller molecule you are decoupling during a free energy calculation.
>> Since interactions at distances beyond the table cannot be computed,
>> they are skipped until they are inside the table limit again. You will
>> only see this message once, even if it occurs for several interactions.
>>
>> IMPORTANT: This should not happen in a stable simulation, so there is
>> probably something wrong with your system. Only change the table-extension
>> distance in the mdp file if you are really sure that is the reason.
>>
>>
>> *em.mdp*
>>
>> ; LINES STARTING WITH ';' ARE COMMENTS
>> title = Minimization ; Title of run
>>   define=-DFLEXIBLE
>>
>> ; Parameters describing what to do, when to stop and what to save
>> integrator = steep ; Algorithm (steep = steepest descent minimization)
>> emtol = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
>> emstep      = 0.01      ; Energy step size
>> nsteps = 50000    ; Maximum number of (minimization) steps to perform
>> energygrps = Protein  ; 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     = 1     ; Frequency to update the neighbor list and long range
>> forces
>> cutoff-scheme   = Verlet
>> ns_type     = grid ; Method to determine neighbor list (simple, grid)
>> rlist     = 1.0 ; Cut-off for making neighbor list (short range forces)
>> coulombtype     = PME ; Treatment of long range electrostatic interactions
>> rcoulomb     = 1.0 ; long range electrostatic cut-off
>> rvdw     = 1.0 ; long range Van der Waals cut-off
>> pbc         = xyz  ; Periodic Boundary Conditions
>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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