[gmx-users] output - em.gro looks very strange
MD
refmac5 at gmail.com
Fri Dec 8 15:26:48 CET 2017
Sorry I didn't copy the complete log after nvt run.
Here it started with several steps before crashing...
I looked up the "blowing up" error on gromacs site and do you think i need
to go back and do more minimization? But the minimization plateaued earlier
and I am not sure why this is still not stable enough..
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006369, max 0.191905 (between atoms 4658 and 4660)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005085, max 0.156266 (between atoms 4658 and 4660)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
starting mdrun 'Protein in water'
50000 steps, 100.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.011373, max 0.373464 (between atoms 4622 and 4640)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4622 4623 32.7 0.1121 0.1193 0.1080
4622 4624 31.5 0.1607 0.1805 0.1538
4622 4640 52.3 0.1634 0.2046 0.1490
4640 4641 44.2 0.1266 0.1179 0.1230
4640 4642 66.4 0.1543 0.1578 0.1345
4642 4643 34.9 0.1039 0.1088 0.0997
Step 1, time 0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.008070, max 0.266870 (between atoms 4656 and 4658)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4622 4623 48.8 0.1193 0.1239 0.1080
4640 4642 34.2 0.1578 0.1540 0.1345
4642 4643 42.4 0.1088 0.1156 0.0997
Step 2, time 0.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.010148, max 0.340368 (between atoms 4660 and 4676)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4620 4621 53.5 0.1062 0.0987 0.0997
4622 4623 74.0 0.1239 0.1167 0.1080
4622 4640 40.6 0.1575 0.1800 0.1490
4640 4641 39.2 0.1264 0.1451 0.1230
4640 4642 51.7 0.1540 0.1664 0.1345
4642 4643 52.1 0.1156 0.1079 0.0997
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.050073, max 1.422370 (between atoms 4678 and 4680)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4584 4585 34.4 0.1017 0.1183 0.0997
4586 4587 46.2 0.1088 0.1531 0.1080
4586 4588 36.5 0.1562 0.1947 0.1538
4586 4604 75.6 0.1600 0.2485 0.1490
4604 4605 70.2 0.1252 0.1139 0.1230
4604 4606 71.0 0.1378 0.2070 0.1300
4610 4611 37.0 0.1103 0.1334 0.1080
4620 4621 91.7 0.0987 0.1218 0.0997
4622 4623 92.5 0.1167 0.1678 0.1080
4658 4659 37.9 0.0976 0.1308 0.0997
4658 4660 126.8 0.1128 0.0328 0.1430
4676 4677 60.1 0.1111 0.0718 0.1230
4676 4678 120.0 0.1111 0.0644 0.1345
4680 4681 79.4 0.1022 0.1278 0.1080
4680 4682 107.3 0.1440 0.0524 0.1538
4680 4688 152.8 0.1399 0.0870 0.1490
4690 4691 41.3 0.0988 0.0680 0.0997
4690 4692 130.9 0.1443 0.0099 0.1430
4692 4693 31.5 0.1111 0.1645 0.1080
Wrote pdb files with previous and current coordinates
On Fri, Dec 8, 2017 at 8:38 AM, MD <refmac5 at gmail.com> wrote:
> If I ignored the messy em.gro and kept running I was able to go to the
> step of nvt run and I got error message and it stopped running.
>
> WARNING: Listed nonbonded interaction between particles 4618 and 4623
> at distance 150.677 which is larger than the table limit 2.431 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.
>
>
> On Fri, Dec 8, 2017 at 8:37 AM, MD <refmac5 at gmail.com> wrote:
>
>> 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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>>
>>
>
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