[gmx-users] mdrun WARING and crash

[Justin Lemkul]

On Monday, March 11, 2013, wrote:

> Hallo Justin,
>
> Thank you for your comments.
> Taking your suggestions, I set nrexcl=1, and comment the [pairs] section,
> because there is no special case of non-bonded interactions to declare,
>  then we try to see what happens.
> Now we minimize it by steep, then by cg, both of the processor are very
> quick done, because after around 7000 steps, the energy can not go further
> down any more.
> Then we finish the mdrun, the energies output are like:
>
>            Step           Time         Lambda
>           10000       10.00000        0.00000
>
>    Energies (kJ/mol)
>         LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
>     1.49468e+05    0.00000e+00    1.49468e+05    8.73890e+03    1.58207e+05
>     Temperature Pressure (bar)
>     4.38208e+02    9.93028e+04
>
> Although this time no running error, we find the outputs are extremely
> wired, for example through
> VMD conf.gro traj.xtc
> we find 0 frame a homogeneous box, starting from the first step, the box
> becomes a lattice, which is far away from our expected the Polymer melt
> system should be.
>
> The force parameters are taken from literature PRL 85(5), 1128(2000), I am
> still very worried about the format of my input files. Could you please
> give me, a very beginner a help.
>
>
Please provide links to images. This is probably not a big deal as long as
the simulation is actually running, since a triclinic representation of the
unit cell is used.

-Justin



> Thanks a lot.
> Kind regards,
> Li
> ________________________________________
> From: gmx-users-bounces at gromacs.org <javascript:;> [
> gmx-users-bounces at gromacs.org <javascript:;>] on behalf of Justin Lemkul [
> jalemkul at vt.edu <javascript:;>]
> Sent: Thursday, February 28, 2013 3:02 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] mdrun WARING and crash
>
> On 2/28/13 6:59 AM, L.Liu at utwente.nl wrote:
> > Hallo Justin,
> >
> > Thank you for you help. I have read the previous discussions on this
> topic, which is very helpful.
> > The link is:
> http://gromacs.5086.n6.nabble.com/What-is-the-purpose-of-the-pairs-section-td5003598.html
> > Well, there are still something I want to make sure, which might be the
> reason of mdrun crash of my system.
> >
> > ###################Introduction of system##############################
> > Linear Polyethylene melt:  each chain contains 16 beads, each bead
> coarse grained 3 monomers. Number of  chain in the box is 64.
> >
> > ####################Force Field##########################
> > ffbonded.itp
> > [ bondtypes ]
> > ; FENE, Ro = 1.5 sigma and kb = 30 epsilon/sigma^2
> > ;   i        j     func        b0 (nm)     kb (kJ/mol nm^2)
> >   CH2   CH2    7           0.795           393.
> >
> > ffnonbonded.itp
> > [ atomtypes ]
> > ; epsilon / kB = 443K
> > ;name  at.num      mass (au)       charge   ptype     sigma (nm)
>  epsilon (kJ/mol)
> >     CH2      1            42.30000       0.000       A           0.5300
>          3.68133
> >
> > [ nonbond_params ]
> >    ; i          j    func  sigma   epsilon
> >     CH2   CH2    1    0.530    3.68133
> >
> > [ pairtypes ]
> >    ;  i          j    func  sigma   epsilon
> >     CH2   CH2    1      0.53    3.68133
> >
> > ############################topology######################
> > [ defaults ]
> > ; nbfunc        comb-rule       gen-pairs       fudgeLJ   fudgeQQ
> >      1                  2                    no              1.0      1.0
> >
> > ; The force field files to be included
> > #include "../forcefield/forcefield.itp"
> >
> > [ moleculetype ]
> > ; name  nrexcl
> >     PE      0
> > [atoms]
> > ;   nr    type   resnr  residu    atom    cgnr  charge
> >       1     CH2       1    PE      C       1      0.0
> >       2     CH2       1    PE      C       2      0.0
> >       3     CH2       1    PE      C       3      0.0
> >       4     CH2       1    PE      C       4      0.0
> >      ......
> >       15    CH2       1    PE      C       15     0.0
> >       16    CH2       1    PE      C       16     0.0
> >
> > [ bonds ]
> > ;  ai    aj              funct           c0           c1
> >      1     2      7      0.795         393.
> >      2     3     7      0.795         393.
> >      3     4     7      0.795         393.
> >     ......
> >      14    15     7      0.795         393.
> >      15    16     7      0.795         393.
> >
> > [ pairs ]
> > ;  ai   --
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