[gmx-users] mdrun WARING and crash
L.Liu at utwente.nl
L.Liu at utwente.nl
Tue Mar 12 18:36:30 CET 2013
Hallo Justin,
One update on the wired snapshot mentioned on previous email.
I checked over the output coordinates and xmgrace it with xy directions, finding that it is not crystal, instead it is a normal homogeneous box. All these give us a clue that it might be the trajectory file goes wrong, cause we calculated the RDF and MSD and view VMD all through traj.xtc.
I am checking the way I output the trajectory. Could you please give me your suggestions if there is something wrong on my .mdp file( included in earlier email).
It seems that the system now is working, though with still some output errors or perhaps further unexpected problems. Well, so far we got a progress, and I want to say thank you very much for all your help.
Kind regards,
Li
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Monday, March 11, 2013 10:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mdrun WARING and crash
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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