[gmx-users] mdrun WARING and crash
L.Liu at utwente.nl
L.Liu at utwente.nl
Tue Mar 12 10:14:29 CET 2013
Hallo Justin,
Thank you for your reply, I uploaded the images, Please find following the link below,
start box:
http://s1279.beta.photobucket.com/user/Li_Liu/media/image0_zpsf95d10fe.jpeg.html?filters[user]=134822327&filters[recent]=1&filters[publicOnly]=1&sort=1&o=1
and snapshot for first step:
http://s1279.beta.photobucket.com/user/Li_Liu/media/image1_zps06f589e6.jpeg.html?filters[user]=134822327&filters[recent]=1&filters[publicOnly]=1&sort=1&o=0
Thanks a lot, and have a nice day.
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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