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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@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-boun...@gromacs.org <javascript:;> [ > gmx-users-boun...@gromacs.org <javascript:;>] on behalf of Justin Lemkul [ > jalem...@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....@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 -- > gmx-users mailing list gmx-users@gromacs.org <javascript:;> > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. 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Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists