Dear all good day. https://drive.google.com/open?id=0B9FUC_dv9IRoTUdHZENEN1FaOHc
In the google drive file i attached all the file with forcefield file. I only deleted the nvt.trr file. As this file size very big. In this run i only use 7 chain of cellulose. to small the calculation step. Still after the energy minimization. When i run the nvt.mdp then the fibril structure broken. All chain aligned one by one. Best regards Md Imrul Reza Shishir On Tue, Jun 7, 2016 at 10:19 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/6/16 9:13 PM, Md. Imrul Reza Shishir wrote: > >> Dear all >> I have a structure file of cellulose nano fibril of 36 chain (each have 40 >> residue). I want to simulate it as a single compound. I try to run the >> simulation with OPLS-AA force field. After energy minimization when i run >> the equilibrium step then the fibril structure broken and all the chain >> aligned in a single chain like structure. I want to restrain the position >> of chain in there original sheet like structure. But I am not able to >> define. >> >> In the dropbox i attached my simulation structure image file. Initially, >> it >> was 7 sheet of 36 cellulose chain (each chain 40 residues). I check the >> structure (gro file) every stage in VMD after new box creation, solvating, >> energy minimization. The initial structure is not broken. But after >> equilibrium stage when I run nvt.mpd it will break it initial stage. And >> all 36 chain aligned like output structure. >> >> *gmx_mpi pdb2gmx -f (filename).pdb -o (filename).gro -water spce -missing* >> >> *gmx_mpi editconf -f test_fibril_processed.gro -o >> test_fibril_newbox.gro -c -d 1.0 -bt cubic *(This box set-up command) >> >> I also attached nvt.mdp, npt.mdp and md.mdp file. This simulation is >> trial run for long time simulation. How should i restrain the position >> of my structure. >> >> >> In the dropbox link i attached nvt.mdp, npt.mdp, md.mdp and also Input >> and output structure image in vmd. >> >> https://www.dropbox.com/sh/skkskzp1pruf227/AADI2a7TG6pzadFzIEE8094na?dl=0 >> >> Thank you very much. >> >> > Please upload the actual coordinate files and any relevant topologies. I > don't see how setting up that structure in a cubic box would lead to such a > structure. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Md Imrul Reza Shishir* Master Student *Inha University* *CRC for NanoCellulose Future Composites* 36 Getbeol-ro, Yeonsu-gu Incheon 21999 South Korea -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.