I need to share you sth which just happened; i run md_pull.mdp in two steps: 1--1nS( dt= 0.001 nsteps=1000000) , 2--then i choosed last frame (conf1000.gro) and run it irst time for 2nS( dt= 0.001 nsteps=2000000) and scond time for 4nS (dt=0.001 nsteps=4000000) and The protein was in normal shape in EVERY steps!
BUT as i told you before when i run just once in 2nS (dt=0.001 nsteps=2000000) periodic boundary conditions make the protein look unusual in for example conf1500.gro?!!! What happened? I've got really confused? Thank ou for your attentions -Rose On Sun, Dec 3, 2017 at 4:31 PM, rose rahmani <rose.rhm...@gmail.com> wrote: > > > On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 11/28/17 12:23 AM, rose rahmani wrote: >> >>> Hello; >>> >>> I took 2000 configuration from trajconv. Amino acid is in its normal >>> shape >>> till almost conf1000.gro(and a little more). But in for example >>> conf1300.gro amino acid was disintegrated. What does it mean? Would you >>> please help me? >>> >> >> Bonds can't break and molecules can't "disintegrate" - what you're seeing >> is probably a result of PBC. >> >> http://www.gromacs.org/Documentation/Terminology/Periodic_Bo >>> undary_Conditions >> >> I don't know why this doesn't work since yesterday?!!!!...anyway... >> > I used trjconv for just one frame for example conf2000; > trjconv -f conf2000.gro -n index.ndx -s pull.tpr -o new_conf2000.gro -pbc > whole > > so protein turned into to its normal shape, but i'm not sure does it makes > sense or not?! is that right? if it's right, another problem is; > protein is getting out of box, should i use trjconv for centering? > > Thank you for your attentions > > >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Virginia Tech Department of Biochemistry >> >> 303 Engel Hall >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalem...@vt.edu | (540) 231-3129 >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >> >> ================================================== >> >> -- >> 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. >> > > -- 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.