Here i am providing you the link of protein structure https://we.tl/X4yEyZq2aR
On Sun, Sep 10, 2017 at 8:59 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/10/17 3:27 AM, ISHRAT JAHAN wrote: > >> Dear Justin >> I have used all the commands given in the link provided by you but unable >> to get the solution. >> commands used by me are- >> trjconv -f prtn_full.xtc -s prtn_md.tpr -o prtn_md_whole.xtc -pbc whole -n >> prtn_drg.ndx >> trjconv -f prtn_md_whole.xtc -s prtn_md.tpr -o prtn_md_cluster.xtc -pbc >> cluster -n prtn_drg.ndx >> trjconv -f prtn_md_cluster.xtc -s prtn_md.tpr -o prtn_md_ref.gro -b 0 -e 0 >> -n prtn_drg.ndx >> >> when i load the prtn_md_ref.gro in vmd i still get the unusual structure >> of >> protein. >> > > What does "unusual" mean? You're probably going to have to post some > pictures online and provide a URL. > > -Justin > > > Please help me if i did not get the point and also check my full.mdp file >> whether it is correct or not, given below- >> ;^M >> title = Yo^M >> cpp = /usr/bin/cpp^M >> constraints = all-bonds^M >> integrator = md^M >> dt = 0.002 ; ps !^M >> nsteps = 50000000 ; total 100000 ps.^M >> nstcomm = 100^M >> nstxout = 25000^M >> nstvout = 500000^M >> nstfout = 500000^M >> nstlog = 500000^M >> nstenergy = 50000^M >> nstxtcout = 50000^M >> xtc-precision = 10^M >> nstlist = 10^M >> ns_type = grid^M >> rlist = 0.9^M >> coulombtype = PME^M >> rcoulomb = 1.2^M >> rvdw = 1.2^M >> fourierspacing = 0.12^M >> fourier_nx = 0^M >> fourier_ny = 0^M >> fourier_nz = 0^M >> pme_order = 4^M >> ewald_rtol = 1e-5^M >> optimize_fft = yes^M >> ; Berendsen temperature coupling is on in two groups^M >> Tcoupl = V-rescale^M >> tc-grps = Protein Non-Protein^M >> tau_t = 0.1 0.1^M >> ref_t = 310 310^M >> ; Energy monitoring^M >> energygrps = Protein Non-Protein >> ; Isotropic pressure coupling is now on^M >> Pcoupl = berendsen^M >> Pcoupltype = isotropic^M >> tau_p = 0.5^M >> compressibility = 4.5e-5^M >> >> 5,1 40% >> ref_p = 1.0^M >> ; Generate velocites is off at 310 K.^M >> gen_vel = no^M >> gen_temp = 310^M >> gen_seed = 173529^M >> ^M >> Thanks in advance >> >> >> >> >> On Sat, Sep 9, 2017 at 7:04 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 9/9/17 1:50 AM, ISHRAT JAHAN wrote: >>> >>> Dear all, >>>> I have done 100ns md simulation of protein with drug using amber99sb.ff >>>> with gromacs-5.1.4 version. After simulation i found my protein broken >>>> into >>>> smaller parts in .gro file but when i load the final xtc file to pr.gro >>>> molecule does not break. I have applied -pbc nojump ,cluster and whole >>>> but >>>> unable to solve the problem. >>>> Will anyone help me to solve the above problem. >>>> >>>> >>> We'll need to see your commands, exactly as issued, to be able to say >>> anything. In general: >>> >>> http://www.gromacs.org/Documentation/Terminology/Periodic_ >>> Boundary_Conditions#Suggested_trjconv_workflow >>> >>> -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. >>> >>> > -- > ================================================== > > 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.
