how can i check whether the structure is whole or not in .tpr file? After trjconv whole stage i got broken structure.
On Sun, Sep 10, 2017 at 9:00 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > You seem to reporting that your system isn't whole. Is it whole after the > trjconv -whole stage? Is the structure in that .tpr whole? > > Mark > > On Sun, Sep 10, 2017 at 9:27 AM ISHRAT JAHAN <jishra...@gmail.com> 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. > > 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. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? 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