My peptide is 26 residue alpha helix obtained from crystal structure .pdb file. I am posting energy minimization, position restarint and full MD simulation .mdp file
Energy minimization cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 3000 ; ; Energy minimizing stuff ; emtol = 1000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.14 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = no Pcoupl = no gen_vel = no Position_restraint.mdp cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds constraintalgorithm = LINCS integrator = md dt = 0.002 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.14 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Full_MD.mdp cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 5000000 ; total 10000 ps. nstcomm = 1 nstxout = 5000 nstvout = 40000 nstfout = 0 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.14 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-protein tau_t = 0.1 0.1 ref_t = 500 500 ; Energy monitoring energygrps = Protein Non-protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 500 K. gen_vel = no gen_temp = 500.0 gen_seed = 173529 shahid On 4/27/10, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > > shahid nayeem wrote: > >> Dear Mark >> Following your advice I started using three peptide in one simulation box. >> Iwas able to add these with genconf as previously in ordered manner, >> generated .gro with genconf, solvated it and after energy minimization I did >> MD run for 10ns. Everything ran well. In the end when I see the trajectory I >> find unfolding of the original chain but the two additional peptide >> introduced through genconf show appearance of new secondary structures. Even >> in these two the secondary structure do not develop at the same point. Why >> the three equivalent peptide behave differently in similar environment. How >> can I explain this observation. why the first peptide does not show any new >> secondary structure. Sholud I go with higher number of molecule. Will it >> make any difference if peptides are added in disordered manner and then >> simulated. >> > > Initial orientation should likely have nothing to do with it. Perhaps this > is even the proper behavior for whatever your peptide is. Is its structure > dynamic? Is the size of your peptides large enough to even believe that > they would be intrinsically stable? Many model peptides, in isolation, have > very transient structures. > > It could also be that your simulation parameters are poorly chosen, so the > force field is breaking down. If you want comments on your .mdp file, > please post it. > > -Justin > > Shahid >> >> On 4/23/10, *Mark Abraham* <mark.abra...@anu.edu.au <mailto: >> mark.abra...@anu.edu.au>> wrote: >> >> On 23/04/10 13:16, shahid nayeem wrote: >> >> Dear All >> I am trying to study inter peptide interaction fpr which I need >> to put >> more than one peptide in one simulation box. I did it with genconf >> command but this inserts peptide in a regular ordered manner I want >> these to be in irregular disordered insertion. Even after using >> genconf >> >> >> Well that's a difficult and atypical scenario. genconf -shuffle will >> allow you to stack the same peptide in a regular array with random >> rotations of the whole box. Then you can solvate, equilibrate and >> run MD at a high temperature to give yourself a quasi-disordered >> starting state. >> >> , I tried to proceed furthe after solvation with spc water. The >> energy >> minimization (steepest descent) failed to converge even after >> 5000 steps >> and theirafter position restraint dynamics failed giving >> segmentation >> fault. Introducing more peptide after generating .gro with -ci >> -nmol >> gives error showing more than one residue in insert molecule. >> Please help me and write commands which I should follow. >> >> >> No, because that's an impossible task. We can't begin to guess the >> reasons for things failing without seeing the actual output (was the >> EM energy large and negative? what was the actual error message >> from -ci -nmol?). >> >> You should be careful to start with a small test case so that you >> can learn the workflow with a manageable problem. Can you get a >> single peptide to equilibrate? Two stacked peptides? It is best to >> learn to walk before trying to run :-) >> >> Mark >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > 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/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/mailing_lists/users.php >
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