On Sat, Dec 16, 2017 at 12:38 PM, rose rahmani <rose.rhm...@gmail.com> wrote:
> and also i want protein get closer to ZnS sheet during pulling in just Z >> direction and straightforward to sheet( like one straight line to sheet), >> is this suitable md_pull.mdp file for this approach? > > is it possible at all?1 > and what about time?is 4nS suitable for each window? > > > Thanks indeed > > On Sat, Dec 16, 2017 at 10:05 AM, rose rahmani <rose.rhm...@gmail.com> > wrote: > >> Hi, >> >> I try to use umbrella sampling for calculating PMF. i change distance >> between protein and ZNS nanosheet. I use gomacsV4.5.4 >> >> after minimization and equilibration. i use: >> >> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr >> >> this is md_pull.mdp: >> >> integrator = md >> dt = 0.002 >> nsteps = 1000000 >> nstxout = 5000 >> nstvout = 5000 >> nstfout = 500 >> nstlog = 500 >> nstenergy = 1000 >> nstxtcout = 1000 >> nstlist = 10 >> rlist = 1.5 >> coulombtype = pme >> rcoulomb = 1.5 >> vdwtype = Switch >> rvdw_switch = 1.0 >> rvdw = 1.2 >> pcoupl = no >> gen_vel = no >> constraints = h-bonds >> ns_type = grid >> pbc = xy >> freezegrps = WAL ZnS >> freezedim = Y Y Y Y Y Y >> energygrp-excl = WAL WAL ZnS ZnS >> energygrps = SOL WAL ZnS Protein NA CL >> nwall = 2 >> wall-atomtype = C C >> wall-type = 9-3 >> wall-density = 150 150 >> wall-ewald-zfac = 3 >> ewald-geometry = 3dc >> fourierspacing = 0.12 >> tcoupl = v-rescale >> tc-grps = System >> tau-t = 0.1 >> ref-t = 300 >> >> ; Pull code >> pull = umbrella >> pull_ngroups = 1 >> pull_group0 = ZnS >> pull_group1 = Protein >> pull_geometry = direction >> pull_vec1 = 0 0 1 >> pull_dim = N N Y >> pull_rate1 = -0.01 >> pull_k1 = 5000 >> pull_start = yes >> pull_nstxout = 50 >> >> then: mdrun -s pull.tpr >> then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep >> >> i got 1000 configuration, i selected 27 of them and foe each of them i >> run md_umbrella.mdp >> >> for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p >> topol.top -n index.ndx -o umbrella0.tpr and then: >> >> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg >> >> >> .This is md_umbrella.mdp file: >> >> ntegrator = md >> dt = 0.002 >> nsteps = 2000000 >> nstxout = 5000 >> nstvout = 5000 >> nstfout = 500 >> nstlog = 500 >> nstenergy = 1000 >> nstxtcout = 1000 >> nstlist = 10 >> rlist = 1.5 >> coulombtype = pme >> rcoulomb = 1.5 >> vdwtype = Switch >> rvdw_switch = 1.0 >> rvdw = 1.2 >> pcoupl = no >> gen_vel = no >> constraints = h-bonds >> ns_type = grid >> pbc = xy >> freezegrps = WAL ZnS >> freezedim = Y Y Y Y Y Y >> energygrp-excl = WAL WAL ZnS ZnS >> energygrps = SOL WAL ZnS Protein NA CL >> nwall = 2 >> wall-atomtype = C C >> wall-type = 9-3 >> wall-density = 150 150 >> wall-ewald-zfac = 3 >> ewald-geometry = 3dc >> fourierspacing = 0.12 >> tcoupl = v-rescale >> tc-grps = System >> tau-t = 0.1 >> ref-t = 300 >> >> pull = umbrella >> pull_ngroups = 1 >> pull_group0 = ZnS >> pull_group1 = Protein >> pull_geometry = direction >> pull_vec1 = 0 0 1 >> pull_dim = N N Y >> pull_rate1 = 0.0 ; 1 nm per ns >> pull_k1 = 5000 >> pull_start = yes >> pull_nstxout = 50 >> ........................................................... >> >> then i use : >> >> wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal >> >> >> i get histo.xvg and profile.xvg file but the profile.xvg contains nan >> vavlue. i don't know why? >> >> >> # This file was created Wed Dec 13 14:54:35 2017 # by the following >> command: # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal >> # # g_wham is part of G R O M A C S: # # GROwing Monsters And Cloning >> Shrimps # @ title "Umbrella potential" @ xaxis label "z" @ yaxis label "E >> (kcal mol\S-1\N)" @TYPE xy 5.723834e-01 -nan 6.714198e-01 -nan 7.704562e-01 >> -nan 8.694925e-01 -nan 9.685289e-01 -nan 1.067565e+00 -nan 1.166602e+00 >> -nan 1.265638e+00 -nan >> >> . >> >> . >> >> . >> >> . >> >> >> Would you please help me? i have not encounter this problem before >> >> Thank you so much >> >> Best regards >> >> Rose >> >> >> >> >> On Mon, Dec 4, 2017 at 1:55 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >>> >>> >>> On 12/3/17 8:42 AM, rose rahmani wrote: >>> >>>> 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? >>>> >>> >>> Read a bit about periodic boundary conditions and what they mean. This >>> is normal behavior. >>> >>> >>> -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? 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