[gmx-users] Umbrella sampling
rose rahmani
rose.rhmn93 at gmail.com
Sat Dec 16 10:13:33 CET 2017
On Sat, Dec 16, 2017 at 12:38 PM, rose rahmani <rose.rhmn93 at 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.rhmn93 at 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 <jalemkul at 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
>>>
>>> jalemkul at 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-request at gromacs.org.
>>>
>>
>>
>
More information about the gromacs.org_gmx-users
mailing list