[gmx-users] Umbrella sampling
rose rahmani
rose.rhmn93 at gmail.com
Sat Dec 16 10:08:03 CET 2017
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? 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
>>
>> ==================================================
>>
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