[gmx-users] Umbrella sampling
rose rahmani
rose.rhmn93 at gmail.com
Sat Dec 16 07:35:04 CET 2017
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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