Rose,
Although in my opinion Justin does know everything, the problem is with
your question. You've posted the same thing over and over (and over),
and noone replied -- this could be an indicator that people simply have
nothing to say. We don't know anything about your system, we don't know
whether it is stable, what is its dynamics, etc, etc. On top of this,
you are using a very outdated Gromacs version.
From my own experience with all versions above 5.0.x, pull in Gromacs
does work well, as long as your system behaves as expected without
pulling, and, once that has been confirmed, you use a properly selected
set of pull parameters. There are basic procedures for checking your
system _prior to_ production simulations involving external stimuli
(fields, pulling, etc) -- please follow them. And please, Please be
mindful of what this message board is, and especially of what it is not.
Good luck!
Alex
On 12/17/2017 1:44 PM, Justin Lemkul wrote:
On 12/17/17 3:39 PM, Rose wrote:
Why you don't answer me?is there anything wrong in my question?
Contrary to popular opinion, I don't know everything :) If I don't
reply to a question, it is because I have nothing useful to contribute.
But since you asked, diagnosing what appears to be buggy behavior in
wildly outdated (and unsupported, as I warned you) versions of the
code is not a wise use of time. Upgrade to the latest version and try
again.
-Justin
Thank you
Sent from my iPhone
On Dec 17, 2017, at 17:36, 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
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?is it possible
at all?
Would you please help me?
Best regards
Rose
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