On 12/18/2017 1:14 AM, João Henriques wrote:
First, you don't need "special computers" to run or compile gromacs. It
helps to have multiple compute nodes at your disposal, but it isn't a
requirement *per se*. Also, you don't need to be root to compile your own
gromacs installation. You can indeed install your own gromacs version on
the cluster you use to run your simulations.
Well, I do need "special computers" to run GMX. :)
Jokes aside, this is a solid point -- even if one uses a Windows
machine, virtualbox+linux+gromacs is always useful to tinker at home for
when you have no access to the "special computer." That, or cygwin,
although that thing nauseates me.
Rose, if you are a student, it would be a good idea to ask for better
instruction from your professors. This board is quite limited in
replacing the kind of instruction you may need. Three months is actually
a reasonable amount of time to get the basics of MD and Gromacs right.
Without those basics, it is completely pointless to try doing any work.
Alex
On Mon, Dec 18, 2017 at 8:57 AM, rose rahmani <rose.rhm...@gmail.com> wrote:
Dear Justin,I don't have special computers to be compatible with these
softwares and run complex calculations.So i have to connect to some
computers which is not mine and the old version is installed there.i can't
update them because i'm just a normal user and not a root one! So there are
two choices; not using GROMACS at all OR be convinced with the old
versions. i choose latter!
WHO don't like an upgraded software sir?! you are not talking with a
headstrong person ;) i like to use V.2018 but it's not possible for me, i
hope you understand me.💜Just this!
You are talking with 3 months experienced student without any experience in
any similar simulation software before!
I agree with you Alex he is a modest person ;)
I understand sometimes it's not possible to say what the problem exactly
is, but i ask to know if you had these problems before how did you solve it
in your system, yes maybe it couldn't be the right answer for another's
system but maybe a clue for someone!
You have helped me many times and i really appreciate you for your
attentions and kindness
Thank you again dear Justin and Alex
Best regards
-Rose
On Mon, Dec 18, 2017 at 12:52 AM, Alex <nedoma...@gmail.com> wrote:
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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