Hi dear lammps users:
I want to use steered MD simulation by pulling special protein through CNT with spring, when I run my system with below input script:
#CNT+protein
boundary p p p
units real
neigh_modify delay 0 every 1 check yes
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data prot.data
group CNT type 41
group protein id 39
special_bonds charmm
fix 1 all nvt temp 300 300 5
fix 2 CNT setforce 0 0 0
fix protein smd cvel 6.022 0.00001 tether 0 0 -28 0
fix_modify 1 energy yes
velocity all create 0.0 12345678 dist uniform
velocity CNT set 0 0 0 units box
thermo 200
thermo_style multi
timestep 0.5
restart 10000 CNT+protein.restart1
dump 1 all xyz 1000 CNT+protein.xyz
#dump_modify 1 image yes scale yes
minimize 1.0e-4 1.0e-6 1000 100000
fix 3 all shake 1e-6 500 0 m 1.0 a 98
run 2000
I faced with this error:
ERROR: could not find fix group ID modify.cpp:601
And when I use ID number for Fix smd command (like 3) I faced with this error:
ERROR: Invalid fix style modify.cpp:668
I read lammps manual bun I can’t find my problem. I need any suggestion/advice about this errors and about something obvious mistake in my input script.
Thanks very much
Xueqing
Hi dear lammps users:
I want to use steered MD simulation by pulling special protein through CNT
with spring, when I run my system with below input script:
#CNT+protein
boundary p p p
units real
neigh_modify delay 0 every 1 check yes
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data prot.data
group CNT type 41
group protein id 39
special_bonds charmm
fix 1 all nvt temp 300 300 5
fix 2 CNT setforce 0 0 0
fix protein smd cvel 6.022 0.00001 tether 0 0 -28 0
Where is the group ""smd""??? The error is obvious...!!!!
fix protein smd ................. ----> fix name-protein
fix
group-smd..
Reverse the names. !!
Sagar
Dear Sagar; first thanks your answer.
I changed the names order but the problem is not fixed. In each of below command line I faced with error (pull and 1 is fix user assign ID, manual page698, fix smd command):
fix smd phosphate cvel 6.022 0.00001 tether 0 0 -27 14 -------------------> ERROR: Invalid fix style modify.cpp:700
fix pull phosphate-smd cvel 6.022 0.00001 tether 0 0 -27 14 -------------------> ERROR: Invalid fix style modify.cpp:700
fix pull smd phosphate cvel 6.022 0.00001 tether 0 0 -27 14 -------------------> ERROR: could not find fix group ID modify.cpp:633
fix 1 phosphate-smd cvel 6.022 0.00001 tether 0 0 -27 14 -------------------> ERROR: Invalid fix style modify.cpp:700
maybe I did not understand your mean.
Xueqing
Dear Sagar; first thanks your answer.
I changed the names order but the problem is not fixed. In each of below
command line I faced with error (pull and 1 is fix user assign ID, manual
page698, fix smd command):
it doesn't work, because you are doing it wrong. the syntax for fixes is:
fix <fix-id> <fix-group> <fix-command> <arguments>
fix smd phosphate cvel 6.022 0.00001 tether 0 0 -27 14
-------------------> ERROR: Invalid fix style <modify.cpp:700>
id=smd
group=phosphate
command=cvel
-> there is no fix cvel
fix pull phosphate-smd cvel 6.022 0.00001 tether 0 0 -27 14
-------------------> ERROR: Invalid fix style <modify.cpp:700>
same as before
fix pull smd phosphate cvel 6.022 0.00001 tether 0 0 -27 14
-------------------> ERROR: could not find fix group ID <modify.cpp:633>
there is no group smd.
fix 1 phosphate-smd cvel 6.022 0.00001 tether 0 0 -27 14
-------------------> ERROR: Invalid fix style <modify.cpp:700>
same as the first.
what you probably want is:
fix pull phosphate smd cvel ...
axel.
Dear axel, thanks your guidance.
I did completely like your advice, but I faced with error:
fix pull phosphate smd cvel 6.022 0.00001 tether 0 0 -27 14 --------------------> ERROR: Invalid fix style (…/modify.cpp:700)
Xueqing
Did you compile in the user-misc package?
Fix smd is an optional feature.
I use windows executable and I don’t know how can I fix this problem in windows?
My UBUNTU 12.04 lammps-daily version does not work, so now I use windows executable.
Xueqing
I use windows executable and I don't know how can I fix this problem in
windows?
My UBUNTU 12.04 lammps-daily version does not work,
"does not work" is a completely useless and unscientific description.
so now I use windows executable.
well, i guess you are between a rock and a hard place then.
unless you use a windows executable from here:
http://git.icms.temple.edu/rpm/windows.html
axel.
I installed my lammps by “sudo apt-get install lammps-daily” command in terminal. Yesterday when I ran some example system for tutorial purpose successful but when I ran my system, the operating system make an error (I do not remember the error but when I check it in lammps mailing list I found this problem is bug) then I removed my lammps-daily package and now I try to compile lammps in my ubuntu 12.04. I compile lammps package with this sequence of command :
(1)make yes-all; (2)make no-lib; (3)make openmpi. so now
How can I compile Fix smd in the user-misc package?
How can I run my system?
(Dear Axel do not be nervous about my silly questions and also discription, I am new user in ubuntu and in lammps I just use tow months from ubuntu and three days from lammps.)
best
Xueqing
I installed my lammps by "sudo apt-get install lammps-daily" command in
terminal. Yesterday when I ran some example system for tutorial purpose
successful but when I ran my system, the operating system make an error (I
do not remember the error but when I check it in lammps mailing list I found
this problem is bug) then I removed my lammps-daily package and now I try to
this is still too vague to comment on.
compile lammps in my ubuntu 12.04. I compile lammps package with this
sequence of command :
(1)make yes-all; (2)make no-lib; (3)make openmpi. so now
How can I compile Fix smd in the user-misc package?
read the LAMMPS manual. i'm not going to read it to you.
How can I run my system?
you probably didn't read my previous e-mail completely. your mistake.
(Dear Axel do not be nervous about my silly questions and also discription,
I am new user in ubuntu and in lammps I just use tow months from ubuntu and
three days from lammps.)
then find somebody local that knows about linux and tutors you with
it. it is pointless to try and solve this over a mailing list. there
are *plenty* of people around that know how to use and compile
software on linux machines, and most of that is easily transferred to
LAMMPS.
do not make the mistake to confuse your lack of experience in linux
with problems in LAMMPS. you have to solve those two things separately
and best get experience in linux *first*. that is *much* easier to do
and then many of the problems that you now perceive as LAMMPS problems
(but are not) will already be gone, or you will understand the advice
be given.
what you are asking for now is equivalent to being a blind person
asking somebody to describe colors. how can you do that?
axel.
Dear Axel; You are completely right.I try to ask my general question from local expert.
Xueqing