Message: 1
Date: Fri, 5 Sep 2008 15:48:12 -0700
From: "Chih-Ying Lin" <[EMAIL PROTECTED]>
Subject: [gmx-users] CPMD- QM MM simulation
To: gmx-users@gromacs.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hi
I read some papers, which the authors use CPMD
gurgo> Vitaly Chaban wrote:
>> Hello,
>>
>> Where can I read about the exact format of the TRR and XTC files. I
>> mean the width and type of every field in the binary trajectory file.
>>
>> I see read_'next_frame(status,&fr)' function in 'template.c'. But
>> where is this fuction defined?
>> Sor
Vasilii Artyukhov wrote:
Hi gmx-users,
Sorry for a not-strictly-GROMACS-related question, but could someone
suggest a program I could use to fit atomic charges to quantum chemistry
results?
antechamber.
Thanks in advance,
Vasilii
-
ravi sharma wrote:
Thanks justin,
but how can identify these groups, i am using fedora core 8,
also Thanks for the Tc-grps,
What groups are you talking about, tc-grps? Please be more specific.
-Justin
regards,
--- On *Sun,
2008/9/8 David van der Spoel <[EMAIL PROTECTED]>
> Vasilii Artyukhov wrote:
>
>> Hi gmx-users,
>>
>> Sorry for a not-strictly-GROMACS-related question, but could someone
>> suggest a program I could use to fit atomic charges to quantum chemistry
>> results?
>>
>> antechamber.
Thanks for a quick
jj beh wrote:
Dear all user
How can I have a force field for simulation of boron-nitride nanotube?
Has anything like that ever been simulated? If it hasn't, there may not be
paramteers for such a species. I don't believe boron exists as an atom type in
any of the force fields provided b
gurgo>> Vitaly Chaban wrote:
>>> Hello,
>>>
>>> Where can I read about the exact format of the TRR and XTC files. I
>>> mean the width and type of every field in the binary trajectory file.
>>>
>>> I see read_'next_frame(status,&fr)' function in 'template.c'. But
>>> where is this fuction define
Dear all user
How can I have a force field for simulation of boron-nitride nanotube?
The pdb file of nanotube is as follow:
HETATM1 N1 UNK 1 1.597 0.000 -5.015 1.00 0.00
N
HETATM2 N2 UNK 1 1.129 1.129 -2.870 1.00 0.00
N
HETATM3 B3 UNK 1 1.1
Of course, there exist a bunch of works simulating B-N NTs. See
papers.
PDB file isn't enough to make a topology for gromacs.
gurgo> Has anything like that ever been simulated? If it hasn't, there may not
be
gurgo> paramteers for such a species. I don't believe boron exists as an atom
type in
Hi all,
may be this is very basic query
I want to calculate order parameters of popc. I have found in archives that
make sn1.ndx(pamitoyl) and sn2.ndx(oleyl) of popc then feed these files to
g_order command. Can anyone tell me that why pamitoyl call as sn1 and oleyl
call as sn2?
Thanks for y
Hello GROMACS users!
I would like to preform arithmetic operations on trajectories which
are output from GROMACS simulations (e.g., to multiply the velocity of
atom 1 by that of atom 2, and average over time). I have read in the
mailing lists references to g_traj and other functions, but think
ravi sharma wrote:
hi
you have written that in my file there are some trailing characters,
how can identify these characters ??
You can see them in the vi editor.
-Justin
;simulated annealing
> annealing = single^M
> annealing_npoints = 5 ^M
> annealing_time = 2 500 100
Hi gmx-users,
Sorry for a not-strictly-GROMACS-related question, but could someone suggest
a program I could use to fit atomic charges to quantum chemistry results?
Thanks in advance,
Vasilii
___
gmx-users mailing listgmx-users@gromacs.org
http://ww
Hi.
Anyway, it would be nice to have a structured manual for the GMX/CPMD
interface. The website http://www.tougaloo.edu/research/qmmm has just a
few basic information and further information in this mailing list under
http://www.gromacs.org/pipermail/gmx-users/2006-June/022329.html are not
that e
Thanks Justin for your reply
you mean to say that C32 of glycerol involves in the palimotyl chain formation
so call as sn1 chain similarly C12,C13 of glycerol involves in the oleyl chain
formation so call as sn2.
Am I correct?
Thanks in advance.
On Mon, 08 Sep 2008 Justin A.Lemkul wrote :
>
>
>m
minnale wrote:
Hi all,
may be this is very basic query
I want to calculate order parameters of popc. I have found in archives
that make sn1.ndx(pamitoyl) and sn2.ndx(oleyl) of popc then feed these
files to g_order command. Can anyone tell me that why pamitoyl call as
sn1 and oleyl call as
minnale wrote:
Thanks Justin for your reply
you mean to say that C32 of glycerol involves in the palimotyl chain
formation so call as sn1 chain similarly C12,C13 of glycerol involves in
the oleyl chain formation so call as sn2.
Am I correct?
More or less, let's just get a few things straig
Thank you! After a day of searches I found the function body I wanted. :)
gurgo> Hello,
gurgo> if you have problems, finding appropiate header files for the
gurgo> functions of gmx, you can perhaps use a development environment like
gurgo> Eclipse, Source-Navigator, KDevelop, Anjuta depending
gurgo> If anyone has a simpler example along the lines of my interests,
gurgo> please send me it!
and to me...
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www
to me too.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Mon, Sep 8, 2008 at 16:30, Vitaly Chaban <[EMAIL PROTECTED]>wrote:
> gurgo> If anyone has a simpler example along the lines of my interests,
> gurgo> please send me it!
>
>
>
OM> to me too.
OM>
OM> Koby Levy research group,
OM> Weizmann Institute of Science.
OM> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
It sounds like an epidemic of analyzing gromacs trajectories. :)
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4,
Dear all,
I would like to ask you help on an installation issue of GROMACS. When I
am running ''make'' after configuring GROMACS, I get the following
error:
/usr/libexec/gcc/i686-apple-darwin8/4.2.1/ld: undefined symbols:
_gmx_fft_3d_real
_gmx_fft_init_3d_real
Collect2: ld returned 1 exit
I am trying to make a radial temperature profile of a given thickness. I
originally used the confout.gro file containing the final output of velocity
and position of each atom to calculate the temperature from the velocity but
would like to take time averages now.
Andy
On Sat, Sep 6, 2008 at 4:21
ravi sharma wrote:
Hello justin,
whether i do correct my md.mdp by vi editor but still it was giving
error well i removed all those groups which coupling to thermostat now
its working (NA+ HEME SOL)
I guess I hadn't even considered that. If you're doing simulated annealing, and
progres
I suggest that we consider ways in which the mailing list can be
optimized. My initial thought is to allow submitters to flag messages
as belonging to some particular topic(s).
e.g.
"program crash"
"force fields"
"protein"
"free energy"
"coarse graining"
"lipids and detergents"
"unknown"
etc.
Hi, Everyone,
I just want to use the clustering tool in amber which only take trj file.
Thanks
-Ranqi
_
Want to do more with Windows Live? Learn “10 hidden secrets” from Jamie.
http://windowslive.com/connect/post/jamiethomson.spac
it's called internet forum... :)
> I suggest that we consider ways in which the mailing list can be
> optimized. My initial thought is to allow submitters to flag messages
> as belonging to some particular topic(s).
>
> e.g.
> "program crash"
> "force fields"
> "protein"
> "free energy"
> "coar
Vitaly Chaban wrote:
it's called internet forum... :)
we've had this discussion before.
On a forum many of the hardcore gromacs people (like me) would probably
not respond anymore.
I suggest that we consider ways in which the mailing list can be
optimized. My initial thought is to allow su
Hey again!
The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm
getting some weird behaviour from grompp where it doesn't set the
output filename correctly. Here is the grompp output from when I run
the demo program, for example (the demo works fine until it gets to
this
Using emails, this might be done "manually" - each user will add to the
TOPIC something like: "tag install", etc`.
Then each user could define his own rule, in his personal email account, how
to deal with messages that contain "tag xxx" & "gromacs" in the topic.
Just a thought... Omer.
Koby Levy r
Are you sure this will be done automaticaly if you'll procide gromacs with
an output file called filename.trj?
There is also the option of converting into PDB: "trjconv -f traj.xtc -o
trajtraj.pdb -s coordinates.gro".
omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizma
Thanks alot Justin for your detailed explanation.
On Mon, 08 Sep 2008 Justin A.Lemkul wrote :
>
>
>minnale wrote:
>>Thanks Justin for your reply
>>you mean to say that C32 of glycerol involves in the palimotyl chain
>>formation so call as sn1 chain similarly C12,C13 of glycerol involves in the
Christopher Daub wrote:
Hey again!
The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm
getting some weird behaviour from grompp where it doesn't set the output
filename correctly. Here is the grompp output from when I run the demo
program, for example (the demo works fine u
Omer Markovitch wrote:
Are you sure this will be done automaticaly if you'll procide gromacs
with an output file called filename.trj?
There is also the option of converting into PDB: "trjconv -f traj.xtc -o
trajtraj.pdb -s coordinates.gro".
omer.
try
trjconv -o blabla.g87 -f something
Kob
Hi all,
I am interested about analyse some of the results with amber and gromacs md
packages. Could anyone tell me how to convert .xtc of gromacs to trajectory
input for amber.
eagerly waiting for reply
Thanks in advance.___
gmx-users mailing list
Hi all,
I am interested about analyse some of the results with amber and gromacs md
packages. Could anyone tell me how to convert .xtc of gromacs to trajectory
input for amber.
eagerly waiting for reply
Thanks in advance.___
gmx-users mailing list
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