Dear All,
I am practising the tutorial 2 of Gromacs ( KALP-15 in DPPC). In the
step Solvate
with water,i made a copy of vdwradii.dat and changed the value of C from
0.15 to 0.375. But i don't know how to input this changed file into genbox.
I saw genbox -h, and i don't find any option for input
jalem...@vt.edu wrote:
On 12/16/12 10:15 PM, Kieu Thu Nguyen wrote:
Dear All,
I am practising the tutorial 2 of Gromacs ( KALP-15 in DPPC). In the
step Solvate
with water,i made a copy of vdwradii.dat and changed the value of C from
0.15 to 0.375. But i don't know how to input
I got it. Thank Justin !
Regards
KT
On Mon, Dec 17, 2012 at 10:28 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote:
Thank Justin !
But i am not clear Is it read automatically when i put it in the working
directory or put it in
$GMXLIB ?.
The same question with gromos53a6_lipid.ff
, Dec 17, 2012 at 8:56 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/17/12 8:53 AM, Kieu Thu Nguyen wrote:
Dear All,
I'm practising the tutorial 2a (protein in water) in the MARTINI tutorial.
After doing step 6 (Do a short energy minimization and position restrained
simulation),i carry out
:
On 12/17/12 9:24 AM, Kieu Thu Nguyen wrote:
Dear All,
When i do the Step Four: Adding Ionsin the tutorial KALP-15 in DPPC,
it
appears the error:
Fatal error:
No such moleculetype W
I checked .top file and included.itp files, they have definded water
molecule type name is W.
What happens
I have just found the right group is 15 (SOL) :-)
Thanks so much and sorry about my stupid question !
On Mon, Dec 17, 2012 at 11:40 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/17/12 11:38 AM, Kieu Thu Nguyen wrote:
Thank Justin ! I found my mistake. But when i type the next command
Thank Justin !
On Tue, Dec 18, 2012 at 7:20 AM, Justin Lemkul jalem...@vt.edu wrote:
On 12/17/12 7:17 PM, Kieu Thu Nguyen wrote:
Dear All,
When i do step EM, the output file .gro is separated into many step.pdb
files . And many errors Water molecule starting at atom XXX can
a
heap of warinngs/notes/errors if structure file and topology don't match.
Erik
Cheers,
Tsjerk
On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen kieuthu2...@gmail.com
wrote:
Dear All,
I don't know which tools used to merge 2 files .gro, 2 files .top ?
Can i use trjcat ?
Thanks !
KT
Thank Justin !
On Tue, Dec 18, 2012 at 10:31 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/18/12 10:30 AM, Kieu Thu Nguyen wrote:
Dear All,
Are there any difference in nvt.mdp and npt.mdp files between MD-CG and
MD-AA ?
Settings in the .mdp file are dictated by the chosen force
Thank Justin so much ! :-)
KT
On Thu, Dec 20, 2012 at 11:54 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/20/12 11:38 AM, Kieu Thu Nguyen wrote:
Dear All,
I convert cg to fg representation by command lines
g_fg2cg -pcg cg.top -pfg fg.top -c cg.gro -n 1 -o fg.grog_fg2cg -pcg
cg.top
But, are there any way using this tool in Gromacs v4.5 ? Since i don't want
to remove version 4.5 and install version 3.3.1
Thank All !
KT
On Fri, Dec 21, 2012 at 6:41 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote:
Thank Justin so much ! :-)
KT
On Thu, Dec 20, 2012 at 11:54 PM, Justin
Thank Tsjerk so much :-)
Merry Christmas !
KT
On Fri, Dec 21, 2012 at 3:52 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Tsjerk
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Sorry, i don't see where is manual for updating.
KT
On Tue, Dec 25, 2012 at 10:24 AM, Justin Lemkul jalem...@vt.edu wrote:
On 12/24/12 10:08 PM, Kieu Thu Nguyen wrote:
Dear All,
When i merge 2 file.gro by command cat, the atom number have not updated
by itself.
Are there any method
I got it. Thank Justin !
On Tue, Dec 25, 2012 at 10:40 AM, Justin Lemkul jalem...@vt.edu wrote:
I don't mean the Gromacs manual, I mean manual in the sense that if you
modify a coordinate file without using one of the Gromacs tools, then you
must manually (i.e. by yourself using some
, 2012 at 6:43 PM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote:
thank all so much :-)
KT
On Tue, Dec 18, 2012 at 4:12 PM, Vedat Durmaz dur...@zib.de wrote:
there's also an executable topology merger available written in python
called gromacs_topology_merger.py as part of a the software package
the created .top might miss some information (tipically
angles and dihedrals)
so I advice you to carefully check the .top file.
Francesco
2012/12/26 Kieu Thu Nguyen kieuthu2...@gmail.com
Dear All,
Are there any method that can convert CHARMM PSF files to Gromacs
topology
files ?
Thank
and no empty lines after the box definition, you have to replace the
second line with the number of lines minus three:
sed '2s/^.*$/'$(wc -l file.gro)'/' file.gro out.gro
Cheers,
Tsjerk
On Tue, Dec 25, 2012 at 7:33 AM, Kieu Thu Nguyen kieuthu2...@gmail.com
wrote:
But i don't see file
too. You can also first
set up an AA model and convert to CG afterwards. However, martinize.py only
works for the protein, so you have to convert the lipids in a different
way.
Cheers,
Tsjerk
On Thu, Dec 27, 2012 at 2:00 AM, Kieu Thu Nguyen kieuthu2...@gmail.com
wrote:
Dear All,
When
Dear All,
When using the command
grompp -f equi.mdp -c membedded.gro -p merged.top -n index.ndx -o
equilibrate.tpr
The error is
Fatal error:
Invalid atom number 6518 in indexfile
How can i fix this ?
Thank so much for any help !
Regards,
KT
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gmx-users mailing listgmx-users@gromacs.org
...@gromacs.org on behalf of Kieu Thu Nguyen
Sent: Fri 1/4/2013 6:51 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] error with indexfile
Dear All,
When using the command
grompp -f equi.mdp -c membedded.gro -p merged.top -n index.ndx -o
equilibrate.tpr
The error is
Fatal
Thank Justin and Peter so much !
Can i make a new box (it's size is not a multiples of the size of the
previous box) from a smaller lipid bilayer box ?
I don't see genconf -nbox can do that.
On Fri, Jan 11, 2013 at 9:20 AM, Peter Lai p...@uab.edu wrote:
Kieu Thu Nguyen kieuthu2...@gmail.com
Thank Justin ! :-)
On Fri, Jan 11, 2013 at 5:26 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/10/13 11:37 PM, Kieu Thu Nguyen wrote:
Thank Justin and Peter so much !
Can i make a new box (it's size is not a multiples of the size of the
previous box) from a smaller lipid bilayer box ?
I
Sorry, i have one more question : Does genbox make new box that the area
per lipid is unchange (the same with the old box) ?
On Fri, Jan 11, 2013 at 7:04 PM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote:
Thank Justin ! :-)
On Fri, Jan 11, 2013 at 5:26 PM, Justin Lemkul jalem...@vt.edu wrote
, Kieu Thu Nguyen wrote:
Sorry, i have one more question : Does genbox make new box that the area
per lipid is unchange (the same with the old box) ?
genbox reads in the old coordinates and uses them to build a grid within
the new box. It will not write partial molecules, so in the case
de Farmacia y Bioquímica
Universidad de Buenos Aires
Junín 956 6º (1113)
TE: 54 011 4964-8273
De: Kieu Thu Nguyen kieuthu2...@gmail.com
Para: Discussion list for GROMACS users gmx-users@gromacs.org
Enviado: miércoles, 16 de enero de 2013 13:09
Asunto: [gmx
jalem...@vt.edu wrote:
On 1/16/13 4:39 PM, Kieu Thu Nguyen wrote:
Thank Justin and Flor so much ! Sorry about my unclear question. I mean
that my boxes is not isotropic. Each box has many types of molecules such
as water, lipid, ... Are those tools that you adviced me available
Thank Justin ! That is APL. How about bilayer thickness ? I made
density.xvg file of headgroup from using g_density.
On Mon, Jan 21, 2013 at 7:31 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote:
Dear All,
I want to know that my lipid bilayer
Thank Felipe ! :-)
On Mon, Jan 21, 2013 at 5:30 PM, Felipe Pineda, PhD
luis.pinedadecas...@lnu.se wrote:
http://www.gromacs.org/**Documentation/How-tos/**Extending_Simulationshttp://www.gromacs.org/Documentation/How-tos/Extending_Simulations
On 01/21/2013 11:20 AM, Kieu Thu Nguyen wrote
in advance !
KT
On Mon, Jan 21, 2013 at 11:03 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/21/13 10:17 AM, Kieu Thu Nguyen wrote:
Thank Justin ! That is APL. How about bilayer thickness ? I made
density.xvg file of headgroup from using g_density.
g_dist with index groups specifying however you
Thank Justin so much ! Sorry about my stupid question. I have looked the
algorithm and i got it.
On Tue, Jan 22, 2013 at 8:05 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/22/13 12:00 AM, Kieu Thu Nguyen wrote:
Thank Justin ! And i used GridMAT-MD as you advised.
I got result The average
,
Tsjerk
On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen kieuthu2...@gmail.com
wrote:
Dear All,
My MD simulation has an error
Warning: Only triclinic boxes with the first vector parallel to the
x-axis
and the second vector in the xy-plane are supported.
Box (3x3
= no
lincs_order = 4
lincs_warnangle = 30
Thanks so much for any help !
Regards,
KT
On Sun, Jan 27, 2013 at 8:26 AM, Justin Lemkul jalem...@vt.edu wrote:
On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote:
Thank Tsjerk so much !
But after being minimized 5 steps
time step.
Cheers,
Tsjerk
On Mon, Jan 28, 2013 at 3:11 AM, Justin Lemkul jalem...@vt.edu wrote:
On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote:
@Justin,
Fmax=8.0226669e+00
OK, that looks good.
the system includes protein, lipid, water, ion Cl-
em.mdp file
I reduced time step in equi.mdp file to 20 ps. But the system is still not
balance. Should i continue reduce time step below 20 ps value ? Thanks so
much for any suggestion about appropriate time step value !
Regards,
KT
On Mon, Jan 28, 2013 at 12:53 PM, Kieu Thu Nguyen kieuthu2
Dear all,
I want to calculate the size of the protein. Which tool should i use for
this purpose ?
Thanks and regards,
KT
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: editconf
- volume: g_sas
Cheers,
Tsjerk
On Fri, Feb 8, 2013 at 5:55 AM, Kieu Thu Nguyen kieuthu2...@gmail.com
wrote:
Dear all,
I want to calculate the size of the protein. Which tool should i use for
this purpose ?
Thanks and regards,
KT
--
gmx-users mailing listgmx
Hi,
What is the specific editconf command should i use to calculate the
dimensions of fitting box of the protein ?
Thanks and regards,
KT
On Fri, Feb 8, 2013 at 2:03 PM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote:
Thank Tsjerk ! I mean that i want to determine the dimensions (x, y, z
:36 PM, Kieu Thu Nguyen wrote:
Dear All,
I want to equilibrate a rectangular box. But after running MD 60 ns, the
system become to be a cubic box mostly. I do not want this happens. Can
anyone tell me how to constrain the boxsize. In that case, the boxsize has
fluctuations but remains
Dear All,
I carry out inserting a protein into lipid membrane by using g_membed tool.
But i have errors :
Fatal error:
(i) Something is wrong with your membrane. Max and min z values are
12.15 and 0.01.
(ii) Maybe your membrane is not centered in the box, but located at the box
edge in
Dear All,
I made a POPC bilayer and carried out embedding a protein into this
membrane. But the fatal error has appeared :
Fatal error:
Something is wrong with your membrane. Max and min z values are 12.342000
and 0.016000. Maybe your membrane is not centered in the box, but located
at the box
, Justin Lemkul jalem...@vt.edu wrote:
On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen kieuthu2...@gmail.com
wrote:
Dear All,
I made a POPC bilayer and carried out embedding a protein into this
membrane. But the fatal error has appeared :
Fatal error:
Something is wrong with your
Dear all,
I want to renumber residue number in file .top (to begin from 1). Have
anyone has a script for this purpose ?
Thankful for any help!
Thu
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Dear users,
Is there command for using many different index.ndx files in one command
line ? I used -n flag many times and gromacs report error.
Thankful for any help!
Thu
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Thank Terry and Justin so much ! I got it :-)
On Tue, May 28, 2013 at 9:20 AM, Justin Lemkul jalem...@vt.edu wrote:
On 5/27/13 10:18 PM, Kieu Thu Nguyen wrote:
Dear users,
Is there command for using many different index.ndx files in one command
line ? I used -n flag many times
Dear users,
What is the algorithm of umbrella sampling simulation ? And can anyone who
had experience in this explain pulling force to me ?
Thankul and regards,
~Thu
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Thank JW so much :-)
On Wed, Jun 12, 2013 at 10:30 PM, JW Gibbs hanniballecte...@gmail.comwrote:
Hi,
Please see the following links:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/
http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WCMS66.html
I think
Dear users,
I make a rectangle bilayer by doubling two equilibrated cubic boxes. But
after minimizing, the system have been crashed. I do not understand why. I
attach the em.mdp below
Thankful for any help !
Thu
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gmx-users mailing listgmx-users@gromacs.org
Dear Justin,
I am testing a umbrella simulation basing on your tutorial. But after using
your distances.pl script, i do not have the file summary_distances.dat.
It only makes many xvg files.
I post the script below:
#!/usr/bin/perl -w
use strict;
# loop g_dist command - measure distance in
Dear users,
How can i fix the system structure while minimizing energy ? I made a
larger system by double a small system. But i can not continue simulation
because the system crashed after EM. Although the small system was
equilibrated well before doubling.
Thankful for any help and regards,
Dear users,
I have a sytem including protein, lipids, and water. My protein is in
center of the box. Now i want it stays at one side of the box. Which tool
or command should i use to pull the protein to a any mong muốn location ?
Thankful for any help !
Thu
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gmx-users mailing list
Dear users,
I want to use g_msd to measure diffusion coefficients of lipid bilayer. But
i do not know how to choose the reference atom per lipid for an any type of
lipid, such as POPC, DOPC,...
Where i can get these references ?
Thanks so much for any help !
~Thu
--
gmx-users mailing list
Thanks so much ! I guessed should i choose it but i am not sure :-)
So, if most people choose it, i think it is ok.
On Mon, Aug 12, 2013 at 4:25 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/11/13 11:26 PM, Kieu Thu Nguyen wrote:
Dear users,
I want to use g_msd to measure diffusion
It depends on what properties of peptides and proteins that you want to
explore.
~Thu
On Mon, Aug 12, 2013 at 7:19 PM, Maria Astón Serrano
m.aston.serr...@gmail.com wrote:
Dear Gromacs users,
We would like to know which is the Force Field which is customarily
preferred for simulations of
Hi,
I also want to try :)
Best regards,
~Thu
On Wed, Oct 23, 2013 at 11:39 PM, houyang chen houyangc...@gmail.comwrote:
Hi Kevin
Can I have a try?
Best
Houyang
On Wed, Oct 23, 2013 at 12:30 PM, Villarealed villarea...@hss.edu wrote:
Sound nice. I would like to try out.
Could You
Dear Kiana,
You can contact with Paissoni Cristina (email: paissoni.crist...@hsr.it) to
get tool using MM/PBSA with GROMACS.
Hope it help :)
Cheers,
Kieu Thu
On Tue, Nov 5, 2013 at 7:18 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/5/13 3:45 AM, kiana moghaddam wrote:
Dear GMX Users
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