So I've removed pbc from the structure and defined new box dims by
editconf. Now how I could cut all atoms which are not inclluded to
that box ( water in upper and lower leaflets) ? As I told when I did
it by means of genbox -cs b2ar_Smaller.gro -box 8.68740 8.41864
9.70145 atom order of the
On Dec 23, 2012, at 11:23 PM, Martin Hoefling martin.hoefl...@gmail.com wrote:
You can have a look at http://www.ncbi.nlm.nih.gov/pubmed/21843471 ,
maybe that does what you want.
On
http://www.mpibpc.mpg.de/grubmueller/compel
you will find installation instructions for the special gromacs
Dear GROMACS Specialists,
We know that one system is at equilibrium state when the variation of Helmholtz
or Gibbs free energy be zero.
May I ask you say me that how I can understand that my system has reached to
equilibrium state in the end of simulation, Please?
Best Regards
Sara
--
On 12/24/12 7:38 AM, Wu Chaofu wrote:
Dear gmxers,
I want to recalculate potential energies for the frames generated
previously. At first, I generate one tpr file with a bit difference
from previous one used for generating those frames. Using this tpr
file, then I restart mdrun with -return
On 12/23/12 10:03 AM, IsaureCB wrote:
Dear gmx-users,
I would like to select, for each residue of a model, the residues that are
within 3.6 A in average over a simulation.
g_mdmat must create this information at some point while generating the
contact diagrams, but I would like to extract
On 12/24/12 10:51 AM, sreelakshmi ramesh wrote:
Dear all,
I am trying repeat a work in which the system is coupled to the
Andersen thermostat in which they say they use a coupling constant p =
0.0003 .
could anyone of you tell me does it mean tau_t is 0.0003. Any help
Hi,
I am running a protein simulation for 70 ns. I had a MPI run but due
to my time constraints on the server, it stopped after 28ns. Now, I
want to continue the simulation from the same point up until I use up
my server time.
I just wanted to confirm that there are two checkpoint files
Hi again,
Sorry for the repetition in email.
When I ran the mdrun command, I got an error of
Attempting to read a checkpoint file of version 13 with code of version 12
Can anyone please help me with this error too?
On Mon, Dec 24, 2012 at 4:35 PM, Ankita naithani
ankitanaith...@gmail.com
On 12/24/12 11:54 AM, Ankita naithani wrote:
Hi again,
Sorry for the repetition in email.
When I ran the mdrun command, I got an error of
Attempting to read a checkpoint file of version 13 with code of version 12
Can anyone please help me with this error too?
This means you are not
Hi Justin,
Thank you so much for your response.
I also noticed that when I type in gmxcheck -f md.cpt to see which
version was used, I get the same fatal error of Attempting to read a
checkpoint file of version 13 with code of version 12.
In my linux machine, the gromacs version is 4.5.5 and
On 12/24/12 12:43 PM, Ankita naithani wrote:
Hi Justin,
Thank you so much for your response.
I also noticed that when I type in gmxcheck -f md.cpt to see which
version was used, I get the same fatal error of Attempting to read a
checkpoint file of version 13 with code of version 12.
In my
Dear GROMACS Users,
I work with NPT ensemble. Is the total energy equal to Gibbs free energy?
Thanks in advance.
Sara
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
Obviosuly not. Total energy in MD = total potential energy + total
kinetic energy. Read basis of MD. There are specific methods to get
free energy which you should aslo read about.
Steven
On Mon, Dec 24, 2012 at 6:21 PM, mohammad agha mra...@yahoo.com wrote:
Dear GROMACS Users,
I work with
Dear Justin,
I am sorry to spell the word. In fact, I had referred to the -return as
-rerun. Could you give me some another suggestion? Thank you very much!
Chaofu Wu
--
View this message in context:
http://gromacs.5086.n6.nabble.com/about-return-of-mdrun-tp5004019p5004035.html
Sent from the
mdrun -rerun your-old-trajectory
works. Unfortunately you're asking us to guess what you did wrong, without
giving us any detail of what you did... that's tricky :-)
Mark
On Tue, Dec 25, 2012 at 12:09 AM, xiaowu759 xiaowu...@gmail.com wrote:
Dear Justin,
I am sorry to spell the word. In
Check out http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
On Mon, Dec 24, 2012 at 5:35 PM, Ankita naithani
ankitanaith...@gmail.comwrote:
Hi,
I am running a protein simulation for 70 ns. I had a MPI run but due
to my time constraints on the server, it stopped after 28ns. Now, I
g_analyze -h probably has relevant things to say
On Mon, Dec 24, 2012 at 10:56 PM, zifeng li lizife...@gmail.com wrote:
Hi, Gromacs users,
I'm using Gromacs 4.5.4 and wondering how is the Err.Est given by
g_energy calculated? Is it roughly
standard deviation/ sqrt N
N is the independent
On 12/24/12 5:53 PM, Steven Neumann wrote:
Dear Gmx Users,
I run pulling simulation of my ligand away from the protein. I
produced 1500 frames and run US windows with 0.1 nm spacing. However,
I have a gap in histograms - I need to use lower value of nstxtcout to
get the proper window where
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 for this problem ?
Manual manipulation requires manual updating.
-Justin
--
Justin A.
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
On 12/24/12 10:38 PM, Kieu Thu Nguyen wrote:
Sorry, i don't see where is manual for updating.
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
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
Dear Steven,
Many thanks from your help. In the manual at the section g_energy has been
written that the gromacs calculate the delta G as is follows:
Delta G = G(N,p,T) - G idgas(N,p,T) = kT ln eˆ(Upot/kT)
But I don't understand why Upot? to calculate of delta S, I know that delta S
=
Dear Steven,
Many thanks from your help. In the manual at the
section g_energy has been written that the gromacs calculate the delta G
as is follows:
Delta G = G(N,p,T) - G idgas(N,p,T) = kT ln eˆ(Upot/kT)
But
I don't understand why Upot? to calculate of delta S, I know that
delta S =
Dear all,
I try to make my residues of interest as an index group using the
command make_ndx -f conf.gro -o index.ndx. I have entered my residues as
r 15 23 27 30 82 84 125 127 129 140 143 184 187 188 191 194 195 198 201
205 206 208 211 228 236 261 263 273 277 282 283 428 429 432 433 438 441 457
But i don't see file gromacs_topology_merger.py in the web Vedat gave me.
Tsjerk, can you give me the script for updating the number of atoms ? I
searched in google, but i have not found it yet. It's really my stupid
question, but i don't know why.
Thanks !
Best regards,
KT
On Tue, Dec 18,
Hi all,
I'm trying to simulate a system of POPC- Protein- Water- Ion following the
Justin's tutorial of Kalp15-DPPC.
I get the system-solved-ion.gro and run energy minimization. I saw some water
molecules in em.gro file, therefore, I erase them and then again save the .gro
file as a new
Hi all,
I'm trying to simulate a system of POPC- Protein- Water- Ion following the
Justin's tutorial of Kalp15-DPPC.
I get the system-solved-ion.gro and run energy minimization. I saw some water
molecules in em.gro file, therefore, I erase them and then again save the .gro
file as a new
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