Hello,
I got an error log when I used gromacs-gpu on npt simulation.
The error is like:
---
Input Parameters:
integrator = md
nsteps = 5000
init_step= 0
ns_type = Grid
n
Uday,
You are reproducing the output of md.csh. I would also like to see the
contents of md.csh to know the gromacs commands therein. This would help to see
where the error is coming. Please paste the file md.csh.
sharada
On 15/12/2010 1:03 PM, Tom Dupree wrote:
Greetings all,
We are looking at setting up Linux desktop in our lab for setting up
some simulations to be run externally, as well some short simulations.
I am new to Linux and Gromos.
I'm going to presume you mean GROMACS.
I have done some readin
Greetings all,
We are looking at setting up Linux desktop in our lab for setting up some
simulations to be run externally, as well some short simulations.
I am new to Linux and Gromos.
I have done some reading of the gmx-users list archive and have a few questions.
I was wondering if there is
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of gromacs [ptf1...@163.com]
Sent: Wednesday, December 15, 2010 9:42 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] HPC mpi how to run
Hi ,
I have installed PSFTP and PuTTY.
gromacs wrote:
Hi ,
I have installed PSFTP and PuTTY. I have seen the Gromacs-4.0.7 in ./opt
in wivenhoe (cluster), and i know how to upload my file to my folder
using PSFTP. However i donot know how to run it in HPC; when i using
Gromacs-4.0.7 in my desktop, if the Gromacs is installed pr
Hi ,
I have installed PSFTP and PuTTY. I have seen the Gromacs-4.0.7 in ./opt in
wivenhoe (cluster), and i know how to upload my file to my folder using PSFTP.
However i donot know how to run it in HPC; when i using Gromacs-4.0.7 in my
desktop, if the Gromacs is installed properly, there will
On Wed, Dec 15, 2010 at 12:53 AM, YUVRAJ UBOVEJA wrote:
> Hello
>
> I am trying to simulate lipase in water in ffamber99sb-ildn. Chosen "cubic"
> as box with distance of 1nm b/w solute n box.
> Protein is going out of the box after equilibration step. Any solution?
>
>
The protein does not diffuse
YUVRAJ UBOVEJA wrote:
Hello
I am trying to simulate lipase in water in ffamber99sb-ildn. Chosen
"cubic" as box with distance of 1nm b/w solute n box.
Protein is going out of the box after equilibration step. Any solution?
FAQ #11.
http://www.gromacs.org/Documentation/FAQs
Please also no
Hello
I am trying to simulate lipase in water in ffamber99sb-ildn. Chosen "cubic"
as box with distance of 1nm b/w solute n box.
Protein is going out of the box after equilibration step. Any solution?
Should i use *freezegrps* option to restrict protein movement. Please
provide some light to this
On 15/12/2010 10:07 AM, Ramachandran G wrote:
Hi Itamar,
Thanks for your help. Without the md.log file i could able to
extend the simulation time but i could not able to append to results
to my old .trr and .edr files.
That is what trjcat and eneconv are for.
Mark
Rama
On Mon, Dec 13,
Hi Itamar,
Thanks for your help. Without the md.log file i could able to
extend the simulation time but i could not able to append to results
to my old .trr and .edr files.
Rama
On Mon, Dec 13, 2010 at 6:39 PM, Itamar Kass wrote:
> Hi,
>
> the log file is not needed for extension. Use someth
On 14/12/2010 8:02 PM, Reinhold Bader wrote:
Hello,
building gromacs 4.5.3 with Cmake 2.6.3 fails because the build system
cannot link
g_analyze
Linking C executable g_analyze
../gmxlib/libgmx.a(gmx_matrix.c.o): In function `matrix_invert':
gmx_matrix.c:(.text+0x1d62): undefined refer
Hi!
Sorry that I missed this discussion, we recently moved the lab and there where
quite many things to attend to.
When we did the implementation of implicit solvent into Gromacs, one of the
strong points was to see how fast we could make it, to speed up conformational
sampling as much as poss
On 14/12/10 19:04, Justin A. Lemkul wrote:
I was going to send a very similar mail -namely, I have a coarse-grain
system in vacuum where I'd like to simulate a charged polymer. My idea
was that of adding a single "ghost" counter-ion with zero VdW
interactions, perhaps keeping it fixed in one corn
devicerandom wrote:
On 14/12/10 18:35, Bob Johnson wrote:
Can anyone answer this question or guide me somewhere with helpful
information?
Thanks,
Bob
I was going to send a very similar mail -namely, I have a coarse-grain
system in vacuum where I'd like to simulate a charged polymer. My idea
On 14/12/10 18:35, Bob Johnson wrote:
Can anyone answer this question or guide me somewhere with helpful
information?
Thanks,
Bob
I was going to send a very similar mail -namely, I have a coarse-grain
system in vacuum where I'd like to simulate a charged polymer. My idea
was that of adding a
Can anyone answer this question or guide me somewhere with helpful
information?
Thanks,
Bob
On Thu, Dec 9, 2010 at 4:52 PM, Bob Johnson wrote:
> Hello everyone,
> I am trying to use implicit solvent with a CG DNA model. The model,
> however, uses explicit charges, which means that the DNA carries
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
-- original message --
I can't understand correctly what we do when we are using umberella sampling
for obtaining PMF.
I explain that ,please modify or complete it.
(I think we define some sampling windo
Poojari, Chetan wrote:
Hello Justin,
I deleted the original file and re ran the script. I did get the output as such:
#DonorAcceptor % Exist.
0.040
ASP1
Tomy van Batis wrote:
Dear all
I have a system consisting of 2 substrates (20 nm distance between them)
and inside them there are polymer chains. I would like during my NVT
simulations the substrates NOT to move (I suppose I have to put the
velocity of the COM of it's substrate to be zero)
On 14/12/2010 6:35 PM, shahid nayeem wrote:
Dear Gromacs User
My pdb is homodimer with Arg as c-terminal residue. With this pdb I
am etting following error in pdb2gmx command
Program pdb2gmx, VERSION 4.0.7
Source code file: pdb2gmx.c, line: 429
Fatal error:
Atom OXT in residue ARG 107 not fou
Dear all
I have a system consisting of 2 substrates (20 nm distance between them) and
inside them there are polymer chains. I would like during my NVT simulations
the substrates NOT to move (I suppose I have to put the velocity of the COM
of it's substrate to be zero).
Does anyone know how to do
Hey there,
just a guess into the blue... did you write that md.csh script yourself?
It very much seems like that script is broken badly (see grompp output).
Use your favorite text editor, open md.csh and paste it's content here.
best,
timo
On 12/14/2010 11:13 AM, udaya kiran wrote:
Hello,
He
The input to your grompp command is wrong. You have selected an invalid
grompp option. Please verify the grompp command and rerun the script.
On Tue, Dec 14, 2010 at 11:13 AM, udaya kiran wrote:
> Hello,
>
> Here I am sending the complete output after the md.csh command with the
> errors in bold
Hello,
Here I am sending the complete output after the md.csh command with the
errors in bold.
COMMAND: csh md.csh
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.5 (-:
W
On Tue, Dec 14, 2010 at 10:07 AM, udaya kiran wrote:
> Hello madam,
>
> The command id
>
> *csh* *md.csh
>
> *
Please paste your md.csh file and the error you get in detail.
> **As I see, there is no error in the command. All other commands are
> properly working (like eq.csh, em.csh etc ).
On Dec 14, 2010, at 7:29, samio wrote:
> Hello
>
> I am trying to perform a CG simulation on the solvated protein but there is
> one question that I would like to ask for suggestion. The problem is: the
> volume of the periodic box varied a lot depending on the Van der Waals
> distance of t
Hello madam,
The command id
*csh* *md.csh
*As I see, there is no error in the command. All other commands are
properly working (like eq.csh, em.csh etc ). The problem is only with
md.csh.
yours sincerely,
uday.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailma
Hello,
building gromacs 4.5.3 with Cmake 2.6.3 fails because the build system
cannot link
g_analyze
Linking C executable g_analyze
../gmxlib/libgmx.a(gmx_matrix.c.o): In function `matrix_invert':
gmx_matrix.c:(.text+0x1d62): undefined reference to `dgetrf_'
gmx_matrix.c:(.text+0x2442): und
Hello Justin,
I deleted the original file and re ran the script. I did get the output as
such:
#DonorAcceptor % Exist.
0.040
ASP1 N SOL171
Hi Mohsen,
for a start, it is always a good idea to read the help
text of a command you are interested in, or to check
the most recent version of the manual. Using Gromacs 4.5
g_wham -h
will guide you to a JCTC paper about g_wham, which
is a nice starting point. Check out this paper as well
as
Dear All
What is the algorithm of g-WHAM?
in the other words ,what is the weighted histogeram analysis method?
Thanks in advance for your reply
Mohsen
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gr
Dear All
I can't understand correctly what we do when we are using umberella sampling
for obtaining PMF.
I explain that ,please modify or complete it.
(I think we define some sampling windows,each related to an reference
distance.
for each distance ,relative to it's distance,we define a spring c
Dear All
I want to know what project any Gromacs user is doing.
In the other words what can we do by Gromacs.
** I am calculating binding free energy of drugs to their corresponding
proteins **
Thanks in advance for your replies
Mohsen
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gmx-users mailing listgmx-users@gromacs.org
http://
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