Dear all, I downloaded GMX from Ubuntu, and it was the 4.0.71 version. Does
anyone know or have the possibility to update UBUNTU with the latest GMX?
Cheers
Sergio
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Please search the archive at
you have generated your em1.tpr file using a newer gromacs version, and are
trying to read it with an older gromacs version. Please make sure you use
the same gromacs version. Try typing which grompp to find out.
On Fri, Dec 24, 2010 at 8:49 AM, shikha agarwal wrote:
> hi ,
> Mr. justin
> thanx
On 24/12/2010 6:49 PM, shikha agarwal wrote:
hi ,
Mr. justin
thanx a lot for ur help!
now i m able to generate system_inflated.gro.
but while i m performing Run energy minimization accorning to
tutorial getting this error
grompp -f minim.mdp -c pope.gro -p topol_pope.top -o em1.tpr
mdrun -
On 24/12/2010 6:45 PM, Sergio Manzetti wrote:
Hi thanks, but if I use make it says make no Makefile found...
Right, so configure didn't work, unlike your statement that it did
work... Troubleshoot the step that failed, not things that came after it...
Mark
On Thu, Dec 23, 2010 at 10:46 PM
On 24/12/2010 8:20 PM, Sergio Manzetti wrote:
Dear all, I downloaded GMX from Ubuntu, and it was the 4.0.71 version.
Does anyone know or have the possibility to update UBUNTU with the
latest GMX?
If it's not in the package manager, than whoever contributed it to
Ubuntu hasn't updated it, I'm
On 22/12/2010 5:44 PM, Qin Qiao wrote:
Dear all,
I posted yesterday but didn't get answer..I guess it's due to my wrong
approach to ask. I would like to explain more and hope I would get
your help.
I'm doing an REMD, and want to have a strong temperature coupling to
make sure every replica
Hi all
I want to simulate more than 1000 molecules of say octane r any alkanes in
gromacs. after doing a little math i find my box dimensions for the
molecules. but when i use genbox to insert multiple molecules in my local
system after running some time it says cannot allocate memory but when the
On 2010-12-24 11.06, vinothkumar mohanakrishnan wrote:
Hi all
I want to simulate more than 1000 molecules of say octane r any alkanes
in gromacs. after doing a little math i find my box dimensions for the
molecules. but when i use genbox to insert multiple molecules in my
local system after runn
On 2010-12-24 11.04, Mark Abraham wrote:
On 22/12/2010 5:44 PM, Qin Qiao wrote:
Dear all,
I posted yesterday but didn't get answer..I guess it's due to my wrong
approach to ask. I would like to explain more and hope I would get
your help.
I'm doing an REMD, and want to have a strong temperatur
>>
>> I'm not sure that PD has any advantage here. From memory it has to
>> create a 128x1x1 grid, and you can direct that with DD also.
>
>See mdrun -h -hidden for -dd.
>
>Mark
>
>> The contents of your .log file will be far more helpful than stdout in
>> diagnosing what condition led to the probl
Dear Gmx users,
I wanted to do a simulation with NVE ensemble but
i want the temprature to be always around 300k but in my simulation the temp
is 380k.can anyone help me out with this.
regards,
sree.
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Not really, there were no errors with ./configure
so I downloaded the version through ubunto sudo -apt get install gromacs
but it was old version
On Fri, Dec 24, 2010 at 10:53 AM, Mark Abraham wrote:
> On 24/12/2010 6:45 PM, Sergio Manzetti wrote:
>
> Hi thanks, but if I use make it says mak
On 24/12/10 10:36, David van der Spoel wrote:
On 2010-12-24 11.04, Mark Abraham wrote:
On 22/12/2010 5:44 PM, Qin Qiao wrote:
Dear all,
I posted yesterday but didn't get answer..I guess it's due to my wrong
approach to ask. I would like to explain more and hope I would get
your help.
I'm doin
On 2010-12-24 13.15, ms wrote:
On 24/12/10 10:36, David van der Spoel wrote:
On 2010-12-24 11.04, Mark Abraham wrote:
On 22/12/2010 5:44 PM, Qin Qiao wrote:
Dear all,
I posted yesterday but didn't get answer..I guess it's due to my wrong
approach to ask. I would like to explain more and hope
On 24/12/2010 9:59 PM, Wojtyczka, André wrote:
I'm not sure that PD has any advantage here. From memory it has to
create a 128x1x1 grid, and you can direct that with DD also.
See mdrun -h -hidden for -dd.
Mark
The contents of your .log file will be far more helpful than stdout in
diagnosing w
On 24/12/2010 9:06 PM, vinothkumar mohanakrishnan wrote:
> Hi all
>
> I want to simulate more than 1000 molecules of say octane r any
> alkanes in gromacs. after doing a little math i find my box dimensions
> for the molecules. but when i use genbox to insert multiple molecules
> in my local syste
Have a good look in acpype, specially its wiki. There you'll see that acpype
is totally new code and among other things it covers amb2gmx.pl and solves
several of its drawbacks. It's not perfect though but for a system created
in tleap, the project is likely to be completed converted to gmx.
Alan
Quoting Sergio Manzetti :
> Not really, there were no errors with ./configure
>
That's simply not possible. The purpose of configuration is to determine
specifications of your system, which are then used to write the Makefile. If
you have no Makefile, then something failed. If you want to try to
Thanks Justin, here is it the copy-out:
ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane..
Quoting Sergio Manzetti :
> Thanks Justin, here is it the copy-out:
>
> ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure
> checking build system type... i686-pc-linux-gnu
> checking host system type... i686-pc-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> chec
Thanks J, I think I will install Ubuntu entirely first, because I just tried
to install FFTW now, and managed only to get to make install, then I got
permission denied messages, so even though I thought I was the admin, I am
seemingly not.
On Fri, Dec 24, 2010 at 2:44 PM, Justin A. Lemkul wrote:
Quoting Sergio Manzetti :
> Thanks J, I think I will install Ubuntu entirely first, because I just tried
> to install FFTW now, and managed only to get to make install, then I got
> permission denied messages, so even though I thought I was the admin, I am
> seemingly not.
>
Before blowing away y
Thanks again J, is that compulsory each time one installs something new?
On Fri, Dec 24, 2010 at 2:50 PM, Justin A. Lemkul wrote:
> Quoting Sergio Manzetti :
>
> > Thanks J, I think I will install Ubuntu entirely first, because I just
> tried
> > to install FFTW now, and managed only to get to m
Well here is the FFTW message at make install:
/usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h'
/usr/bin/install: cannot remove `/usr/local/include/fftw3.h': Permission
denied
/usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f'
/usr/bin/install: cannot remove `/usr
Justin, THe FFTW messagte was AFTER sudo make install.
On Fri, Dec 24, 2010 at 2:53 PM, Sergio Manzetti <
sergio.manze...@vestforsk.no> wrote:
> Well here is the FFTW message at make install:
>
> /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h'
> /usr/bin/install: cannot rem
Quoting Sergio Manzetti :
> Justin, THe FFTW messagte was AFTER sudo make install.
>
Then you're not an admin. You can always do the installations in your home
directory (for both FFTW and Gromacs) by specifying an appropriate --prefix
during configuration.
-Justin
> On Fri, Dec 24, 2010 at
Thanks, but I will start from scratch.
On Fri, Dec 24, 2010 at 3:13 PM, Justin A. Lemkul wrote:
> Quoting Sergio Manzetti :
>
> > Justin, THe FFTW messagte was AFTER sudo make install.
> >
>
> Then you're not an admin. You can always do the installations in your home
> directory (for both FF
Dear Gmx users,
I wanted to do a simulation with NVE ensemble but
i want the temprature to be always around 300k but in my simulation the temp
is 380k.I am usng leap frog as integrator .can anyone help me out with
this.how to do the velocity rescaling
regards,
sree.
--
hello
I m unable to update the [ molecules ] directive of topol_pope.top .
grompp -f minim.mdp -c system_inflated.gro -p topol_pope.top -o em1.tpr
Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 20782)
does not match topology (topol_pope.top, 37867)
On Fri, 24 Dec 2010 06:36:03 -0800
sreelakshmi ramesh wrote:
> Dear Gmx users,
> I wanted to do a simulation with NVE
> ensemble but i want the temprature to be always around 300k but in my
> simulation the temp is 380k.I am usng leap frog as integrator .can
> anyone help
Quoting shikha agarwal :
> hello
>
>
> I m unable to update the [ molecules ] directive of topol_pope.top .
>
> grompp -f minim.mdp -c system_inflated.gro -p topol_pope.top -o em1.tpr
>
>
> Fatal error:
> number of coordinates in coordinate file (system_inflated.gro, 20782)
> does not
what is velocity rescaling and how to use it in nve simulations.
thanks in advance.
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Please search the archive at
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Please don't
Quoting sreelakshmi ramesh :
> what is velocity rescaling and how to use it in nve simulations.
>
Velocity rescaling is a method for controlling temperature by modifying the
kinetic energy. In an NVE simulation, thermostats are not used.
-Justin
> thanks in advance.
>
===
On 24/12/10 12:26, David van der Spoel wrote:
I'm not an expert, but isn't Berendsen usually not used because it
doesn't give a correct ensemble? I may be partial because I personally
know Giovanni Bussi, but it seems from what I've heard that v-rescale is
the best choice usually.
V-rescale is
On 12/24/10 6:40 PM, ms wrote:
On 24/12/10 12:26, David van der Spoel wrote:
I'm not an expert, but isn't Berendsen usually not used because it
doesn't give a correct ensemble? I may be partial because I personally
know Giovanni Bussi, but it seems from what I've heard that v-rescale is
the bes
mustafa bilsel wrote:
Hi,
I have a problem with dssp programme.
I have the programme in /home/m/DSSP. When I write
export DSSP=/usr/local/bin
and then I check /usr/local/bin I couldn't see dssp.
How can I handle this problem. I have caheceked gromacs website
export DSSP=/path/to/dssp
setenv D
Dear Justin,
I have added your last reply to the end of this message.
my shell type is bash.
my dssp exe file is in /home/m/DSSP/dssp
I wrote export DSSP=//home/m/DSSP/ as in gromacs web page, then I did
do_dssp I have the below error. Although the dssp exe is in /usr/local/bin
and also I did expor
Hi,
What is the meaning of the below message after I completed minimization?
Does it mean minimization is successful?
In my input parameters nsteps=10,000,000 but minimization stops at about
14,000 th step. Is 10,000,000 very large? What is the typical value for it?
And also what is the meaning of
mustafa bilsel wrote:
Dear Justin,
I have added your last reply to the end of this message.
my shell type is bash.
my dssp exe file is in /home/m/DSSP/dssp
I wrote export DSSP=//home/m/DSSP/ as in gromacs web page, then I did
This is still wrong. As I quoted in the previous message, the DSS
mustafa bilsel wrote:
Hi,
What is the meaning of the below message after I completed minimization?
Does it mean minimization is successful?
In my input parameters nsteps=10,000,000 but minimization stops at about
14,000 th step. Is 10,000,000 very large? What is the typical value for it?
Thanks a lot!
It says Nose-hoover coupling generates the correct canonical ensemble, and
that's the reason why I used it. I wonder whether v-rescale can also get the
correct ensemble. Could you tell me?
I'm quite curious how to choose the frequency of the T-coupling in REMD.
Though it seems the h
hello
Merry Christmas.
this is my topol_pope.top file
; Include chain topologies
#include "forcefield.itp"
#include "pope.itp"
; Include water topology
#include "spc.itp"
; Include ion topologies
#include "ions.itp"
; System specifications
[ system ]
340-Lipid POPE Bilayer
[ molecules ]
;
Dear All
I want to pull my ligand from protein which is docked to it for generating
configurations for umbrella sampling.
But my ligand is located in a hole inside of protein.
If I pull it along the line which is connecting COMs of them,the ligand may
be arrested(constraint)inside of hole.
Am I for
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