On 9/4/16 2:52 PM, Atila Petrosian wrote:
Dear Justin,
Thanks for your good guidance (There is only one program now.).
My previous problem was solved.
Now, I have another question.
I used two times following commands for my system (protein):
gmx_mpi mdrun -v -deffnm npt >& npt_1.job &
gm
Dear Justin,
Thanks for your good guidance (There is only one program now.).
My previous problem was solved.
Now, I have another question.
I used two times following commands for my system (protein):
gmx_mpi mdrun -v -deffnm npt >& npt_1.job &
gmx_mpi mdrun -nb gpu -v -deffnm npt >& npt_2.j
On 9/4/16 1:45 PM, Atila Petrosian wrote:
Dear Mark,
In /usr/local/gromasc/bin directory, there are only
demux.pl
gmx-completion.bash
gmx-completion-gmx_mpi.bash
gmx_mpi
GMXRC
GMXRC.bash
GMXRC.csh
GMXRC.zshxplor2gmx.pl
In this directory, there is gmx_mpi rather than gmx. It is true based
on
Dear Mark,
In /usr/local/gromasc/bin directory, there are only
demux.pl
gmx-completion.bash
gmx-completion-gmx_mpi.bash
gmx_mpi
GMXRC
GMXRC.bash
GMXRC.csh
GMXRC.zshxplor2gmx.pl
In this directory, there is gmx_mpi rather than gmx. It is true based
on the
http://manual.gromacs.org/documentation/5
Dear Mark,
> you still need to source the GMXRC from the version you want to use > > in
> the terminal you want to use it from.
I used source /usr/local/gromacs/bin/GMXRC,
But, when I use gmx pdb2gmx command, I encountered with:
-bash: gmx: command not found
Best,
Atila
--
Gromacs Users mail
Hi,
Like the installation instructions say, you still need to source the GMXRC
from the version you want to use in the terminal you want to use it from.
Mark
On Sun, 4 Sep 2016 16:02 Atila Petrosian wrote:
> Dear Justin,
>
> Thanks for your answer.
>
> I know several programs have been renamed
Dear Justin,
Thanks for your answer.
I know several programs have been renamed in new version such as
pdb2gmx --> gmx pdb2gmx. But when I use gmx pdb2gmx,
-bash: gmx: command not found
Best,
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_L
On Sunday, September 4, 2016, Atila Petrosian
wrote:
> Dear Mark,
>
> Thanks for your quick answer.
>
> Now, how to use gromacs 5.1.3 commands?
>
> The reason of my question:
>
> There is gromacs 4.5.4 (in /opt/bio directory) in my Rocks cluster system
> by default.
>
> I used source /usr/local/g
Dear Mark,
Thanks for your quick answer.
Now, how to use gromacs 5.1.3 commands?
The reason of my question:
There is gromacs 4.5.4 (in /opt/bio directory) in my Rocks cluster system
by default.
I used source /usr/local/gromacs/bin/GMXRC,
then
pdb2gmx
Unfortunately, pdb2gmx related to gromac
Hi,
Yes.
http://manual.gromacs.org/documentation/5.1/ReleaseNotes/removed-features.html#removed-temporary-symlinks-from-pre-5-0-tool-names
Mark
On Sun, Sep 4, 2016 at 3:19 PM Atila Petrosian
wrote:
> Dear Mark,
>
> Thanks for the guidance.
>
> I updated gcc using your proposed link (https://ed
Dear Mark,
Thanks for the guidance.
I updated gcc using your proposed link (https://ed.braaten.net/blog/
2014-05-28-devtools-for-centos/).
Now my Rocks cluster system has following info:
Rocks 6.2
CentOS 6.6
Cuda 7.5 and 8 (/usr/local/cuda)
gcc 4.8.2
I installed gromacs 5.1.3 based on followin
Dear James,
Thank you for your reply. I have tried the trjconv for fixing PBC and it
works fine. I posted this query because I came across the following very
old thread
https://redmine.gromacs.org/issues/165
thus I wanted to make sure everything is fine.
Thanking you,
Prithvi
> -
>
> Messag
Hi,
I think some crystal water molecules are important to my the system. Can I
keep the crystal water molecules when I run a MD simulation with implicit
water model?
Thank you in advance!
Best regards!
Dading Huang
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.
13 matches
Mail list logo