[gmx-users] gnuplot

Tim Harder mail at tim-harder.de
Sun Feb 6 10:51:16 CET 2011


you want to install gnuplot on your local system. As most of the 
analysis, plotting is most
likely done on our local machine.

Without knowledge of your system this is just a stab in the dark.
For linux, open a terminal and type
sudo apt-get install gnuplot
or open the software install panel from the menu and install it from there.

If you have no sudo rights on your machine, you will either have to 
install it manually or
ask your sys admin to help you.


On 2/6/11 10:43 AM, delara aghaie wrote:
> Dear gromacs users
> I am using hpc system of our university to work on molecular dynamics 
> simulation with gromacs. The gormacs has been installed there and I 
> can connect to the hpc system and submit my jobs.
> Now I want to know that for using gnuplot to have my graphs, the 
> gnuplot program should be installed on my office pc or on the hpc 
> system and let me know how to do that? If it should be installed on 
> hpc let me know pls. how should it be installed ?
> Thanks for your time
> D.M
> --- On *Sat, 2/5/11, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
>     From: Justin A. Lemkul <jalemkul at vt.edu>
>     Subject: Re: [gmx-users] Porting Amber parmbsc0 force field to Gromacs
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Date: Saturday, February 5, 2011, 8:53 PM
>     william Stebbeds wrote:
>     > Hello,
>     >
>     > I would like to use the parmbs0 Amber forcefield to Gromacs,
>     specifically the nucleic acid parameters.
>     >
>     > Is this likely to come in a future release?
>     >
>     Force fields are only implemented if a developer has a compelling
>     reason to do so, and then take the time to validate it.  As such,
>     new force fields are not often introduced.
>     > I appreciate that this will likely be a difficult process but if
>     anyone can point me in the right direction I would be very grateful.
>     >
>     You can probably take an existing Amber force field and modify
>     it.  Chapter 5 is your friend here.  By modifying existing files,
>     you don't have to come up with all the syntax by yourself.
>     -Justin
>     > Will - Cranfield University
>     >
>     -- ========================================
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>     ========================================
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