Re: [gmx-users] Output of Gromacs Demo

2011-02-13 Thread majid hasan
Okay, thanks. I will install it again in some other directory. Majid From: Justin A. Lemkul To: Gromacs Users' List Sent: Sun, February 13, 2011 1:39:16 PM Subject: Re: [gmx-users] Output of Gromacs Demo majid hasan wrote: > Thanks, Justin! Sudo

Re: [gmx-users] Output of Gromacs Demo

2011-02-13 Thread Justin A. Lemkul
Justin Best, Majid *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Sun, February 13, 2011 9:30:52 AM *Subject:* Re: [gmx-users] Output of Gromacs Demo majid hasan wrote: > I have attached the output of demo, and another Okay, I just ran the demo and kept pressing

Re: [gmx-users] Output of Gromacs Demo

2011-02-13 Thread majid hasan
Thanks, Justin! Sudo seems to have solved my problem, I do get the outputs now. Best, Majid From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Sun, February 13, 2011 9:30:52 AM Subject: Re: [gmx-users] Output of Gromacs Demo majid hasan

Re: Fw: [gmx-users] Output of Gromacs Demo

2011-02-13 Thread Tsjerk Wassenaar
Hi Majid, Maybe it's a good idea to find somebody around that can help you get started with using linux. You should get acquainted with that before trying to use some specialized software. Cheers, Tsjerk On Feb 13, 2011 6:38 PM, "Justin A. Lemkul" wrote: majid hasan wrote: > > I have attached

Re: Fw: [gmx-users] Output of Gromacs Demo

2011-02-13 Thread Justin A. Lemkul
majid hasan wrote: I have attached the output of "demo", and "water" with the message. I just ran the demo and kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here is what I got. You seem to have the DISPLAY variable is set, so we will pop up a window with the outp

Fw: [gmx-users] Output of Gromacs Demo

2011-02-13 Thread majid hasan
I have attached the output of "demo", and "water" with the message. I just ran the demo and kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here is what I got. You seem to have the DISPLAY variable is set, so we will pop up a window with the output of the pdb2gmx pr

Re: [gmx-users] Output of Gromacs Demo

2011-02-13 Thread Justin A. Lemkul
majid hasan wrote: I have attached the output of demo, and another Okay, I just ran the demo and kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here is what I got. You seem to have the DISPLAY variable is set, so we will pop up a window with the output of the pdb2

Re: [gmx-users] Output of Gromacs Demo

2011-02-13 Thread majid hasan
I have attached the output of demo, and another Okay, I just ran the demo and kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here is what I got. You seem to have the DISPLAY variable is set, so we will pop up a window with the output of the pdb2gmx program Press St

Re: [gmx-users] Output of Gromacs Demo

2011-02-12 Thread Tsjerk Wassenaar
Hi Majid, Check whether you have writing permissions where you're doing the demo. Cheers, Tsjerl On Feb 13, 2011 6:14 AM, "TJ Mustard" wrote: Majid, Can you post the exact executions you did. ie grompp .. mdrun .. This will help alot. On February 12, 2011 at 7:29 PM majid

Re: [gmx-users] Output of Gromacs Demo

2011-02-12 Thread TJ Mustard
Majid, Can you post the exact executions you did.   ie grompp .. mdrun ..   This will help alot. On February 12, 2011 at 7:29 PM majid hasan wrote: Dear

[gmx-users] Output of Gromacs Demo

2011-02-12 Thread majid hasan
Dear All, I installed the gromacs on Ubuntu, and ran the demo. But every time it produces an output file, I get this error: "output.pdb2gmx: Permission denied.", so I can't view the output. I am also unable to locate the .trr file, which is supposed to be the ultimate output of demo. Could anyo