..After all Gromacs can not start.
On Fri, May 13, 2016 at 12:53 PM, Elsaid Younes wrote:
> Hi all,
>
> I have installed gromacs like the quick and dirty installation. I have a
> 16.04 version of ubuntu. I can not start it.
> I used to do the same procedure in ubunt
Hi all,
I have installed gromacs like the quick and dirty installation. I have a
16.04 version of ubuntu. I can not start it.
I used to do the same procedure in ubuntu 15.10, and it worked fine.
/Elsaid
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/Elsaid
On Sun, Feb 21, 2016 at 3:56 AM, Elsaid Younes wrote:
> Sorry
> Once, I added .tpr to the md_0_1 then it gave me the above message then I
> did as you said without .tpr.
> That error was obtained:
>
> Fatal error:
ot do appending
because of this condition.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
/Elsaid
On Sun, Feb 21, 2016 at 3:38 AM, Elsaid Younes wrote:
&g
It says:
No previous checkpoint file present, assuming this is a new run.
Reading file md_0_1.tpr, VERSION 5.0.4 (single precision)
Changing nstlist from 10 to 20, rlist from 1 to 1.03
then start..
/Elsaid
On Sun, Feb 21, 2016 at 3:21 AM, Elsaid Younes wrote:
> Ok, How can I use md_
Ok, How can I use md_0_1.tpr instead of topol.tpr
/Elsaid
On Sun, Feb 21, 2016 at 2:59 AM, Elsaid Younes wrote:
> Hi,
>
> The mdrun I did was gmx mdrun -deffnm md_0_1
> I write the command
> mdrun -cpi md_0_1_prev.cpt -append
> I tried to use -noappend, but still doesn
Hi,
The mdrun I did was gmx mdrun -deffnm md_0_1
I write the command
mdrun -cpi md_0_1_prev.cpt -append
I tried to use -noappend, but still doesn't work.
/Elsaid
On Sun, Feb 21, 2016 at 2:43 AM, Elsaid Younes wrote:
> Still asks for topol.tpr? Can I have that file
>
>
> /El
Still asks for topol.tpr? Can I have that file
/Elsaid
On 2/20/16 6:49 PM, Elsaid Younes wrote:
>* Hi,
*>>>* If I have this file md_0_1_prev.cpt What is the text exactly? It asks
*>* for topol.tpr
*
I gave you the command-line options that are new to the mdrun command
line. Run
Hi,
If I have this file md_0_1_prev.cpt What is the text exactly? It asks
for topol.tpr
On 2/20/16 5:32 PM, Elsaid wrote:
>* The simulation has the time, which is time of the wanted simulation. But the
*>* job was killed by the server.
*
If the simulation terminated prior to completion, you don'
Hi all,
I need to extend a previous simulation, and its directory is the same with
all inputs and outpts. That simulation can not be complete due to the
maximum time of the job which is limited by the server. I use gromacs 5,
when using the command gmx convert-tpr, an error is obtained.
Command
Hey all,
I wish I can find a way to help me writing a script to the gromacs. I mean
by scripts "the commands that one writes to gramacs terminals and the
choices, which are prompted after command's processing, all collected in
one file"
I do simulation like lysozyme in water tutorial.
Looking forw
Hi all,
I can not do ssh over X, although my sshd-config is:
# Package generated configuration file
# See the sshd_config(5) manpage for details
# What ports, IPs and protocols we listen for
Port 22
# Use these options to restrict which interfaces/protocols sshd will bind to
#ListenAddress ::
Hi,
Can anyone please tell me how to remove a file from directory?
rm doesn't work.
for example:
rm/prss/sss/topol.top
There are three files of it.
/Elsaid
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Hi,
I deleted the old one and moved another one using box.com since scp doesn't
work, but I got the same results.
Any ideas?
/Elsaid
On Tue, Nov 10, 2015 at 3:02 AM, Justin Lemkul wrote:
>
>
> On 11/9/15 7:59 PM, Elsaid Younes wrote:
>
>> Hi,
>>
>> i
Hi,
it gives me file input/output error 1aki.pdb.
Elsaid
On Mon, Nov 9, 2015 at 8:20 PM, Elsaid Younes wrote:
> Thank you!
>
> On Mon, Nov 9, 2015 at 8:18 PM, Samuel Flores
> wrote:
>
>> Oh that makes sense!
>>
>> Elsaid, issue:
>>
>> module
g_pme_error g_rms_dg_select
> g_tcaf_d g_xrama make_editrjcat
> >>
> >>
> >> Elsaid,
> >>
> >> Regarding Justin’s suggestion, on Uppmax I believe the full path would
> be:
> >>
> >> source /sw/apps/gromacs/4.6
Hi,
Thank you for your response.
When writing gmx, it gives the command not found. (Note I use windows)
Elsaid
On Mon, Nov 9, 2015 at 3:31 PM, Justin Lemkul wrote:
>
>
> On 11/9/15 5:23 AM, Said wrote:
>
>> Hi,
>>
>> I have a gateway access to uppmax. I could have copied 1aki.pdb to my
>> acco
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