Hi,
Further to what Justin said, I see a lot of people crafting complex bash
scripts to run their whole project in the same directory, and as part of
that the scripts do approximately what
gmx mdrun -cpi -noappend
does - name the output files so that they include a part number, and will
need to
t and output files to
the same basename (in your case md"$i"; note the lack of the ".tpr"). After
setting to "-deffnm md$i", Gromacs will expect the checkpoint file
(requested in your case by "-cpi md$j.cpt") to be called md"$i".cpt.
Cheer
On 1/29/18 12:01 PM, Myunggi Yi wrote:
Hi,
The following is a part of my bash script to automate extended running.
(not appending or not crashed simulations)
script---
# em
...
# heating
...
# npt equilibration
gmx grompp -f npt.mdp -c nvt.gro -r ../mono.gro -t n
Hi,
The following is a part of my bash script to automate extended running.
(not appending or not crashed simulations)
script---
# em
...
# heating
...
# npt equilibration
gmx grompp -f npt.mdp -c nvt.gro -r ../mono.gro -t nvt.cpt -p ../mono.top
-n ../index.ndx -o np
Thank you all.
Have a great day.
Myunggi
On Mon, Jan 29, 2018 at 9:40 AM, Mark Abraham
wrote:
> Hi,
>
> See
> http://manual.gromacs.org/documentation/2018-latest/user-guide/managing-
> simulations.html#extending-a-tpr-file
>
> Mark
>
> On Mon, Jan 29, 2018 at 3:37 PM Myunggi Yi wrote:
>
> >
Hi,
See
http://manual.gromacs.org/documentation/2018-latest/user-guide/managing-simulations.html#extending-a-tpr-file
Mark
On Mon, Jan 29, 2018 at 3:37 PM Myunggi Yi wrote:
> Thank you for your help.
>
> Then how can the simulation be continued without previous cpt file
> (information)?
>
> Or
Thank you for your help.
Then how can the simulation be continued without previous cpt file
(information)?
Or, should I use another way to extend the simulations?
Myunggi
On Mon, Jan 29, 2018 at 9:10 AM, Justin Lemkul wrote:
>
>
> On 1/29/18 9:07 AM, Myunggi Yi wrote:
>
>> Dear users,
>>
>>
On 1/29/18 9:07 AM, Myunggi Yi wrote:
Dear users,
I am using gromacs2018
I've got the following error message.
Command line:
gmx convert-tpr -s md1.tpr -f md1.cpt -n ../index.ndx -o md2.tpr -extend
2.0
---
Program: gmx conve
Dear users,
I am using gromacs2018
I've got the following error message.
Command line:
gmx convert-tpr -s md1.tpr -f md1.cpt -n ../index.ndx -o md2.tpr -extend
2.0
---
Program: gmx convert-tpr, version 2018
Source file: src/groma
Hi
I think it should be like this:
tpbconv -s previous.tpr -extend timetoextendby -o new.tpr
mdrun -s new.tpr -cpi previous.cpt
On Tue, Dec 22, 2015 at 2:07 PM, Mark Abraham
wrote:
> Hi,
>
> Please start with
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
> Mark
>
> On
Hi,
Please start with
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
Mark
On Tue, Dec 22, 2015 at 9:10 PM masoud keramati
wrote:
> sorry with my question
>
> is it true that for extending simulation use the following code?
>
> gmx grompp -f md.mdp -c md.gro -t md.trr -p top
sorry with my question
is it true that for extending simulation use the following code?
gmx grompp -f md.mdp -c md.gro -t md.trr -p topol.top -o md2.tpr
gmx mdrun -deffnm md2
*md.gro and md.trr is files for first run
On 12/22/15, Justin Lemkul wrote:
>
>
> On 12/21/15 7:00 PM, Soumya Lipsa Rat
On 12/21/15 7:00 PM, Soumya Lipsa Rath wrote:
Dear Mark and Chandan,
Thank you so much for the information. I was indeed using a wrong tpr file.
I will include the -cpi state.cpt flag during the tpbconv step.
You don't need -cpi with tpbconv, only in mdrun.
-Justin
Thanks,
Soumya
On Mo
Dear Mark and Chandan,
Thank you so much for the information. I was indeed using a wrong tpr file.
I will include the -cpi state.cpt flag during the tpbconv step.
Thanks,
Soumya
On Mon, Dec 21, 2015 at 12:30 PM, Soumya Lipsa Rath wrote:
> Dear Gromacs users,
>
> I am trying to extend my simul
Hi Soumya,
I think you also need to mention -cpi state.cpt flag in the tpbconv command.
Chandan
On Mon, Dec 21, 2015 at 9:00 AM, Soumya Lipsa Rath
wrote:
> Dear Gromacs users,
>
> I am trying to extend my simulation for 200ns by using:
>
> tpbconv_mpi -s topol.tpr -extend 20 -o topol2.tpr
Hi,
Sounds like you haven't used the .tpr you think you are using. (But if your
production simulations require the use of -maxwarn 5, then you probably
have much bigger problems...)
Mark
On Mon, Dec 21, 2015 at 2:32 PM Soumya Lipsa Rath
wrote:
> Dear Gromacs users,
>
> I am trying to extend my
Dear Gromacs users,
I am trying to extend my simulation for 200ns by using:
tpbconv_mpi -s topol.tpr -extend 20 -o topol2.tpr
mdrun_mpi -s topol2.tpr -cpi state.cpt -append -maxwarn 5 >&
grompp_output.log
However, my simulation has only extended for 50ns. Am I doing something
wrong?
Thanks,
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