Thank you very much Dr. Lemkul,
I downloaded your file and it works!
Actually I downloaded the previous file from Gromacs web:
http://www.gromacs.org/Downloads/User_contributions/Force_fields
Thanks again for your help!
On Fri, Aug 16, 2019 at 6:22 AM Justin Lemkul wrote:
>
>
> On 8/16/19
On Mon, Aug 5, 2019 at 5:00 PM Stefano Guglielmo
wrote:
>
> Dear Paul,
> thanks for suggestions. Following them I managed to run 91 ns/day for the
> system I referred to in my previous post with the configuration:
> gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 4 -ntmpi 7 -npme 1 -gputasks
>
Thanks both of you for your useful suggestions. I'll check accordingly.
Thanks again for help.
Dhrubajyoti
On Fri, 16 Aug 2019 at 15:50, Justin Lemkul wrote:
>
>
> On 8/16/19 6:09 AM, Dhrubajyoti Maji wrote:
> > Hi all,
> > I have a simulated trajectory of 50 ns but my desired property
On 8/16/19 2:15 AM, Lei Qian wrote:
Sorry for this basic question.
I read previous emails and tried to make pdb2gmx find ffG43a1p.ff.
I added #include "ffG43a1p.itp" in FF.dat in ffG43a1p.ff folder. Also tried
to create a file called forcefield.doc and wrote "ffG43a1p" into it.
I put these
On 8/16/19 6:09 AM, Dhrubajyoti Maji wrote:
Hi all,
I have a simulated trajectory of 50 ns but my desired property is not
well converged. Therefore, I want to extend the run for another 50 ns. As
far as I know if I use the last output files as input files for next run, I
can finally have
Hi,
you can generate a new .tpr file by extend flag ( time is in ps) then run
your code again. Please replace the names carefully. Also, check this link :
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-convert-tpr.html
gmx convert-tpr -s last.tpr -o new.tpr -extend 1
gmx mdrun
Hi all,
I have a simulated trajectory of 50 ns but my desired property is not
well converged. Therefore, I want to extend the run for another 50 ns. As
far as I know if I use the last output files as input files for next run, I
can finally have two 50 ns run trajectory files. But if I want a
got it.
Thank you all for your help.
On Fri, Aug 16, 2019 at 12:40 PM Bratin Kumar Das <
177cy500.bra...@nitk.edu.in> wrote:
> Hi..
> The command is given below
> gmx make_ndx -f *.gro -o *.ndx
> You need to see inside the gro file what are the residue index
> corresponding to the particular
Sorry for this basic question.
I read previous emails and tried to make pdb2gmx find ffG43a1p.ff.
I added #include "ffG43a1p.itp" in FF.dat in ffG43a1p.ff folder. Also tried
to create a file called forcefield.doc and wrote "ffG43a1p" into it.
I put these files in working directory
and
