Dear Mark,
I see. pcoupl = No is obvious. That means when I create tpr file from
grompp.mdp, the pcoupl setting was No instead of berendsen.
Thank you very much.
Best regards,
Changwoon Jang
On Tue, Jan 5, 2016 at 3:41 PM, Mark Abraham
wrote:
> Hi,
>
> Look at what md.log says about the va
Hi,
Look at what md.log says about the value for pcoupl it read from your .tpr.
:-)
Mark
On Tue, Jan 5, 2016 at 9:39 PM Chang Woon Jang
wrote:
> Dear Mark,
>
> I obtained the tpr file with gro and topology file using grompp -v.
>
> The following is from md.log file.
>
> Best regards,
> Changwo
Dear Mark,
I obtained the tpr file with gro and topology file using grompp -v.
The following is from md.log file.
Best regards,
Changwoon Jang
Log file opened on Fri Nov 13 13:52:29 2015
Host: c438-702.stampede.tacc.utexas.edu pid: 8923 rank ID: 0 number of
ranks: 64
GROMACS:mdrun_mpi,
Hi,
On Tue, Jan 5, 2016 at 7:15 PM Chang Woon Jang
wrote:
> Dear Gromacs Users,
>
>
> I have a low density polymer system initially. I would like to fit the
> correct liquid density using NPT simulation.
>
> I used Pcoupl=berendsen for 22 ns but the box size in confout.gro is still
> the same as
Dear Justin,
The following is from .mdf file.
; VARIOUS PREPROCESSING OPTIONS
include =
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit= 0
dt = 0.001
nsteps
On 1/5/16 2:51 PM, Chang Woon Jang wrote:
Dear Justin,
Please take a look at the file. I modified mdp file provided from VOTCA
tutorial. I think that mdp file is ok.
The mailing list does not accept attachments. Copy and paste the .mdp contents.
-Justin
Thank you very much.
Best rega
Dear Justin,
Please take a look at the file. I modified mdp file provided from VOTCA
tutorial. I think that mdp file is ok.
Thank you very much.
Best regards,
Changwoon Jang
On Tue, Jan 5, 2016 at 2:45 PM, Chang Woon Jang
wrote:
> Dear Justin,
>
> Please take a look at the files. I modified
On 1/5/16 2:25 PM, Chang Woon Jang wrote:
Dear Justin,
I am curious about resizing the box. My system contains 15000 atoms
representing liquid polymer with very low density (maybe gas phase due to
very low density). Does this very low density affect the simulation not to
converge the box?
Dear Justin,
I am curious about resizing the box. My system contains 15000 atoms
representing liquid polymer with very low density (maybe gas phase due to
very low density). Does this very low density affect the simulation not to
converge the box? Or, do the initial conditions (Pcoupl=berendsen
On 1/5/16 1:42 PM, Chang Woon Jang wrote:
Dear Abhishek Khetan,
Thank you for your answer. It means that Gromacs does not automatically
adjust the box size even though NPT ensemble is employed. Am I right?
This is incorrect. The box size will change under the influence of pressure.
Its
Dear Abhishek Khetan,
Thank you for your answer. It means that Gromacs does not automatically
adjust the box size even though NPT ensemble is employed. Am I right?
Different from Gromacs, Lammps automatically adjust box size when NPT
ensemble is applied during the simulation. Therefore, the den
To rescale the box.gro to a desired size using the actual density 543.21
kg/l of the solvent and get a new scaled.gro file, I use this command:
$ gmx editconf -f box.gro -density 543.21 -o scaled.gro > logfile
On Tue, Jan 5, 2016 at 7:05 PM, Chang Woon Jang
wrote:
> Dear Gromacs Users,
>
>
> I
Dear Gromacs Users,
I have a low density polymer system initially. I would like to fit the
correct liquid density using NPT simulation.
I used Pcoupl=berendsen for 22 ns but the box size in confout.gro is still
the same as the input size of conf.gro.
Initial in conf.gro (10.0 10.0 9.8)
output i
Dear Gromacs Users,
I have a low density polymer system initially. I would like to fit the
correct liquid density using NPT simulation.
I used Pcoupl=berendsen for 22 ns but the box size in confout.gro is still
the same as the input size of conf.gro.
Initial in conf.gro (10.0 10.0 9.8)
output i
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