Den 2018-07-11 kl. 18:40, skrev SHYANTANI MAITI:
Dear all,
If the autocorrelation function is zero for a particular simulation, is
there any problem in the simulation? Can autocorrelation come out to be
zero for a simulation?
What autocorrelation function?
--
David van der Spoel, Ph.D., Profes
Have you try make_ndx tool of Gromacs?
On Wed, Jul 11, 2018, 00:09 Chetan Puri wrote:
> Can someone guide me in how to make a group for atoms number 1566, 1567,
> 1569,1571,1574&1579, which all belong to a tyrosine residue number 128 of
> protein.
>
> Since I need to measure distance between two
Dear all,
If the autocorrelation function is zero for a particular simulation, is
there any problem in the simulation? Can autocorrelation come out to be
zero for a simulation?
--
Best regards,
*Shyantani Maiti*
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Gromacs Users mailing list
* Please search the archive at
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Hi,
The flat bottom potential acts in both directions out from the center you
specify, so you should only need one potential - see figure 4.14 in the
reference manual, panel A. Use a positive r value and positive force
constant.
Kevin
On Wed, Jul 11, 2018 at 6:09 AM, Joe Wu wrote:
> Yes I am!
I think you can manually insert that into the index file (.ndx).
On Tue, Jul 10, 2018 at 12:09 PM, Chetan Puri wrote:
> Can someone guide me in how to make a group for atoms number 1566, 1567,
> 1569,1571,1574&1579, which all belong to a tyrosine residue number 128 of
> protein.
>
> Since I need
https://www.urbandictionary.com/define.php?term=btw :) He wants you to try
never version 2018.2:
ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.2.tar.gz
Also try different fftw options.
On cmake line add:
-DGMX_FFT_LIBRARY=xxx
where xxx can be fftw, mkl or fftpack. You also need proper stuff inst
Sorry, but... what is BTW 2018.2? Another software?
El mié., 11 jul. 2018 a las 6:50, Mark Abraham ()
escribió:
> Hi,
>
> I haven't seen that, and don't know how to guess what might make it work.
> BTW 2018.2 is a better idea to install.
>
> Mark
>
> On Wed, Jul 11, 2018 at 3:34 AM Maximiliano Se
Yes I am!
On Wed, Jul 11, 2018 at 5:47 PM, Mark Abraham
wrote:
> Hi,
>
> Are you telling grompp to use your restraint.gro?
>
> Mark
>
> On Wed, Jul 11, 2018 at 9:43 AM Joe Wu wrote:
>
> > Hi Justin (or anyone else who can help),
> >
> > There was a post where Justin told us to look through the
Hi,
Are you trying to observe something about the transition, or merely the
different end points?
Mark
On Tue, Jul 10, 2018 at 4:12 PM Soham Sarkar wrote:
> Dear all,
> I am planning to do a simulation where after 50ns of simulation I want to
> add some other chemicals in the system and conti
Hi,
I haven't seen that, and don't know how to guess what might make it work.
BTW 2018.2 is a better idea to install.
Mark
On Wed, Jul 11, 2018 at 3:34 AM Maximiliano Sebastián Castillo <
mcasti...@itba.edu.ar> wrote:
> Hello,
> I have the next problem:
> [ 1%] No patch step for 'fftwBuild'
>
Hi,
Are you telling grompp to use your restraint.gro?
Mark
On Wed, Jul 11, 2018 at 9:43 AM Joe Wu wrote:
> Hi Justin (or anyone else who can help),
>
> There was a post where Justin told us to look through the archive for
> detailed steps as to how to set up flat bottom restraints, but I canno
Try running this command from the directory where topolgen.pl script is
present.
On 11/07/2018 09:43, farial tavakoli wrote:
Dear gromacs users
I am trying to run a simulation on my complex which has small molecule as a ligand ,
using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then in
Dear gromacs users
I am trying to run a simulation on my complex which has small molecule as a
ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then
installed perl script on linux. then typed "perl -v" to check if it is
installed. the perl 5.20.1 is installed.
but when I typed
Hi Justin (or anyone else who can help),
There was a post where Justin told us to look through the archive for
detailed steps as to how to set up flat bottom restraints, but I cannot
find it. I've been looking through the entire archive for that post where
he explains in detail. Can anyone help ou
Hi,Although I have read the manual and I have wrote programs with mpi, the
gromacs use of mpi is confusing.
Is it mandatory to use mpirun before gmx_mpi or not?
Can someone shed a light on that?
Regards,
Mahmood
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