Group selection depends on what you want to see in the output
trajectory. What I am trying to say is that per se nothing wrong seems
to be happening -- you just have things crossing periodic boundaries.
The messages about inconsistent shifts could also mean atom shifts
across boundaries, which
Dear Alex,
Which group I should select (system, CNT or lig)?
After selecting each of them:
There were 44 inconsistent shifts. Check your topology
I'm confused.
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Thank you!
I see these:
linux-vdso.so.1 => (0x7ffc4f0df000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x7f10b6b51000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7f10b694d000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x7f10b6745000)
libcufft.so.8.0
Hi,
CMake will link to whatever it is allowed to find. What does ldd on the
executable report as the libraries being dynamically linked? Those are the
ones that cmake found for which there were apparently no static equivalents.
Mark
On Sun, Jul 22, 2018, 18:16 Shayna Hilburg wrote:
> Hi all,
>
Your ligand seems to be crossing a periodic boundary, which is normal.
Try trjconv -pbc whole.
On 7/22/2018 1:35 PM, Atila Petrosian wrote:
Dear gromacs users,
After doing NVT md simulation of CNT + LIG + WATER molecules, I encountered
with unusual structure of LIG molecule in some frames in
Dear gromacs users,
After doing NVT md simulation of CNT + LIG + WATER molecules, I encountered
with unusual structure of LIG molecule in some frames in trajectory viewing
using VMD.
https://1drv.ms/u/s!AveJH4Y30cH0sQu08knJYk7TGc7g
My mdp file for this md is as follows:
define = -DPOSR
Hi,
On Sun, Jul 22, 2018, 14:15 Mijiddorj B wrote:
> Dear Mark,
> Thank you bery much for your reply. I do not know which tool is useful for
> the counting a time series of atom number.
Me neither, but first you need to have made the selections of atoms to
count. Maybe gmx select or gmx analyz
Hi all,
I'm trying to install GROMACS 2018 for use on GPUs. We typically keep the
software on the master node and just call it through a mounted drive on the
compute nodes. However, despite using static library tags, it appears there
are still dependencies. It works fine on our master node but not
Dear Mark,
Thank you bery much for your reply. I do not know which tool is useful for
the counting a time series of atom number. I think that gmx select is a
possible one. However, I could not specify water molecules.
If you have any experience of gmx select ... , please advise me on
specifing wate
Hi,
Your working directory is the one in which you are doing your work. You are
making a copy of the normal force field folder, so that next time you use
it, you know it is unchanged from what GROMACS provides. Having made the
copy, edit the files in the copy.
Mark
On Sun, Jul 22, 2018, 09:49 工业
No I didn't try it. Its a nice idea.. I will try it.
On Sun, Jul 22, 2018 at 3:28 AM wrote:
> Have you tried the "insert-chemicals-after-md" command ?
>
> PB
>
> > On Jul 11, 2018, at 4:50 AM, Mark Abraham
> wrote:
> >
> > Hi,
> >
> > Are you trying to observe something about the transition, o
dear all
I am a new user,I was doing this
tutorial(http://www.mdtutorials.com/gmx/membrane_protein/index.html) it said
{To use the parameters in lipid.itp, we will have to make some changes to our
pre-packaged GROMOS96 53A6 force field files (in $GMXLIB/gromos53a6.ff). Make a
copy of th
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