Thank you sir for the valuable input. I will look into the matter and get
to you.
On Thu, Apr 11, 2013 at 2:40 AM, Mark Abraham wrote:
> You have a box with negligible dimensions, so as forecast above, your
> conversion process from AMBER was not as effective as it might have been.
> As you can
You have a box with negligible dimensions, so as forecast above, your
conversion process from AMBER was not as effective as it might have been.
As you can see with g_rdf -h, it defaults to using periodic boundary
conditions. You need to do something different.
Mark
On Wed, Apr 10, 2013 at 2:38 P
Sir
I truncated my file so it has only 10 molecules of water and 5 frames.
gmxcheck gives the following information
Checking file test.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time0.000
# Atoms 30
Last frame 5 time0.500
Item#frames Timestep
On Tue, Apr 9, 2013 at 8:33 AM, Dr. Vitaly Chaban wrote:
> So there is a problem with your trajectory file. Try to understand what
> kind of problem it is.
e.g. by using gmxcheck and/or gmxdump (on a small version of your
data!) to see what information is present.
Mark
>
> I can recollect that
So there is a problem with your trajectory file. Try to understand what
kind of problem it is.
I can recollect that I experienced something like that why translating CPMD
trajectory to GROMACS. Maybe, it does not write time for each frame at the
right place -- just a guess.
Dr. Vitaly Chaban
Sir
I tried g_msd, after asking for group selection the program appears not to
read the frames as it remains stuck at reading frame 0, time 0.00.
What to do?
Thanks
On Mon, Apr 8, 2013 at 11:16 PM, Dr. Vitaly Chaban wrote:
> Do you experience this problem with g_rdf only, or with all gromac
Do you experience this problem with g_rdf only, or with all gromacs
analysis utilities?
On Mon, Apr 8, 2013 at 7:33 PM, Venkat Reddy wrote:
> Sir
>
> I loaded the trajectory. There doesn't seem to be anything wrong with it.
> Have no clue whats going wrong
>
> Thanks
>
>
> On Mon, Apr 8, 2013 a
Sir
I loaded the trajectory. There doesn't seem to be anything wrong with it.
Have no clue whats going wrong
Thanks
On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban wrote:
> I believe the problem is in the way which you used to convert AMBER
> trajectory to the GROMACS trajectory
>
> I wo
I believe the problem is in the way which you used to convert AMBER
trajectory to the GROMACS trajectory
I would suggest to try gmxdump and see what your trajectory looks like. Oe
maybe even better - try to visualize it in VMD to see if the format is
correct.
Dr. Vitaly Chaban
Sir
>
> I wa
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