Huyjin,
If you look in your log file from the rerun you will see that when running
using the GPU, energy groups are ignored or unused for energy reporting. Thus
for this to work you need to run it on the CPUs.
This is what I get in my output md.log when trying the same thing...
NOTE: With
or invalidate your modeling
observations.
Best of luck!
Jesper
On May 5, 2013, at 9:47 PM, shahid nayeem msnay...@gmail.com wrote:
It is a peptide.
Shahid
On Mon, May 6, 2013 at 4:46 AM, Jesper Sørensen jesoren...@ucsd.edu wrote:
Shahid,
This must be system dependent then because
Shahid,
This must be system dependent then because there are experimental methods, e.g.
NMR and CD, that can help determine the secondary structure of
proteins/peptides are various pH ranges.
What is your system? A peptide? A globular protein?
Best,
Jesper
On May 3, 2013, at 7:33 PM, shahid
Is it really fair to call this a circle? A circle is a 2D object. What you are
describing here is a disc.
Jesper
On May 2, 2013, at 1:13 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de
wrote:
There are indeed circular lipid bilayer structures possible, but they are
not found very
The shape is a sphere not a circle, what the picture is showing is a cut
through the vesicle. Have you googled lipid vesicles?
I don't know of a place that will have template systems like this for you. But
you should be able to get these by making a large enough system with enough
lipids to
HI George,
For AMBER you can use the parameters by Meagher, Redman, and Carlson they were
developed with this force field in mind. They are available on the Bryce group
amber parameter database below, although you will have to port them to Gromacs
format yourself.
Hi Richard,
Thanks for the reply. It was very helpful.
I've looked at the updated manual regarding the x-modifiers and that cleared it
up for me.
Best regards,
Jesper
On Apr 13, 2013, at 4:48 AM, Broadbent, Richard
richard.broadben...@imperial.ac.uk wrote:
On 12/04/2013 21:50, Jesper
Hi Berk and others,
Sorry it has been a long time since this issue was posted, but I got
side-tracked from this issue with other projects. And I want to make sure I
understand this correctly before venturing into more simulations. So this gets
a little long winded, but I hope you will help me
Dear GMX developers,
Thanks so much for the GMX 4.6 release. Testing on GPUs has shown impressive
speed-ups.
I have a question however, regarding the missing switching and shifting for
non-bonded interactions.
I looked at the developer zone website and saw this comment below:
Hi Berk,
I am running membrane simulations using both the CHARMM36 and MARTINI v. 2.1
parameters.
So both those cut-off treatments are important to me, but if there are ways
around it I'd be happy to explore them to be able to use the GPUs. The place it
would be most effective would probably
Hi Sebastian,
This may just be my take, but the Keppler Cards are not supported yet as far as
I understand it.
They are at least not mentioned on the GROMACS GPU page in the Supported Cards
section - granted that page has not been updated in quite a while.
Specifically, does this work when you
that forcing the device does work but it does not seem to
be the case.
Probably I have to wait for an update or the 4.6 version.
All the best,
Sebastian
On 10/29/2012 05:50 PM, Jesper Sørensen wrote:
Hi Sebastian,
This may just be my take, but the Keppler Cards are not supported yet
I would say looking at the CHARMM force field website would be the first thing
to do. Google: CHARMM FORCE FIELD, and you should get the relevant pages... The
articles are listed on the website...
/Jesper
On May 11, 2012, at 9:19 PM, Shima Arasteh wrote:
Dear gmx users,
Anybody can guide
Hi,
I am trying to extend the run time in tpr file to include more steps using
tpbconv
This has worked well for a while, but now I get two errors
One is that it writes now -207466 steps, which doesnt make sense
why is this number negative
Also, You've simulated long enough.
for the extension you need ... you can
give trr and edr files to grompp so the tpr file is a continuation of
earlier one ...
XAvier.
On Feb 24, 2011, at 11:50 AM, Jesper Sørensen wrote:
Hi,
I am trying to extend the run time in tpr file to include more steps using
tpbconv
This has worked well
2011/2/24 Jesper Sørensen li...@jsx.dk:
Hi Xavier,
That worked, thanks
Would it also work if I just gave the old
state.cpt file to mdrun?
Jesper
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org
]
On Behalf Of XAvier Periole
Sent: 24. februar 2011 12:19
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