It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have
an impact. I've tried being gentle, slowly turning up the force constant
and running for 1 ns for each value but as soon as the force constant
approaches 100 it crashes.
The starting structure was generated with the same re
I may have just come across this issue as well. I have no time to
investigate, but my guess is that it's related to some thread-safety
issue with thread-MPI.
Could one of you please file a bug report on redmine.gromacs.org?
Cheers,
--
Szilárd
On Thu, Aug 8, 2013 at 5:52 PM, Brad Van Oosten wro
Hello,
I would like to calculate angle tetrahedral order parameter of water
molecules as defined by Chau et al (eq 3). I am using g_hydorder of
gromacs 4.6.3 with my index group containing all oxygen atoms of water:
g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out
file_2.out -n i
On 9/1/13 1:30 PM, Nidhi Katyal wrote:
I have created my files long time ago using version 4.0.7. But now
analyzing the same files using g_hbond/g_mindist using version 4.5.5
Try 4.6.3. If it still doesn't work, you can feel free to file a bug report on
redmine.gromacs.org, or otherwise ju
I have created my files long time ago using version 4.0.7. But now
analyzing the same files using g_hbond/g_mindist using version 4.5.5
On Sun, Sep 1, 2013 at 10:48 PM, Justin Lemkul wrote:
>
>
> On 9/1/13 1:17 PM, Nidhi Katyal wrote:
>
>> Even after giving same cutoff radius of 0.35nm in both,
On 9/1/13 1:17 PM, Nidhi Katyal wrote:
Even after giving same cutoff radius of 0.35nm in both, I am getting around
400 contacts per timeframe with mindist but 0 contacts with g_hbond.
What version of Gromacs are you using?
-Justin
On Sun, Sep 1, 2013 at 10:40 PM, Justin Lemkul wrote:
Even after giving same cutoff radius of 0.35nm in both, I am getting around
400 contacts per timeframe with mindist but 0 contacts with g_hbond.
On Sun, Sep 1, 2013 at 10:40 PM, Justin Lemkul wrote:
>
>
> On 9/1/13 1:08 PM, Nidhi Katyal wrote:
>
>> The two groups are: protein and cosolvent mo
On 9/1/13 1:08 PM, Nidhi Katyal wrote:
The two groups are: protein and cosolvent molecules. With g_mindist -on ,
I am getting values of around 6500 per timeframe. But then why g_hbond
giving different results.
Are you using the same cutoff radius for both?
-Justin
On Sun, Sep 1, 2013 at
The two groups are: protein and cosolvent molecules. With g_mindist -on ,
I am getting values of around 6500 per timeframe. But then why g_hbond
giving different results.
On Sun, Sep 1, 2013 at 10:23 PM, Justin Lemkul wrote:
>
>
> On 9/1/13 12:50 PM, Nidhi Katyal wrote:
>
>> Hello,
>> I would
On 9/1/13 12:50 PM, Nidhi Katyal wrote:
Hello,
I would like to calculate number of contacts between two groups, for which
I am using following command:
g_hbond -f *.xtc -s *.tpr -num *.xvg -contact -b 49000 -e 5
I am getting 0 as the output. But when I am calculating number of hydrogen
bond
trjorder might be of some help to deal with the exchange events.
Best,
João
On Sun, Sep 1, 2013 at 5:28 PM, Albert wrote:
> On 09/01/2013 06:03 PM, Justin Lemkul wrote:
>
>> Maybe g_msd or g_rmsf, but I don't think there's anything specifically
>> designed to address water molecules, and the t
Why not calculate the hydration map?
On 1 September 2013 19:29, Justin Lemkul wrote:
>
>
> On 9/1/13 12:28 PM, Albert wrote:
>
>> On 09/01/2013 06:03 PM, Justin Lemkul wrote:
>>
>>> Maybe g_msd or g_rmsf, but I don't think there's anything specifically
>>> designed to address water molecules, a
Hello,
I would like to calculate number of contacts between two groups, for which
I am using following command:
g_hbond -f *.xtc -s *.tpr -num *.xvg -contact -b 49000 -e 5
I am getting 0 as the output. But when I am calculating number of hydrogen
bonds between the same two groups by using the a
On 9/1/13 12:28 PM, Albert wrote:
On 09/01/2013 06:03 PM, Justin Lemkul wrote:
Maybe g_msd or g_rmsf, but I don't think there's anything specifically
designed to address water molecules, and the term "flexibility" can have far
too many meanings ;)
-Justin
thanks a lot for kind messages.
b
On 09/01/2013 06:03 PM, Justin Lemkul wrote:
Maybe g_msd or g_rmsf, but I don't think there's anything specifically
designed to address water molecules, and the term "flexibility" can
have far too many meanings ;)
-Justin
thanks a lot for kind messages.
but there are a lot of water molecul
On 9/1/13 11:36 AM, Albert wrote:
Hello:
I've finished a MD with Gromacs and I found that the water molecules inside
certain region of my protein is very flexible: the movement of them are very
fast; in other region there are very stable. I am just wondering is there any
tool in Gromacs can
Hello:
I've finished a MD with Gromacs and I found that the water molecules
inside certain region of my protein is very flexible: the movement of
them are very fast; in other region there are very stable. I am just
wondering is there any tool in Gromacs can differentiate the water
molecules'
On 9/1/13 8:23 AM, mjm136...@yahoo.com wrote:
Hi
I am in MD simulation step and use of command:
grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tprmdrun
-deffnmmd_0_1
(50 step-1000.0 ps)
but in runing,program stop and give a error:
File input/output error:
Cannot write tra
Hi
I am in MD simulation step and use of command:
grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tprmdrun
-deffnmmd_0_1
(50 step-1000.0 ps)
but in runing,program stop and give a error:
File input/output error:
Cannot write trajectory frame; maybe you are out of quota?
pleas
On 9/1/13 1:39 AM, Shima Arasteh wrote:
Hi,
I ran US on an ion through a channel inserted in a bilayer.
I used g_wham and got the profile output. In the visualized profile, I see a
region that the plot shows a flat line and it seems the data is missed there.
Would you please let me know wh
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