thank you informing about g_rdf...
Is it possible to dump the structure with those average water molecules
interacting with the residues. I generated the hbond.log file which gives
the details but I need to generate a figure for this ??
On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul wrote:
>
On 11/10/13 8:38 PM, bharat gupta wrote:
But trjorder can be used to calculate the hydration layer or shell around
residues ... Right ??
Yes, but I also tend to think that integrating an RDF is also a more
straightforward way of doing that. With trjorder, you set some arbitrary cutoff
tha
But trjorder can be used to calculate the hydration layer or shell around
residues ... Right ??
On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul wrote:
>
>
> On 11/10/13 8:30 PM, bharat gupta wrote:
>
>> Thanks for your reply. I was missing the scientific notation part. Now
>> everything is fine
On 11/10/13 8:30 PM, bharat gupta wrote:
Thanks for your reply. I was missing the scientific notation part. Now
everything is fine.
Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
to protein.
I wouldn't try to draw any sort of comparison between the output of trjo
Thanks for your reply. I was missing the scientific notation part. Now
everything is fine.
Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
to protein.
On Mon, Nov 11, 2013 at 10:12 AM, Justin Lemkul wrote:
>
>
> On 11/10/13 7:18 PM, bharat gupta wrote:
>
>> I check
On 11/10/13 7:18 PM, bharat gupta wrote:
I checked the file hbnum.xvg file and it contains three columns - time,
hbonds, hbonds that donot follow the angle criteria. In that case SS1 is
The third column is not actually H-bonds, then ;)
the average of actual hbonds (2nd column ) and SS2 is t
Justin, thank you very much for your kind help about LIE and PME
Williams
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I checked the file hbnum.xvg file and it contains three columns - time,
hbonds, hbonds that donot follow the angle criteria. In that case SS1 is
the average of actual hbonds (2nd column ) and SS2 is the average of 3rd
column. Am I right here or not ??
I tried to calculate the h-bond for residues 1
Hi All,
I am experiencing a few problems in membrane simulations wrt COM removal. I
downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all the
accompanying files. I then carried out the following steps:
1) energy minimization
2) NVT Eq - 100 ps
3) NPT Eq - 250 ps (Berendsen temp, Pres c
On 11/10/13 9:14 AM, shahab shariati wrote:
Dear Justin
Very thanks for your reply.
What you described earlier should not be attempted with "distance"
geometry. It won't work very well. The use of restraints is almost
NEVER necessary, especially in the case where the reference group > is
mu
Dear Justin
Very thanks for your reply.
> What you described earlier should not be attempted with "distance"
> geometry. It won't work very well. The use of restraints is almost
> NEVER necessary, especially in the case where the reference group > is
much more massive than the pulling group.
I w
Hi,
There's nothing GROMACS-specific here - something about your MPI
installation, configuration or use is pretty wrong, but we can't help work
out what.
Mark
On Sun, Nov 10, 2013 at 12:31 PM, S.Chandra Shekar <
chandrashe...@iisertvm.ac.in> wrote:
> Dear all
>
> I encounter a problem while ru
On 11/10/13 5:31 AM, shahab shariati wrote:
Dear Justin
Thanks for your reply.
You are right. I should not extrapolate too literally from your tutorial
to my system.
But, I have a general question:
There is 2 groups in COM pulling method (reference group + pull group).
If I want to use pu
On 11/10/13 12:20 AM, bharat gupta wrote:
Hi,
I used the command g_hbond to find h-bond between residues 115-118 and
water. Then I used g_analyze to find out the average and it gives the value
for the hbonds like this :-
std. dev.relative deviation of
Dear all
I encounter a problem while running command mdrun_mpi -v -deffnm em in
gromacs.
I am new to the gromacs. i just ran test calculation, *simulation of
lyzozyme in water*. i am able to generate gro, tpr files. But in the final
step i got following error.
Thanks in advance.
[localhost.l
Thank you Justin for your kind help. The simple reason for considering only
gromos parameter sets is that the parameters for the metal ions (in my
protein) are not defined in other force fields.
On Sat, Nov 9, 2013 at 7:18 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5012376...@n6.nabble.com>
Dear Justin
Thanks for your reply.
You are right. I should not extrapolate too literally from your tutorial
to my system.
But, I have a general question:
There is 2 groups in COM pulling method (reference group + pull group).
If I want to use pull_geometry = distance, so, I should fix referen
On Sun, Nov 10, 2013 at 5:28 AM, Dwey Kauffman wrote:
> Hi Szilard,
>
> Thank you very much for your suggestions.
>
> >Actually, I was jumping to conclusions too early, as you mentioned AMD
> >"cluster", I assumed you must have 12-16-core Opteron CPUs. If you
> >have an 8-core (desktop?) AMD CPU
On Nov 10, 2013 10:04 AM, "Mark Abraham" wrote:
> Yes (unless you are using AMD cpus), per the installation instructions,
> although you will probably do slightly better with GCC 4.7, and should not
> do a new install of 4.6.2 after 4.6.3 is released. In particular, 4.6.2 has
> an affinity-relate
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