Friends,
I am interested in setting the permittivity of the external surface.
With the previous posting in the forum, i am able understand the
meaning of the epsilon_surface parameter.
I would like to know if someone could suggest me some articles that
address the role of this parameter.
Thanks,
B
starting point as the reference and
calculate the msd of each succeeding points with respect to the
starting.
Thanks
Bala
On Wed, Aug 22, 2012 at 6:16 PM, Justin Lemkul wrote:
>
>
> On 8/22/12 12:12 PM, Bala subramanian wrote:
>>
>> Hi justin,
>> Thanks for the suggesti
lt;=0.5
thanks
On Wed, Aug 29, 2012 at 11:59 AM, Mark Abraham wrote:
> On 29/08/2012 7:43 PM, Bala subramanian wrote:
>>
>> Hi,
>> I read the examples. I find that one example shows the usage of rdist
>> keyword. But i am not getting the right syntax to use it. I tried
-select 'resname SOL and within (rdist >= 0.25 and rdist <= 0.5) of
group "Protein"'
-select 'resname SOL and within {0.25 to 0.5} of group "Protein"'
On Tue, Aug 28, 2012 at 5:56 PM, Mark Abraham wrote:
> On 29/08/2012 1:37 AM, Bala subramanian w
Friends,
I read the documentation of g_select and previous questions, but I
could nt find how to extract the index of water layer around the
protein. While i understand that i can use 'within' keyword to get
water layer around protein, my need is slightly different in a sense
that i have specify a
, Justin Lemkul wrote:
>
>
> On 8/21/12 10:01 AM, Bala subramanian wrote:
>>
>> Friends,
>> I have calculate the mean sq. displacement of water molecules in the first
>> hydration shell around the protein (distance of .25nm). I want to write
>> the
>&
Friends,
I have calculate the mean sq. displacement of water molecules in the first
hydration shell around the protein (distance of .25nm). I want to write the
code but i dnt know how to manipulate the coordinates to account for the
pbc. Any guidance from anyone would be a great help.
Thanks in ad
Friends,
I have a completed simulation for 30ns (done with gro. 4.5.4), Now I
want to extend the simulation for another 30ns. In gromacs page (Ext.
simulations), I found the following procedure to extend the
simulations
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr
Friends,
I read in many articles explaining the behaviour of water in the first (or
second etc) hydration layers around a protein. I am curious to know if
there is any way to obtain/guess the thickness of this layer. How does one
defines the thickness ?
Thanks,
Bala
--
C. Balasubramanian
--
gmx
Hi,
Read the error information carefully. Probably you are trying to read a
amber trajectory. Try installing vmd and set the VMD_PLUGIN_PATH variable
to the plugin directory inside vmd installation. Gromacs can then read the
trajectory using the vmd plugin.
On Sat, May 26, 2012 at 6:42 PM, a a wr
Dear gmx-users, I have some doubts on the manual pages. Kindly help to
understand the same.
Section 5.7.1 Page 129
1) gen-pairs: Setting ‘yes’ generates 1-4 parameters that are not present
in the pair list from normal Lennard-Jones parameters using fudgeLJ.
Is there any way that I can see/write
Friends,
I have created the top (attached) file for a tripeptide using pdb2gmx tool
of gromacs. However in the top file, i dnt see the pdb2gmx writing the ff
parameters.
I guess that the ff parameters are read directly from the ff.itp given in
the given as #include "amber03.ff/forcefield.itp". Is
Friends,
I am a newbie to gromacs, trying to calculate the Schlitters entropy
calculation using the following commands.
g_covar -f mytraj.xtc -s structure.pdb -n index.ndx -b 0 -e 4000 -mwa
-ref
g_anaeig -entropy -temp 300
When i used the above commands, i get the Schlitter entropy value for
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