Hi justin
in the tutorail you have
It is not necessary to run a complete energy minimization procedure on the
bilayer, although you can if you want. The .tpr file contains information
about bonding and periodicity, so it can, in a sense, be used to reconstruct
"broken" molecules.
when i tried
never mind , added both names and worked. did not work first time but then
it did
thank you
On Thu, Aug 18, 2011 at 12:00 PM, Sara baretller <
sarabiocomputat...@gmail.com> wrote:
>
>
> what do i write on the top of the system.gro file before the number of the
> molecules. do
what do i write on the top of the system.gro file before the number of the
molecules. do i add the name of protein and the name of bilayer or somthing
else to represent both systems in one system
Thank you
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eck the file system.gro it has the protein and the lipid
coordinates, however when i load to vmd to veiw , the VMD does not
show anything , does any body have an idea what s wrong
Thank you
>
>
>
>
>
> On Wed, Aug 17, 2011 at 4:19 PM, Sara baretller <
> sarabiocomputat..
19 PM, Sara baretller <
sarabiocomputat...@gmail.com> wrote:
> ok i did find the script
>
> thank you
>
>
>
> On Wed, Aug 17, 2011 at 4:03 PM, Sara baretller <
> sarabiocomputat...@gmail.com> wrote:
>
>> Thank you
>>
>> yes i removed the Re
ok i did find the script
thank you
On Wed, Aug 17, 2011 at 4:03 PM, Sara baretller <
sarabiocomputat...@gmail.com> wrote:
> Thank you
>
> yes i removed the Remove unnecessary lines ... i found the inflategro.pl
> when i click on the rl inflategro.pl it gives me Fire
Thank you
yes i removed the Remove unnecessary lines ... i found the inflategro.pl
when i click on the rl inflategro.pl it gives me Firefox can't find the
server at inflategro.pl.
<http://inflategro.pl/>
On Wed, Aug 17, 2011 at 3:17 PM, Justin A. Lemkul wrote:
>
>
>
I am doing the protein in lipid tutorial .
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html
Pack the lipids around the protein, i dont see where is the script perl
inflategro.pl
I googled It and did not find it. Can you please send me the sc
Hi Justin you mentioned in the past email that i can not use the measure
hbond;
do you suggest any other way to find the hbond??
thank you
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do you suggest any other way to find the hbond?? is the cut of distance of 3
or less something i can do in this case or not??
thank you
On Tue, Aug 2, 2011 at 1:58 PM, Justin A. Lemkul wrote:
>
>
> Sara baretller wrote:
>
>>
>> does the g_hbond work for course gr
does the g_hbond work for course grained file. i tried this command and it
gave me nothing but an error it does not matter wich selection
On Tue, Aug 2, 2011 at 1:01 PM, Justin A. Lemkul wrote:
>
>
> Sara baretller wrote:
>
>> I have a question about the g-hbond selection
I have a question about the g-hbond selection . after i typed in the g_hbond
, it asked me to choose two groops and i am wondering what is difference
between Protein and Protein-H ?
Thank you
Specify 2 groups to analyze:
Group 0 ( System) has 7722 elements
Group 1 (Protei
e output coordinate file contain ions? The topology
> will not be modified because genion is not being told to (i.e. through the
> use of -p).
>
> -Justin
>
>
> Warren Gallin
>>
>> On 2011-07-26, at 2:49 PM, Sara baretller wrote:
>>
>> thanks bu
thanks but i want to neutralize the system , why genion -s file.tpr -conc
0.2 -neutral -o file.gro -random does not neutralize the system to 0 .
On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul wrote:
>
>
> Sara baretller wrote:
>
>> Hi
>>
>> this a part of th
uring standard C nonbonded kernels...
Testing ia32 SSE2 support... present
On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul wrote:
>
>
> Sara baretller wrote:
>
>> Hi All
>>
>> I used the genion command using like this "genion -s file.tpr -conc 0.2
>> -neutral
ne genion -s file.tpr -conc
0.2 -neutral -o file.gro -random .
Sara
On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul wrote:
>
>
> Sara baretller wrote:
>
>> Hi all
>>
>> I used the genion to add a concentration and to neutalize the system in
>> the same ti
Hi all
I used the genion to add a concentration and to neutalize the system in the
same time by using the
*genion -s file.tpr -conc 0.2 -neutral -o file.gro -random
so it did add the NA and Cl but it did not neutralize the system,
the net charge of the system still the same negative.
s
between 2.2 and 2.7 M.
Thank you
On Fri, Jul 15, 2011 at 5:40 PM, Justin A. Lemkul wrote:
>
>
> Sara baretller wrote:
>
>> thank you for your help, will it be alot to add 700 ions to a system made
>> of water and proteins that is 4000 molecules
>>
thank you for your help, will it be alot to add 700 ions to a system made of
water and proteins that is 4000 molecules
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yes
i had X M and i convert it to X molecule / mol using Avogadro's number. but
how do i get only molecules or ions
On Fri, Jul 15, 2011 at 1:52 PM, Justin A. Lemkul wrote:
>
>
> Sara baretller wrote:
>
>> Hi All
>>
>> I have a question about adding ions
Hi All
I have a question about adding ions to the system. using Genion one can add
ions but how can you convert molecule/mol to number of molecules or ions ??
let say 2 e 23 molecule/mol to X number of molecule or ions
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