Hi Salam,
Please get acquainted with SI units and prefixes. And don't forget to use
your brains. It says there that 1000 ps is 1 ns. So now, how to go from 1
to 10 and match the ps and nsteps?
Cheers,
Tsjerk
On Jan 30, 2015 8:55 AM, "salam pradeep" wrote:
> Dear Gromacs user,
>
> I am a new us
Hi all,
I used g_polystat command in gromacs to compute persistence length and I
define atom group in index.ndx file. The result is like
Average end to end distance: 0.203 (nm)
Average radius of gyration: 0.051 (nm)
Average persistence length: *2.00 bonds* (? why not in nm?)
Regards,
--
Gr
Thx a lot Tsjerk
On Fri, Jan 30, 2015 at 1:38 PM, Tsjerk Wassenaar wrote:
> Hi Salam,
>
> Please get acquainted with SI units and prefixes. And don't forget to use
> your brains. It says there that 1000 ps is 1 ns. So now, how to go from 1
> to 10 and match the ps and nsteps?
>
> Cheers,
>
> Tsj
On 1/30/15 3:10 AM, Christian Bope Domilongo wrote:
Hi all,
I used g_polystat command in gromacs to compute persistence length and I
define atom group in index.ndx file. The result is like
Average end to end distance: 0.203 (nm)
Average radius of gyration: 0.051 (nm)
Average persistence
On 1/30/15 1:55 AM, ashish bihani wrote:
Hello,
I understand that .itp is a topology file. But the swissparam pack does not
have a .gro file. How do I create solvated.gro ? (which has to be used in
grompp)
Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say
wheth
Thank you justin for reply. I have read and follow the second paragraph and
use this command
*g_polystat -s tmp.tpr -f tmp.xtc -n index.ndx -p persist.xvg*
On 30 January 2015 at 19:14, Justin Lemkul wrote:
>
>
> On 1/30/15 3:10 AM, Christian Bope Domilongo wrote:
>
>> Hi all,
>>
>> I used
Hi Adam
I have a SVL script to convert a gromacs trajectory in pdb format to mdb.
Contact me offline.
Best
Sandeep
On Wed, Jan 28, 2015 at 5:43 AM, adam wrote:
> Hi
>
>
>
> Does anyone have experience/tips/ideas about importing a Gromacs trajectory
> into MOE ? I can obviously port everyth
Dear Gromacs users,
We are simulating a large nanofiber assembly composed of repeating units of
peptides, and we have been trying to see how the addition of calcium would
affect its behavior. We have already tried adding calcium ions in a random
distribution, which we successfully did.
But we a
Dear Gromacs users,
I'm trying to see the part of a protein that are accessible to an average
size antibody and to do that I'm calculating the Solvent Accessible Surface
Area using a bigger probe (-probe 1.5 ).
The problem is that every time (and with different machines) I have
"Segmentation fault
Dear Gromacs users,
I'm trying to see the part of a protein that are accessible to an average
size antibody and to do that I'm calculating the Solvent Accessible Surface
Area using a bigger probe (-probe 1.5 ).
The problem is that every time (and with different machines) I have
"Segmentation fault
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