Wassenaar tsje...@gmail.com
Hi Nawel,
g_rmsdist calculates the RMSD of distances, and distances are invariant to
translation and rotation.
Cheers,
Tsjerk
On Sun, Jun 2, 2013 at 1:45 PM, Nawel Mele nawel.m...@gmail.com wrote:
Hi,
THanks for your answers. I already seen the help
provided
with the option -s.
Cheers,
Tsjerk
On Mon, Jun 3, 2013 at 12:39 PM, Nawel Mele nawel.m...@gmail.com wrote:
Hi,
THanks for your answers.
Just for be sure, with g_rmsdit the reference structure correspond to the
frame at time 0??
Because in the manual the rmsd equation show
Hello everyone.
During the calculation of the rms with g_rmsdist command , the reference
and the current structure are aligned before calculating??
Regards,
--
*Mlle* Mele Nawel
Master 2 In Silico Drug Design
University of Paris Diderot/Strasbourg
--
gmx-users mailing list
On Sun, Jun 2, 2013 at 12:29 PM, Nawel Mele nawel.m...@gmail.com wrote:
Hello everyone.
During the calculation of the rms with g_rmsdist command , the reference
and the current structure are aligned before calculating??
Regards,
--
*Mlle* Mele Nawel
Master 2 In Silico Drug
HI,
I would like to compute an umbrella sampling simulation for o protein
divided in two domain, with Center of mass pulling using as constraint
between the two domains. And the constraint is applied instead of a
harmonic potential
I create a pull.mdp file with this option for the pull:
title
Thanks a lot for your answer.
2013/5/10 Justin Lemkul jalem...@vt.edu
On 5/10/13 4:24 AM, Nawel Mele wrote:
Hi,
I am trying to understand what is the difference between g_rms and
g_rmsdist commands.
I have looked at the manual and all I can find is that:
*g_rms*: The root mean square
Hi all,
I am performing a simulation of protein at air/water interface.
For create an air-water interface I just expand the box in the z direction.
So,aAfter minimization we can noticed that water molecules moved out of
bulk water in the z direction.
Why you just need to expand the z-axis for
, Nawel Mele wrote:
Hi all,
I am performing a simulation of protein at air/water interface.
For create an air-water interface I just expand the box in the z
direction.
So,aAfter minimization we can noticed that water molecules moved out of
bulk water in the z direction.
Why you just need
...@vt.edu
On 5/13/13 8:01 AM, Nawel Mele wrote:
So we just compute an interface vacuum-water like the picture in attach in
increase the coordinate value of the z-axis of the box?
The list does not accept attachments. If you want to post an image or
file, provide a public link to access
Hi,
I am trying to understand what is the difference between g_rms and
g_rmsdist commands.
I have looked at the manual and all I can find is that:
*g_rms*: The root mean square deviation (RM SD) of certain atoms in a
molecule with respect to a reference
structure can be calculated with the
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