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
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 11/9/13 9:38 AM, shahab shariati wrote:
Dear Justin
Thanks for your explanation.
My system contains lipid bilayer + drug + water molecules.
I want to calculate Potential of mean force as a function of the distance
between the centers of mass of drug and the lipid bilayer.
Box vector alon
On 11/9/13 8:22 AM, shahab shariati wrote:
Daer Justin
I studied your tutorial (Umbrella Sampling). It is very beneficial for me.
The system you considered was the dissociation of a single peptide from the
growing end of an protofibril.
You considered following parameters:
Chain_B: referenc
On 4/29/13 6:42 AM, Shima Arasteh wrote:
Dear Justin,
About Umbrella sampling tutorial, would you please let me know why you created
an index file contains of chain A and chain B?
Also, what's the meaning of 19 and 20 created by a text editoras groups.txt
file? I can not understand this.
As I know, it is not necessary to restrain neither reference nor pulled
group. When you apply pulling force, it means you have restrained both of
them.
Dariush
On Mon, Jan 9, 2012 at 4:15 PM, przemek bartha wrote:
> Hello,
> According to Justin's tutorial on umbrella sampling,
> link:
> http://w
przemek bartha wrote:
Hello,
According to Justin's tutorial on umbrella sampling,
link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html
could anyone explain, if the molecules are restrained in any way in the
umbrella sampling part?
The umbrel
Steven Neumann wrote:
Hey Gmx Users,
I went through Justin tutorial of umbrella sampling with spacing of 0.2 nm:
Time COM distance
0 - 0.5
208 - 0.7
218 - 0.92
225 - 1.119
231 - 1.41
235 - 1.61
239 - 1.81
246 - 2.09
253 - 2.3
261 - 2.51
268 - 2.71
276 - 2.91
289 - 3.11
307 - 3.3
325
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