I increased the potential to 2350 instead of 1000 in my md_umbrella.mdp (the
other parameters kept unchanged), then the movement of my protein was less than
the previous one, which we can see from pullx.xvg (attached). But it still not
reach to the designed region. So I am going to increase the
*.mdp files.
Jiangfeng.
Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
The Netherlands
md_umbrella.mdp
Description: md_umbrella.mdp
md_p
Thank you for your reply, Thomas. Under your explanation, I am well understood
of the terms: pull_k and pull_rate.
Here I upload both md_umbrella.mdp and md_pulling.mdp.
I have to mention that it is coarse gained system with Martini force field.
At the same time, i am going to run a simulation
On 5/22/12 9:36 AM, Du Jiangfeng (BIOCH) wrote:
Dear Justin,
Based on your questions to my simulation, I posted here yesterday hopefully
it was the correct way to reply in this forum.
You've still replied to the entire digest message (which I've cut out); please
make sure to keep replies f
Dear Justin,
Based on your questions to my simulation, I posted here yesterday hopefully it
was the correct way to reply in this forum.
In this morning I got a list of new windows of umbrella sampling, the overlap
is sufficient enough, but I saw another problem: In the histogram figure, the
b
On 5/21/12 10:05 AM, Du Jiangfeng (BIOCH) wrote:
Please don't reply to the entire digest message; copy and paste only the
relevant parts.
On 5/16/12 4:08 AM, Du Jiangfeng (BIOCH) wrote:
Dear Sir/Madam,
I have performed umbrella pulling and umbrella sampling my protein from a
DOPC/DOPS mem
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