On 30/12/2011 1:06 AM, leila karami wrote:
Dear gromacs users
I want to calculate error estimates using block averaging for output
from g-dist
(distance between donor atom of protein and acceptor atom of dna).
I used g_analyze -f dist.xvg -ee
there are 3 columns in output file.
anyone give
On 30/12/2011 5:30 AM, Olivia Waring wrote:
Hi Mark,
Thanks for your reply! I'm sorry, you're right, as far as I know the
manual doesn't actually mention Buckingham pairs generation... but
when I set gen-pairs to "yes" and run grompp, I get the following error:
"Generating pair parameters is
On 30/12/2011 7:49 AM, Yun Shi wrote:
Hello everyone,
I am using g_cluster with gromos method to do some clustering, and by
default, -cl writes the central structure of each cluster obtained.
So I wonder what 'central structure' mean? Assuming that I cluster
based on RMSD values relative to
Hello everyone,
I am using g_cluster with gromos method to do some clustering, and by
default, -cl writes the central structure of each cluster obtained.
So I wonder what 'central structure' mean? Assuming that I cluster based on
RMSD values relative to the starting conformation, and that I then
d how to solve that error.
thank you in advanced
Bests
-Zahra
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Message: 3
Date: Thu, 29 Dec 2011 0
Hi Mark,
Thanks for your reply! I'm sorry, you're right, as far as I know the manual
doesn't actually mention Buckingham pairs generation... but when I set
gen-pairs to "yes" and run grompp, I get the following error:
"Generating pair parameters is only supported with LJ non-bonded
interactions"
Dear gromacs users
I want to calculate error estimates using block averaging for output from
g-dist
(distance between donor atom of protein and acceptor atom of dna).
I used g_analyze -f dist.xvg -ee
there are 3 columns in output file.
anyone give me more explain about these columns?
how to e
On 29/12/2011 9:43 PM, michael zhenin wrote:
Hello,
I would like to run a simulation using the shell option.
I tried to restraint solvent molecules which were found within the
range of 5-10 angstroms from the box center. I couldn't find any
way to do so. I didn't find any inf
Hey :)
Just some side notes. Make sure to distinguish between 'statistical
error' or 'standard error of the mean', which is a measure of how
'correct' your estimate of the average is, and the standard deviation
or the variance, which is a measure of the natural spread. The latter
is not an error!
Hello,
I would like to run a simulation using the shell option.
I tried to restraint solvent molecules which were found within the range
of 5-10 angstroms from the box center. I couldn't find any way to do
so. I didn't find any information about this topic anywhere else
i.e. GROMACS manual, onlin
On 29/12/2011 8:24 PM, Zahra M wrote:
Sorry ...I forget to announce that my potential energy is positive, is
it logical?
No.
*From:* Zahra M
*To:* "gmx-users@gromacs.org"
*Sent:* Thursday, December 29, 2011 12:52 PM
*
Sorry ...I forget to announce that my potential energy is positive, is it
logical?
From: Zahra M
To: "gmx-users@gromacs.org"
Sent: Thursday, December 29, 2011 12:52 PM
Subject: positive potential energy
Hi dear all
I'm simulating a system containing CNT,
Hi dear all
I'm simulating a system containing CNT, when I put CNT in a unit cell and want
to run energy minimization in a vacuum, I encounter with such an error: "The
optimal PME mesh load for parallel simulations is below 0.5 and
for highly parallel simulations between 0.25 and 0.33, for h
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