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
Sorry ...I forget to announce that my potential energy is positive, is it
logical?
From: Zahra M s_zahra_mous...@yahoo.com
To: gmx-users@gromacs.org gmx-users@gromacs.org
Sent: Thursday, December 29, 2011 12:52 PM
Subject: positive potential energy
Hi dear
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 s_zahra_mous...@yahoo.com
*To:* gmx-users@gromacs.org gmx-users@gromacs.org
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
I
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
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,
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
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!
that error.
thank you in advanced
Bests
-Zahra
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Message: 3
Date: Thu, 29 Dec 2011 01:24:14 -0800
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
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
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 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
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