On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos -
REMD). I have to perform the REMD simulation with 35 different
temperatures.
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos -
REMD). I have to perform the REMD simulation with 35
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos -
If I preped the tpr using amber forcefields, could that be the reason?
The mdrun I am using does not have any force field libraries in its
directory.
On Sat, Dec 26, 2009 at 11:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
Jack Shultz wrote:
I preped this ligand using acpypi followed by
Hi GMX users,
I want to fix a group in a truncate octahedron. How can I dealt with the
questions below,
1. I hope the box corresponds to an inscribed circle of cubic of size
40*40*40, how to calculate the box vectors?
2. One spherical rigid body consists of face-center cubic lattices is fixed
Hi Wende, please do not double post. If you are unsure if your post
got through, you can easily see the list at
http://lists.gromacs.org/pipermail/gmx-users/2009-December/date.html.
You did not put units beside 40, so I suppose that you mean 40 A,
whereas gromacs uses nm.
1. Make a box
Dear GMX users,
it is recommended the use of two-step procedure
for decoupling the solute from the solvent in hydration
free energy calculation: first decreasing the charges in the solute, without
soft core,
and after that, the same procedure is used for the LJ interactions.
In version Gromacs 4,
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a
'protein in
water' system. I am following instructions
Jack Shultz wrote:
If I preped the tpr using amber forcefields, could that be the reason?
No.
The mdrun I am using does not have any force field libraries in its
directory.
That's irrelevant. Only non-mdrun tools care about the contents of
$GMXLIB or local force field files. The point of
Hi Marc,
I figured it out. I tried upir suggestion and tested the gmxcheck but
got the following errors
gmxcheck.exe -s1 topol.tpr
Please give me TWO run input (.tpr/.tpa/.tpb) files
or specify the -m flag to generate a methods.tex file
gmxcheck.exe -s1 topol.tpr -m
Jack Shultz wrote:
Hi Marc,
I figured it out. I tried upir suggestion and tested the gmxcheck but
got the following errors
gmxcheck.exe -s1 topol.tpr
Please give me TWO run input (.tpr/.tpa/.tpb) files
or specify the -m flag to generate a methods.tex file
gmxcheck.exe -s1 topol.tpr -m
Dear all,
I want to convert the difference of two rmsf data sets into B-factor of a
coordinate (to illustrate their difference by coloring the structure by
B-factor), can anyone tell me how to do it?
Thanks in advance!
Antonio--
gmx-users mailing listgmx-users@gromacs.org
AntonioLeung wrote:
Dear all,
I want to convert the difference of two rmsf data sets into B-factor of
a coordinate (to illustrate their difference by coloring the structure
by B-factor), can anyone tell me how to do it?
g_rmsf -h
Mark
--
gmx-users mailing listgmx-users@gromacs.org
On Mon, 28 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a
I know how to calculate, and have calculated the RMSF of two trajectories (of
the same molecule), and I want to compare the two RMSFs. I want convert their
discrepancy into B-factors. Can you tell me more detailed?
-- Original --
From: Mark
Dear all,
I am trying to do a simulation of protein OMPA. At the step grompp, it shows a
fatal error stated Fatal error: Atomtype 'HC' not found!
I tried to configure the error but i failed. So, hope that anyone can help me
in this.
Thnaks..
bharat v. adkar wrote:
On Mon, 28 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica
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