--
Message: 1
Date: Wed, 20 Mar 2013 12:55:45 +0100
From: Thomas Schlesier schl...@uni-mainz.de
Subject: [gmx-users] Umbrella sampling with large pulling distance
(larger than half of the box size)
To:
Dear all,
I am running a 9000 atom system with GBSA (Gromacs 4.5.5) in a
Blue Gene/Q cluster. I got the speed 1.002 ns/day with 8 cores.
However, in my own workstation with 8 cores the same system can reach
nearly 10 ns/day (Intel(R) Xeon(R) CPU E5620 @ 2.40GHz). Can anyone
tell me what's
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On 17/07/2012 5:00 PM, DeChang Li wrote:
Dear all,
I am running a 9000 atom system with GBSA (Gromacs 4.5.5) in a
Blue Gene/Q cluster. I got the speed 1.002 ns/day with 8 cores.
However, in my own workstation with 8 cores the same system can reach
at all. Does this affact my calculation?
=
Dechang Li , Ph.D
Biomechanics and Biomaterials Laboratory
Department of Applied Mechanics
School of Aerospace Engineering
Beijing Institute of Technology
Beijing 100081, P. R. China
Hi all,
Just as the title, can Gromacs do Targeted MD simulations? If Yes, how
to set up the simulation procedure?
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Please search the archive at
) between some
small molecules (e.g. ligand A and its replica). How can Gromacs to do this?
Any suggestion will be very appreciated.
Best regards,
=
Dechang Li, Ph.D
Biomechanics and Biomaterials Laboratory
Department of Applied Mechanics
School of Aerospace
Dear all,
What is the difference between the option Distance and Direction in
Umbrella Sampling?
In my opinion, the option Direction means that pulling the pull_group1
through the direction related to the reference group. Right? But how about
the option Distance?
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gmx-users mailing
Message-ID: 4ce280b6.2080...@vt.edu
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DeChang Li wrote:
Dear all,
What is the difference between the option Distance and Direction in
Umbrella Sampling?
In my opinion, the option Direction means that pulling
Dear all,
I want to use umbrella sampling to calculate the PMF of the
conformational transition of a protein. What temperature coupling method and
pressure coupling method should I use? Berendsen temperature coupling or
Nose-Hoover temperature coupling? Or each one is OK?
--
gmx-users
Message: 6
Date: Tue, 19 Oct 2010 09:30:47 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Umbrella sampling with temperature and
pressurecoupling method problem
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
Message-ID: 4cbdd022.6020...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
DeChang Li wrote:
Message: 6
Date: Tue, 19 Oct 2010 09:30:47 -0400
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Subject: Re: [gmx-users] Umbrella sampling
Dear all,
Does the following three options do the same things in the pull code of
Gromacs 4.0:
1. pull_dim = Y Y Y
pull_vec1 = 1 0 0
**
2. pull_dim = Y N N
pull_vec1 = 1 0 0
**
3. pull_dim = Y N N
pull_vec1 = 1 0.5 0.5
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gmx-users
Dear all,
I used g_nmeig to diagonalize the Hessian matrix, that I got the
eigenvalues. However, I found that in the file 'eigenval.xvg' the unit of
the eigenvalues are Eigenvalue [Gromacs units]. What is the '[Gromacs
units]'?
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Dear gmx-users,
Are there any comparisons of the code speed between Gromacs 3.0 and
Gromacs 4.0. In my calculation, I got a speed about 3.5ns/day of a system have
about 50,000 atoms, using 8 CPUs with Gromacs 3.3.1. In contrast, the speed can
reach up to 7.3ns/day when switch to
?
Best regards,
2009-1030
=
Dechang Li, Ph.D Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
P.R. China
Tel: +86-10-62773574(O)
Email: lid...@mails.tsinghua.edu.cn
24.0190.1102782
26.0190.1115073
28.0190.1304575
30.0190.1173159
Best regards,
=
Dechang Li, Ph.D Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
P.R. China
Tel: +86-10-62773574(O
Message: 1
Date: Mon, 25 May 2009 01:15:44 -0700
From: Zhanglin Ni z...@u.washington.edu
Subject: [gmx-users] force field parameter for ligands
To: gmx-users@gromacs.org
Message-ID: 009701c9dd11$012c1ae0$0301a...@zn3
Content-Type: text/plain; format=flowed; charset=iso-8859-1;
,
=
Dechang Li, Ph.D Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
P.R. China
Tel: +86-10-62773574(O)
Email: lidc02 at mails.tsinghua.edu.cn
=
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gmx-users mailing listgmx
the energy from the file ener.edr, does the cutoff affect the values
of the energy? For example, when the cutoff is set to 1.2 nm and the PME method
is used, does the energy term Coul-SR read by g_energy contain the long range
part ?
Ran.
Dechang Li wrote:
Dear all,
When we do a MD simulation
be displayed by the arrowhead and the length of the arrows? If NO,
how can I do this work with other package?
Thanks in advance!
Best regards,
2009-3-5
=
Dechang Li, Ph.D Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
P.R. China
=
Dechang Li, Ph.D Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
P.R. China
Tel: +86-10-62773574(O)
Email: lid...@mails.tsinghua.edu.cn
to a reference strucutre firstly, and then calculate S2 using command
'g_rotacf'? If YES, what the reference structure is? The average
structure in the trajectory?
Best regards,
2009-3-3
=
Dechang Li, Ph.D Candidate
Department of Engineering Mechanics
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773574(O)
Email: lid...@mails.tsinghua.edu.cn
=
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gmx-users mailing list
Dechang Li wrote:
Dear all,
I want to use g_rotacf to calculate the order parameter(S2, N-H bond
in
main chian).
The tool g_rotacf needs an index.ndx file that contains two vectors.
g_rotacf wants the index number of two atoms to calculate the order
parameter of an NH vector
=flowed
On Sun, 04 Jan 2009 13:38:33 +1100
Mark Abraham mark.abra...@anu.edu.au wrote:
Dechang Li wrote:
Dear all,
I want to use g_rotacf to calculate the order parameter(S2, N-H bond in
main chian).
The tool g_rotacf needs an index.ndx file that contains two vectors.
g_rotacf wants
,
2009-1-3
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773779(O)
Email: li.d...@gmail.com
regards,
2009-1-4
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773779(O)
Email: li.d...@gmail.com
column?
Best regards,
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773779(O)
Email: [EMAIL PROTECTED
ffamber99 to simulate the system
which contains
proteins and DNAs?
Best regards,
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773779(O)
Email: [EMAIL PROTECTED
;charset=utf-8;format=flowed
Dechang Li wrote:
Dear all,
I used command g_hbond to calculated the distance distribution of
hbonds
in my system. There are two columns in the file hbdist.xvg, as showed
follow:
@title Hydrogen Bond Distribution
@xaxis label Hydrogen
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773779(O)
Email: [EMAIL PROTECTED]
=
___
gmx-users
about 5 angstrom? Is that possible in
Gromacs?
Best regards,
2008-4-20
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773779(O)
Email: [EMAIL PROTECTED
Dear all,
How can I calculate the number of water molecules around the
protein with a distance about 5 angstrom? Is that possible in
Gromacs?
Best regards,
2008-4-20
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua
gmx-users-request,您好!
Message: 1
Date: Sat, 5 Apr 2008 11:48:15 +0800
From: DeChang Li [EMAIL PROTECTED]
Subject: [gmx-users] RMSD VS. parallel simulation
To: gmx-users@gromacs.org
Message-ID:
[EMAIL PROTECTED]
Content-Type: text/plain; charset=ISO-8859-1
Dear all,
I
the person managing the list at
[EMAIL PROTECTED]
When replying, please edit your Subject line so it is more specific
than Re: Contents of gmx-users digest...
Today's Topics:
1. RMSD VS. parallel simulation (DeChang Li)
2. Re: RMSD VS. parallel simulation (Mark Abraham
simulation, the RMSD of protein at t=0 was about
0.1 nm, why not equal to zero? I used the initial structure for the
least squares fit.
Best regards,
2008-4-5
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773779(O)
Email: [EMAIL PROTECTED]
=
___
gmx-users mailing
,
2007-12-2
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773779(O)
Email: [EMAIL PROTECTED
resolve it?
Best regards,
2007-11-11
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773779(O)
Email: [EMAIL PROTECTED
@gromacs.org
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=UTF-8; format=flowed
Dechang Li wrote:
Dear all,
I used Gromacs-3.3.1 to do a simulation. When it finished, I used
command g_dist to calculate two groups distance VS time. But at time
9408ps, it stopped and showed
-
|
H
Best regards,
2007-10-17
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773779(O)
Email: [EMAIL PROTECTED
, another one is the script.
They are in a compressed file in the attached.
The command used may be:
./amb2gmx.pl --prmtop XK.prmtop --crd XK.prmcrd --outname XK
Best regards,
2007-10-13
=
Dechang Li, PhD
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773779(O)
Email: [EMAIL PROTECTED
replying, please edit your Subject line so it is more specific
than Re: Contents of gmx-users digest...
Today's Topics:
1. Gromacs for Aerosol Particle Agglomeration (Lorenzo Isella)
2. Re: Gromacs for Aerosol Particle Agglomeration (Yang Ye)
3. ANTECHAMBER GAFF (Dechang Li)
4. Re
= 0.2
tc-grps = protein
ref_t = 300.0
Thank you for your answers.
Dechang Li
[EMAIL PROTECTED]
2007-04-16
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hi,
Can anyone tell me what does this error mean?
ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not
implemented
my md.mdp file was set:
ns_type = grid
pbc = xyz
Thank you very much!
Li,DC
Department of Engineering Mechanics
Tsinghua University
Beijing
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