>--
>
>Message: 1
>Date: Wed, 20 Mar 2013 12:55:45 +0100
>From: Thomas Schlesier
>Subject: [gmx-users] Umbrella sampling with large pulling distance
>(larger than half of the box size)
>To:
>Message-ID: <5149a3c1.2000...@
plain; charset=ISO-8859-1; format=flowed
>
>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 w
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 wr
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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ions) 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 Aeros
sers
> Message-ID: <4ce280b6.2080...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> DeChang Li wrote:
> > Dear all,
> >
> > What is the difference between the option Distance and Direction in
> > Umbrella Sampling?
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 list
S users
> 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
> Message: 6
> Date: Tue, 19 Oct 2010 09:30:47 -0400
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] Umbrella sampling with temperature and
>pressurecoupling method problem
> To: Discussion list for GROMACS users
> Message-ID: <4cbd9d87.6080...@vt.edu>
> Content-Type: text/p
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 mailing
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 mailing
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 Gromac
ward" etc. mean?
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...@m
, the unit of pull rate is (dt*nm)/(1fs*ps)? Right? I used
Gromacs-3.3.1 for the simulation. Thanks!
Best regards,
2009-8-8
=====
Dechang Li, Ph.D Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
P.R. China
Tel: +86-10-627
1630
22.0190.1270466
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 100
>
>Message: 1
>Date: Mon, 25 May 2009 01:15:44 -0700
>From: "Zhanglin Ni"
>Subject: [gmx-users] force field parameter for ligands
>To:
>Message-ID: <009701c9dd11$012c1ae0$0301a...@zn3>
>Content-Type: text/plain; format=flowed; charset="iso-8859-1";
> reply-type=original
>
>Dear all,
>where
Gromacs to
read 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
,
=
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
=
___
gmx-users mailing listgmx
0 ?
Best regards,
2009-3-5
=========
Dechang Li, Ph.D Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
P.R. China
Tel: +86-10-62773574(O)
Email
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
he protein
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 E
sults reasonable?
Best regards,
2009-1-11
=====
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
=
>>>> 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
>On Sun, 04 Jan 2009 13:38:33 +1100
> Mark Abraham 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 f
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
0.974 0.831 0.967 0.974
Thanks alot!!!
Best regards,
2009-1-3
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR
in third column sometimes smaller than
the number in second column?
Best regards,
=====
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
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
EMAIL PROTECTED]>
>Content-Type: text/plain;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. Th
m I right?
Best regards,
2008-5-17
=========
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86
you know. ^_^
>
>> Message: 3
>> Date: Sun, 20 Apr 2008 21:01:57 +0800
>> From: Dechang Li <[EMAIL PROTECTED]>
>> Subject: [gmx-users] the number of water molecules
>> To: "gmx-users"
>> Message-ID: <[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
&g
AIL PROTECTED]
>
>You can reach the person managing the list at
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>
>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. paralle
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
the pulled group
and the reference group. How can I achieve it using Gromacs-3.3.1?
Best regards,
Dechang Li
2007/1/9
=========
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-6
=
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
[EMAIL PROTECTED]>
>Subject: Re: [gmx-users] Incomplete header: nr 3078 time 9408
>To: Discussion list for GROMACS users
>Message-ID: <[EMAIL PROTECTED]>
>Content-Type: text/plain; charset=UTF-8; format=flowed
>
>Dechang Li wrote:
>> Dear all,
>>
>
e problem? How can I 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)
Ema
-
|
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
nt to do a simulation such as a protein in the explicit
water, which option would be better? Or it will be the same?
Thank you for your reply.
Best regards,
2007-10-14
=
Dechang Li, PhD Candidate
Department of E
nd the .prmcrd file, 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
=
2. Re: Gromacs for Aerosol Particle Agglomeration (Yang Ye)
> 3. ANTECHAMBER & GAFF (Dechang Li)
> 4. Re: ANTECHAMBER & GAFF (Mark Abraham)
> 5. Re: ANTECHAMBER & GAFF (Yang Ye)
> 6. Re:
9-29
=
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773779(O)
Email: [EMAIL PROTE
= berendsen
tau_t = 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 1000
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