ether he delivered the code for 3D-WHAM or not
>
>Best,
>
>On Thu, Feb 20, 2020 at 2:58 AM Qing Lv wrote:
>
>> Dear Colleagues,
>>
>>
>> I am doing an umbrella sampling of an enzymatic reaction using QM/MM.
>> However, as the reaction coordinate exceed
Dear Colleagues,
I am doing an umbrella sampling of an enzymatic reaction using QM/MM. However,
as the reaction coordinate exceeds a certain value, an unexpected reaction,
which is obviously unreasonable, often occurs during the umbrella sampling. So,
how to deal with such problem? The only me
н, 13 янв. 2020 г., 17:35 Qing Lv :
>
>> Dear All,
>>
>>
>> I wonder if the error bars are necessary for umbrella sampling in PMF
>> calculation? If yes, how should the error bars be calculated? Need I do 2~3
>> repeats (with different random initial velo
Dear All,
I wonder if the error bars are necessary for umbrella sampling in PMF
calculation? If yes, how should the error bars be calculated? Need I do 2~3
repeats (with different random initial velocites assigned)?
Thanks,
Qing
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21:29:23, "Justin Lemkul" wrote:
>
>
>On 1/10/20 11:02 AM, Qing Lv wrote:
>> Dear Colleagues,
>>
>>
>> I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic
>> reaction. The initial coordinates (with solvents and ions) for each
Dear Colleagues,
I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic
reaction. The initial coordinates (with solvents and ions) for each sampling
window were extracted from previous trajectories. The reaction coordinate (bond
length difference) of each initial frame was c
defaults] sections. You can #include files, but
>they have to follow the structure of the example in chapter 5 of the manual
>(and every tutorial). Defaults, then atomtypes and parameters, then
>moleculetypes, then system.
>
>Mark
>
>On Fri, Jun 23, 2017 at 5:47 AM Qing Lv wrote:
&
At 2017-06-23 21:55:39, "Justin Lemkul" wrote:
>
>
>On 6/23/17 9:53 AM, Qing Lv wrote:
>> I tried pdb2gmx -merge interactive or -chainsep interactive, but neither
>> work...
>
>There is no chain information in a .gro so this approach cannot work. If you
I tried pdb2gmx -merge interactive or -chainsep interactive, but neither work...
Qing
At 2017-06-23 17:19:55, "Fitsiou, Eleni" wrote:
>Hi ,
>Rename your chains and you could use -merge interactive and the -ter flag
>Best
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>
>* Please search the archive at
>ht
ot; in PDB), pdb2gmx might
regard all aminoacids as one single chain.
Sorry for not having explained clearly in previous emails. Any suggestions?
Many thanks,
Qing
At 2017-06-23 16:24:13, "Qing Lv" wrote:
>Dear Mark,
>
>
>Actually I had tried the method you suggested, but g
manually renaming atoms.
>
>Mark
>
>On Fri, Jun 23, 2017 at 3:55 AM Qing Lv wrote:
>
>> Hi,
>>
>>
>> Gromos 54a7 force field has built-in topologies for some small molecules,
>> like ATP. In these topologies, many atoms have names of up to 5 letters,
>
d defaults directive.
P.S.
My topology file includes ATP, Protein, and Mg2+. I tried to remove Mg2+
(probably inappropriate) but still got the same errors.
Thanks,
Qing
At 2017-06-23 09:46:49, "Qing Lv" wrote:
>Dear All,
>
>
>I am setting up a simulation of pr
Hi,
Gromos 54a7 force field has built-in topologies for some small molecules, like
ATP. In these topologies, many atoms have names of up to 5 letters, such as
AO1PA and AO2PB. However, PDB files seem do not support 5-letter atom names.
So, if I name an atom "AO2PB" in PDB, it will be truncated
Dear All,
I am setting up a simulation of protein-ATP complex. I manually combined the
coordinates and topologies of the protein and ATP together, and ran editconf
and solvate successfully. However, when I ran grompp, errors occurred:
Syntax error - File forcefield.itp, line 4
Last line read:
'
mx-rms.html
>You can have a look at rms.xvg file, it contains rmsd values.
>
>Best regards,
>Dading Huang
>
>
>On Wed, Jun 14, 2017 at 7:05 PM, Qing Lv wrote:
>
>> I generated a .dat file with the following command:
>> gmx rms -s .pdb -f 1.xtc -f2 2.xtc -n in
I generated a .dat file with the following command:
gmx rms -s .pdb -f 1.xtc -f2 2.xtc -n index.ndx -o rms.xvg -m rms.xpm -bin
rms.dat
But how to read the binary file rms.dat?
The reason is that,
I found the lowest RMSD in RMSD matrix (rms.xpm) is 0.52 nm; how to know which
frame in 1.xtc a
Thank you. I have just received the response from Dr. Jochen Hub and solved
this problem.Qing
At 2017-05-14 22:42:30, "Qing Lv" wrote:
>Hi Colleagues,
>
>I am trying to compile FMA (Functional Mode Analysis), developed by Dr. Jochen
>Hub. However, I met difficulti
Hi Colleagues,
I am trying to compile FMA (Functional Mode Analysis), developed by Dr. Jochen
Hub. However, I met difficulties in the installation. According to the
instructions, I installed Gromacs 4.0.5 (also tried 4.0.7) and the related
libraries (libf2c, lapack, mpich, etc).
Firstly, cmake
Dear all,
I am trying to compile IED (Interactive essential dynamics) according to the
instructions of
http://mccammon.ucsd.edu/ied/
However, I always got such errors:
--
vmd > gopython
Info) Starting Python...
Traceback (most recent call last):
File "",
Thank you so much, Justin. I will look into PLUMED.
Qing
At 2017-04-08 19:05:28, "Justin Lemkul" wrote:
>
>
>On 4/8/17 1:46 AM, Qing Lv wrote:
>> Thank you, Justin.
>>
>>
>> My goal is to investigate the conformation transition of a 30aa loop be
divide the loop into many small segments (pull-groups) and define the
pull coordinates separately? This seems horrible...
Thanks,
Qing
At 2017-04-08 09:06:46, "Justin Lemkul" wrote:
>
>
>On 4/7/17 8:56 PM, Qing Lv wrote:
>> Dear Colleagues,
>>
>>
>> I a
ne can provide a template of pull code for such simulations?
Thanks a lot
Qing Lv
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Dear Colleagues,
I am now compiling GMX 2016.1 on CentOS 6, with devtoolset-3 and -4. When
executing 'make' , I got such errors:
[ 98%] Building CXX object share/template/CMakeFiles/template.dir/template.cpp.o
Linking CXX executable ../../bin/template
../../lib/libgromacs.so.2.1.0: undefined ref
Hi,
I am trying to compile GMX 2016.1 on CygWin, but failed.
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs2016.1
-DGMX_BUILD_OWN_FFTW=ON
make
/tmp/cctDFyCD.s: Assembler messages:
/tmp/cctDFyCD.s:49: Error: invalid register for .seh_savexmm
Makefile:745: re
on a different
>machine than you were running on... Does $builddir/bin/mdrun-test pass?
>Does the terminal output mention SIMD?
>
>Mark
>
>On Fri, Feb 3, 2017 at 1:29 PM Qing Lv wrote:
>
>> Mark,
>>
>>
>> The results are:
>> $ ./simd-test.exe
>> Se
t;
>Mark
>
>On Fri, Feb 3, 2017 at 6:52 AM Qing Lv wrote:
>
>> Thank you, Mark. I am now trying to install devtoolset-2.
>>
>>
>> Regarding Cygwin version, I must clarify that, although the compilation is
>> successful, I got an error message when per
m libraries alone on redhat systems, and instead compiling with
>the devtoolset packages.
>
>Thanks for the Cygwin report. People often report problems that look like
>they come from broken systems, and we rarely hear of a resolution.
>
>Mark
>
>On Fri, 3 Feb 2017 05:55 Qing L
Hi Colleagues,
I am trying to build GMX 5.1.x (tried 5.1.4, 5.1.1, & 5.1) on a Redhat 6.5
server; I have updated GCC compiler and all dependent libraries (tried GCC
4.9.4 and GCC 6.3.0). (The built-in compiler of Redhat 6.5 is GCC 4.4.7, which
is too old.)
I used the commmand
export CC=gcc
exp
on the road. But if you observe yourself in a car
>crash every day, now you have evidence that you need driving lessons... If
>you had a car crash once every hundred days, and reported only that single
>day as evidence you need lessons... that'd be wrong on many levels.
>
>Mark
Hi,
I did a 200-ns MD for a protein and found an interesting conformation
transition, and according to NMR study in literature, it is believed that 10 us
~ ms scale simulations are needed to get this conformation transition.
However, when I tried to reproduce this conformation transition, I was
Hi,
I did a 200-ns MD for a protein and found an interesting conformation
transition, and according to NMR study in literature, it is believed that 10 us
~ ms scale simulations are needed to get this conformation transition.
However, when I tried to reproduce this conformation transition, I was
I see. Thanks.
Qing
At 2015-07-11 05:07:27, "Justin Lemkul" wrote:
>
>
>On 7/9/15 11:00 PM, Qing Lv wrote:
>>> It means to evaluate quantities over successive blocks of time (e.g. using
>>> -b and -e that all GROMACS analysis tools support) and check to s
ze of blocks I need to divide in such an analysis? e.g., for a 100-ns
trajectory, is it appropriate to divide it into 5-ns or 10-ns blocks to see if
it has converged?
Qing
At 2015-07-10 01:39:42, "Justin Lemkul" wrote:
>
>
>On 7/9/15 10:11 AM, Qing Lv wrote:
>>
Hi Brett,
I think the following command will work:
trjconv -f source.xtc -skip 5 -o target.xtc
Qing
At 2015-07-10 10:10:39, "Brett" wrote:
>Dear All,
>
>
>Will you please show me the command based on the following cited content from
>the website on how to convert a xtc file with 1 frame per
help?
Best,
Qing
At 2015-07-09 19:41:09, "Justin Lemkul" wrote:
>
>
>On 7/8/15 9:48 PM, Qing Lv wrote:
>> Hi,
>>
>> I did a 70-ns MD simulation. I wonder how to justify when the trajectory
>> reached equilibrium...
>> Seen from RMSD-time curve
Hi,
I did a 70-ns MD simulation. I wonder how to justify when the trajectory
reached equilibrium...
Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and
kept stable after that. Could I justify that the system reached equilibrium at
12 ns? Are there any methods/criteri
Hi,
I did a 70-ns MD simulation. I wonder how to justify when the trajectory
reached equilibrium...
Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and
kept stable after that. Could I justify that the system reached equilibrium at
12 ns? Are there any methods/criteri
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