[gmx-users] Bond lengths

[suniba shuaib]

Dear Users
I have performed a 200 ns MD simulation of a protein and a small molecule
inhibitor of 30 atoms, using GROMOS 43a1 ff and Gromacs v 5.0. Taking
reference from a number of papers and similar systems, I have used LINCS
algorithm to constrain all bond lengths.
I have reported interactions like pi-pi and hydrogen bonding between
protein and ligand plus some other analysis and  recently i submitted my
article. Reviewers have asked few question one of which is:

*Q: Why you have constrained all bond lengths? A good force field should
permit free variation of the bond lengths and only high frequency motions
(C-H) should be constrained.*

As i visited mailing list, I found an answer by Justin Lemkul:

*"The effects of H-bond vibrations aren't of interest for the problems
at hand; if you want to model bond formation, you can't accept a model
that has no "electron vibrations," and *that* drives your choice of
time step."*

Another reply by Mark Abraham:
"*Force field parameters are (unfortunately) co-optimized with and
dependent on*

*implementation issues like size of time step and lengths of cut-offs. The
use of constraints=all-bonds couples constraints across a whole polymer; if
that's a protein simulated using a spatial domain decomposition, those
atoms are widely distributed on the machine and the communication required
for the iterative constraint solver can become rate limiting at extreme
scale. Reducing the constraint iteration to a single node is unattractive
if the rest of the machine lies idle - which is part of why we'd like to
improve the ability to deploy task parallelism in GROMACS at scale. The
main alternative is using shorter time steps (maybe no constraints at all!)
- if they only way you can get 10x greater sampling rate for a single
simulation is by using 100x the hardware at one tenth of the time step,
then that could be a serious option.

I think that feeling that "constrained H bonds" is natural and "constrained
heavy-atom bonds" is artificial is wrongly conflating experience with
correctness."*


After reading these answers, I am little confused how should i respond
to the raised question. In my case, I believe, it was not necessary to
keep the system unconstrained. Plus, from Mark's answer, I concluded
that it is better to keep all bonds constrained? Please clear my
confusion.

Thank You

Suniba
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Re: [gmx-users] couple-intramol

[Qasim Pars]

Hi,

Thanks. If I want to calculate the intramolecular energy of the ligand, I
need to choose Coul-14:LIG-LIG, LJ-14:LIG-LIG, Coul-SR:LIG-LIG and
LJ-SR:LIG-LIG in the .edr file. Am I wrong?

On 4 January 2017 at 04:03, Justin Lemkul  wrote:

>
>
> On 1/3/17 2:40 PM, Qasim Pars wrote:
>
>> Dear users,
>>
>> I got a little bit confused about the use of "couple-intramol". If I set
>> it
>> to "no", the intramolecular intractions of the ligand are "on" when the
>> ligand is decoupled, right? It means that I don't need to set [
>>
>
> More specifically, intramolecular interactions are not a function of
> lambda; they are always in the A-state.  Only intermolecular interactions
> are modulated by lambda.
>
> nonbond_params ] part for the ligand?
>>
>>
> You should never have to do anything with [nonbond_params] in these
> systems.
>
> -Justin
>
> ; Free energy
>> free-energy  = yes
>> init-lambda  = 0
>> delta-lambda = 0
>> sc-alpha = 0.5
>> sc-power = 1
>> sc-sigma = 0.3
>> sc-coul  = yes
>> couple-moltype   = ligand
>> couple-intramol  = no
>> couple-lambda0   = vdw-q
>> couple-lambda1   = none
>> nstdhdl  = 100
>>
>> Thanks in advance,
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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-- 
Qasim Pars
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Re: [gmx-users] force calculations in PMF

[Alex]

Since I don't use WHAM or even know what it is, I can only guess that 
feeding pullf data sets the COM force as a function of time. Conversely, 
GMX reports COM pullf data when pulling is set up via pull code. And 
that is the pulling force acting upon the COM of the _pulled object_. 
So, I can guess here that you're supplying the force data for the COM of 
_the group subject to pulling_. It makes very little sense to me that a 
force would be prescribed for the entire system when the objective is to 
artificially move one subsystem relative to another.


This assumes I understood your question. :)

Alex


On 1/3/2017 8:22 PM, deepak bapat wrote:

HI Alex!



OK.. :-)

Let me try to put it this way.

In WHAM method we supply pullf files.

I had doubt regarding forces listed in those files.

Whether these values are for the entire system or the forces acting on the
particular group which is being pulled away.

Regards

Deepak






On Wed, Jan 4, 2017 at 8:46 AM, Alex  wrote:


There's a reason no one is replying: we can't understand your question. :)



On 1/3/2017 8:09 PM, deepak bapat wrote:


Dear Gromacs users

I had a doubt regarding pull code.

Which force values are considered while calculations? ensemble average
values of the entire system or the forces acting on the group/atoms under
consideration.

Regards

Deepak


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Re: [gmx-users] force calculations in PMF

[deepak bapat]

HI Alex!



OK.. :-)

Let me try to put it this way.

In WHAM method we supply pullf files.

I had doubt regarding forces listed in those files.

Whether these values are for the entire system or the forces acting on the
particular group which is being pulled away.

Regards

Deepak






On Wed, Jan 4, 2017 at 8:46 AM, Alex  wrote:

> There's a reason no one is replying: we can't understand your question. :)
>
>
>
> On 1/3/2017 8:09 PM, deepak bapat wrote:
>
>> Dear Gromacs users
>>
>> I had a doubt regarding pull code.
>>
>> Which force values are considered while calculations? ensemble average
>> values of the entire system or the forces acting on the group/atoms under
>> consideration.
>>
>> Regards
>>
>> Deepak
>>
>
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-- 
Deepak U. Bapat
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Re: [gmx-users] force calculations in PMF

[Alex]

There's a reason no one is replying: we can't understand your question. :)


On 1/3/2017 8:09 PM, deepak bapat wrote:

Dear Gromacs users

I had a doubt regarding pull code.

Which force values are considered while calculations? ensemble average
values of the entire system or the forces acting on the group/atoms under
consideration.

Regards

Deepak


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[gmx-users] force calculations in PMF

[deepak bapat]

Dear Gromacs users

I had a doubt regarding pull code.

Which force values are considered while calculations? ensemble average
values of the entire system or the forces acting on the group/atoms under
consideration.

Regards

Deepak
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Re: [gmx-users] couple-intramol

[Justin Lemkul]

On 1/3/17 2:40 PM, Qasim Pars wrote:

Dear users,

I got a little bit confused about the use of "couple-intramol". If I set it
to "no", the intramolecular intractions of the ligand are "on" when the
ligand is decoupled, right? It means that I don't need to set [


More specifically, intramolecular interactions are not a function of lambda; 
they are always in the A-state.  Only intermolecular interactions are modulated 
by lambda.



nonbond_params ] part for the ligand?



You should never have to do anything with [nonbond_params] in these systems.

-Justin


; Free energy
free-energy  = yes
init-lambda  = 0
delta-lambda = 0
sc-alpha = 0.5
sc-power = 1
sc-sigma = 0.3
sc-coul  = yes
couple-moltype   = ligand
couple-intramol  = no
couple-lambda0   = vdw-q
couple-lambda1   = none
nstdhdl  = 100

Thanks in advance,



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] mdrun initialises, fails to run, no error message

[Justin Lemkul]

On 1/3/17 10:43 AM, Natalie Tatum wrote:

Dear all,

I'm hoping you can shed light on (a) what my mdrun problem is and (b) where
to start fixing it.

I'm simulating different mutants of a protein dimer on DNA, for 10 ns
a-piece. I have successfully run this protocol on the wild-type protein, on
two single residue mutants, and on a double mutant. I came to run the same
on a fourth, single site mutant. I have followed the same protocols and
utilised the same MDP settings throughout. All were subject to 5000 steps
of steepest-descent energy minimisation, then 200 ps of equilibration in
the NVT ensemble, then the same in the NPT. For this particular mutant
there were no issues apparent going into production MD. Therefore, I don't
think it's an issue of my MDP setup or system...

So I have two compatible (OpenCL 1.2) AMD Radeon HD Firepro D300 GPUs, and
I have one mutant (run/process) assigned to each.

For this mutant I call mdrun with:

gmx mdrun -deffnm md -gpu_id 1 &

Whereas the other is on -gpu_id 0, and walk away. This worked successfully
in the week prior for two other systems. It's New Year, then I come back to
what should be completed simulations this morning to get my hands dirty in
analysis.

Run on gpu 0 has completed successfully, all is grand.

Mutant on gpu 1 has not. Attempts to resume/restart fail (on either GPU, or
both, or calling neither explicitly). All output looks like this:

GROMACS:  gmx mdrun, VERSION 5.1.3

Executable:   /usr/local/gromacs/bin/gmx

Data prefix:  /usr/local/gromacs

Command line:



  gmx mdrun -deffnm md



From the .log, it appears your command was not what you think it was.  Is it 
possible that the job failed because mdrun tried to consume all available 
hardware and got hung up?





GROMACS version:VERSION 5.1.3

Precision:  single

Memory model:   64 bit

MPI library:thread_mpi

OpenMP support: disabled

GPU support:enabled

OpenCL support: enabled

invsqrt routine:gmx_software_invsqrt(x)

SIMD instructions:  AVX_256

FFT library:fftw-3.3.4-sse2

RDTSCP usage:   enabled

C++11 compilation:  disabled

TNG support:enabled

Tracing support:disabled

Built on:   Mon  1 Aug 2016 17:20:18 BST

Built by:   natalie@t 
hemachineIuse.here.there [CMAKE]

Build OS/arch:  Darwin 15.5.0 x86_64

Build CPU vendor:   GenuineIntel

Build CPU brand:Intel(R) Xeon(R) CPU E5-1650 v2 @ 3.50GHz

Build CPU family:   6   Model: 62   Stepping: 4

Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx
msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2
sse3 sse4.1 sse4.2 ssse3 tdt x2apic

C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/
XcodeDefault.xctoolchain/usr/bin/cc Clang 7.3.0.7030031

C compiler flags:-mavx-Wall -Wno-unused -Wunused-value
-Wunused-parameter -Wno-unknown-pragmas  -O3 -DNDEBUG

C++ compiler:   /Applications/Xcode.app/Contents/Developer/Toolchains/
XcodeDefault.xctoolchain/usr/bin/c++ Clang 7.3.0.7030031

C++ compiler flags:  -mavx-Wextra -Wno-missing-field-initializers
-Wpointer-arith -Wall -Wno-unused-function -Wno-unknown-pragmas  -O3
-DNDEBUG

Boost version:  1.60.0 (external)

OpenCL include dir: /System/Library/Frameworks/OpenCL.framework

OpenCL library: /System/Library/Frameworks/OPENCL.framework

OpenCL version: 1.2


And there it ends. No files except the log shown above - and though this
initial output looks identical in content to the beginnings of logs for
successful simulations, mdrun does not then seem to engage with the
GPU/CPUs available.

There are no error messages, no apparent indication as to where this has
gone wrong... And now I can't run mdrun at all, for any system.



Test whether or not your GPU is still accessible and capable of running test 
programs.


-Justin


I've checked my disk space (fine, >100 GB available), I'm able to call and
execute other gmx commands, but mdrun does the above.

The closest error I can find with my google-fu is three years ago where
this user (
http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/FEdWd6gC/mdrun-no-error-but-hangs-no-results
) got no error but a killed process, but I don't even get as far as
detection of CPUs/GPUs or domain decomposition.

Any suggestions much appreciated,

Natalie



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] couple-intramol

[Qasim Pars]

Dear users,

I got a little bit confused about the use of "couple-intramol". If I set it
to "no", the intramolecular intractions of the ligand are "on" when the
ligand is decoupled, right? It means that I don't need to set [
nonbond_params ] part for the ligand?

; Free energy
free-energy  = yes
init-lambda  = 0
delta-lambda = 0
sc-alpha = 0.5
sc-power = 1
sc-sigma = 0.3
sc-coul  = yes
couple-moltype   = ligand
couple-intramol  = no
couple-lambda0   = vdw-q
couple-lambda1   = none
nstdhdl  = 100

Thanks in advance,

-- 
Qasim Pars
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Re: [gmx-users] About the number of step in Argon Molecular Dynamic -Phase transition

[Romulo Leoncio Cruz Simbron]

Hi Mark,
Thank you very much for your reply. It seems to me very strange what
happens precisely because the equilibria of Temperature and Pressure were
realized to me to look with success during time of equilibration of almost
10 ns for the case of NVP that allowed a equilibration of the pressure and
temperature that was corroborated by the graph of pressure.xvg and
temperature.xvg.
I have reviewed the bibliography and found the article: https://www.
omicsgroup.org/journals/molecular-dynamics-investigation-visualization-
on-the-phase-transition-of-a-lennard-jones-fluid-2168-9806.
1000103.php?aid=8141

In the paper it happens that the temperature of change of phase is not
correct , around 50 K (the boiling point of argon correct is around 87K).

 Adiotionally , the paper,
http://www.pci.uni-heidelberg.de/bpc2/pdfs/paper2011/Schubert2011.pdf
, is showing the dependency of the average melting temperature on the
heating rate.

Could it be very important to perform annealing slowly in order to achieve
a proper equillibrium?

Best REgards

Romulo L. Cruz Simbron
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[gmx-users] The Rg does not change at all during the umbrella sampling

[faride badalkhani]

Dear all,

I want to perform pulling simulations on a polymer-drug system. I have
performed simulations on polymer and polymer+drug for 30 ns and then set up
system for pulling. After generating configurations I chose some of them
and performed a 10 ns of MD for each window. However, when I plot the Rg
for the system it does not change during the simulation and autocorrelation
function of Rg is zero, as well.

I have performed another PMF simulation on a similar system (the only
difference is in the terminal groups of polymers) and I did not have this
problem. I would appreciate any suggestions on how to solve this issue.

Regards,
Farideh
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Re: [gmx-users] Reading tpx file (md_0_1.tpr) version 110 with version 100 program

[Mark Abraham]

Hi,

You can only generate an old tpr format with the version of the code that
produced that. So you want to either upgrade the version on your cluster,
or install the old version on your laptop for your convenience.

Mark

On Wed, Dec 28, 2016 at 10:11 PM Zhang, Cheng  wrote:

> Dear Gromacs,
>
> I use "gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o
> md_0_1.tpr" to generate the tpr file on my own PC. Then I submitted it to
> our university computer cluster, in which an older version is installed,
> and I got the Fatal error:
>
>
> Reading tpx file (md_0_1.tpr) version 110 with version 100 program
>
>
> I know I should use the same old version to generate the tpr file. But
> should I unstall the newer one, and install the older one?
>
>
> Can I use the newer Gromacs to generate the old tpr file? Thank you.
>
>
> Yours sincerely
>
> Cheng
>
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Re: [gmx-users] New inGromacs

[Mark Abraham]

Hi,

We'd be quite happy to consider organizing a GROMACS activity in e.g.
Africa if there's a suitable number of users it would help and a way to pay
travel expenses. We may have ways to find money, if people have communities
they want to expose further to GROMACS.

Mark

On Thu, Dec 29, 2016 at 3:59 AM Fredrick Oghenebrorie 
wrote:

> Hi every one. am new with Gromacs, for going to 4 months now.
> i have been working through the online tutorials to get some of the
> commands of Gramacs.
> i see different conferences and seminars being organized in different parts
> europe.
> am from Nigeria and stay here in nigeria,
> butno conference/seminar has been organized here in nigeria
> is the Gromacs Administrators not interested in developing the software
> around african countries?.
> i really want to know the Gromacs in details
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Re: [gmx-users] Exploding temp/pressure.

[Mark Abraham]

Hi,

P-R coupling is only stable if the system is already near equilibrium, so I
would always vary other stuff (like step size) while using NVT or Berendsen
P coupling (or both in successive stages).

Although your observations are consistent with an initial structure that
has reached a reasonable local minimum, a possibility is that the
configuration is still frustrated somehow and that it is easier for a
larger time step to get over a saddle point towards a deeper minimum. But
then that time step could be too large for the resulting forces (which
would certainly be made even worse by P-R). Expending effort into
constructing a more reasonable original starting structure might pay off.
Simulated annealing at the small step size would be another possibility to
consider.

Mark

On Sun, Jan 1, 2017 at 5:02 PM Nash, Anthony  wrote:

> Hi all,
>
> I¹m trying to equilibrate a Martini CG simulation from an initial
> atomistic structure. Eq and Fc values were derived using an atomistic
> system. I¹ve started the dt at 0.0005 for 60 steps, moving through
> 0.001, 0.0015 and 0.002 for the same number of steps, using the .mdp
> details below (with the exception of the time step and the output
> delimiters - the remaining settings are from the Martini website). During
> these steps the temperature dropped from approx 6K down to 310K and
> the potential energy dropped from positive figures down to around
> -1.4*10^6. A final 60 steps with dt = 0.002 showed a converged temp,
> pressure, volume, potential energy (and total energy), and very little
> change in the unit dimensions.
>
> I now want to move the time step up to 0.025. I¹ve tried various dt values
> (0.005, 0.01, 0.015Š 0.025) using the below setup, but each time dt causes
> almost immediately structural explosion. The temperature and the pressure
> rockets up. I changed the pressure coupling to berendsen and the same
> happens. I have been through dozens of tau_p and tau_t combinations, each
> one yields a trajectory of varying length before exploding (the protein
> Œexplodes¹ at the exact time the the pressure and temperature increases).
> I have also changed the thermostat to berendsen and Nose-Hoover, using a
> range of 5*(dt*nsttcouple) and 20(dt*nsttcouple), respectively.
>
>
> I would appreciate any thoughts or suggestions on how to solve my
> temperature/pressure problem when I try increasing the dt to a CG value.
>
> Thanks
> Anthony
>
>
> title= Martini
> integrator   = md
> dt   = 0.025
> nsteps   = 30
> nstcomm  = 100
>
>
> nstxout  = 1
> nstvout  = 1
> nstfout  = 0
> nstlog   = 1
> nstenergy= 1
> nstxout-compressed   = 0
> compressed-x-precision   = 0
> ;compressed-x-grps=
> energygrps   = collagen solvent
> cutoff-scheme= Verlet
> nstlist  = 20
> ns_type  = grid
> pbc  = xyz
> verlet-buffer-tolerance  = 0.005
> coulombtype  = PME ;reaction-field
> rcoulomb = 1.1
> fourierspacing   = 0.16 ;0.2  ;0.12
> epsilon_r= 15   ; 2.5 (with polarizable water)
> epsilon_rf   = 0
> vdw_type = cutoff
> vdw-modifier = Potential-shift-verlet
> rvdw = 1.1
>
> tcoupl   = v-rescale ;berendsen ;v-rescale
> tc-grps  = collagen solvent
> tau_t= 0.4 0.4 ;2.0 2.0
> ref_t= 310 310
>
> Pcoupl   = parrinello-rahman
> Pcoupltype   = semiisotropic
> tau_p= 12.0  ;parrinello-rahman is more stable with
> larger tau-p, DdJ, 20130422
> compressibility  = 4.5e-5 0
> ref_p= 1.0 1.0
> refcoord_scaling = com
>
> gen_vel  = no
> gen_temp = 310
> gen_seed = 473529
> continuation = yes
> constraints  = none
> constraint_algorithm = lincs
> lincs-warnangle = 45
> lincs-order=18
> lincs-iter=4
>
>
>
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Re: [gmx-users] Exploding temp/pressure.

[Daniel Bauer]

Did you forget to set an initial temperature distribution? In your mdp you
set gen_vel to no. So it will not create an initial velocity distribution
matching your temperature. For the first simulation of your workflow, you
should set gen_vel: yes and continuation: no. Then for all simulation that
build on top of that simulation you use the velocities from the last
timestep of the previous one (mdrun -t flag) and disable gen_vel + set
continuation to yes.

Also consider running your first simulation with berenden barostat to
quickly equilibrate the pressure. For actual sampling of the configuration
space you should then switch to parrinello since berendson doesnt sample
the ensemble correctly.

Both temperature and pressure should equilibrate very quickly in a martini
simulation, allowing to increase the timestep to 3 fs or more rather
quickly.


Hope this helps!
Daniel
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[gmx-users] About GTX-Titan-X(Pascal)

[양창원]

Dear gromacs users.

Does the latest version of gromacs support GTX-Titan-X(pascal) or not?

It’s code name is GP102-400, different from GTX1080 or GTX1070.(GP104-200
or GP104-400)

Thanks a lot. 

 

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[gmx-users] About GTX-Titan-X(Pascal)

[양창원]

Dear gromacs users.

Does the latest version of gromacs support GTX-Titan-X(pascal) or not?

It’s code name is GP102-400, different from GTX1080 or GTX1070.(GP104-200
or GP104-400)

Thanks a lot. 

 

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[gmx-users] relative reorientation calculation

[Md. Imrul Reza Shishir]

Dear all
Good day.

I am working one 36 chain fibril cross section. I want to calculate
relative reorientation with respect to the center chain. For my simulation,
i use position restrain in the center chain. I am little confused how I
calculate relative reorientation (Δφ/Δr). Do I have to calculate average
distance and angle by gmx distance and gmx gangle with respect time, then
calculate the relative reorientation.

I have another quarry about gmx distance and gmx gangle. When we select a
group what is it mean by number of position is not even (gmx distance) or
divided by 3 (gmx gangle).

-- 
*Md Imrul Reza Shishir*
Master Student
*Inha University*
*CRC for NanoCellulose Future Composites*
36 Getbeol-ro, Yeonsu-gu
Incheon 21999
South Korea
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