[gmx-users] Polymerization in gromacs

[이영규]

Dear users,

I am currently having trouble with polymerization, joining the nearby atoms
if they are within the polymerization distance. My system consists of 2
monomers. The procedure what I did was that first put monomers in the box
and equilibrate it by extending box size. After I get the final box size
and equilibrate the system, I have to connect monomers. This point is what
I am stuck and here's my question.

Q. Is there any command or procedure that I can do with gromacs about the
polymerization? If not, does anyone let me know how to do or the software
doing this polymerization?

Thanks in advance
-- 

Yeongkyu Lee

M.S student

Department of Physics

501, Jinjudaero, Jinju, Gyeongnam
,
52828, Korea

Email: monsterpl...@gmail.com

Phone: +82-10-8771-2190
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[gmx-users] Simulation is very slow

[이영규]

Dear gromacs users,

I installed gromacs 2019 today. When I run gromacs, it is really slow. I
don't know the reason. I am using GTX 1080 TI and TITAN XP for GPU and I
have 8 cores. Please help me.

Sincerely

-- 

Yeongkyu Lee

M.S student

Department of Physics

501, Jinjudaero, Jinju, Gyeongnam
,
52828, Korea

Email: monsterpl...@gmail.com

Phone: +82-10-8771-2190
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[gmx-users] How to calculate tetrahedral order parameter?

[이영규]

Dear gromacs users,

Hello. I am working on bulk water system simulation. I am trying to
calculate tetrahedral order parameters in gromacs by using "gmx hydorder"
command. Dose anyone know how to process outputs generated by "hydorder"
command? It is in the form of output.xpm file.

Thanks in advance.
-- 
YK Lee
351-101
Department of physics
Institute of natural science
Gyeong sang National University
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[gmx-users] How to calculate double donor and double acceptors in gromacs?

[이영규]

Dear gromacs users,

These days, I am working on bulk water system problem. One point than I
want to know is is there a way to calculate double donor and double
acceptors in gromacs? Actually I tried to use "gmx hydorder" command but I
could't know how to use ouput, for instance output.xmp file. Could anyone
help me to figure out this problem?

Best regards,
-- 
YK Lee
351-101
Department of physics
Institute of natural science
Gyeong sang National University
-- 
Gromacs Users mailing list

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[gmx-users] How to use reduced unit in gromacs?

[이영규]

Dear gromacs users,

These days, I am working on supercritical fluid of lennard jones fluid. I
want to make a system of supercritical fluid by using gromacs with reduced
units. However, I am lost defining those parameters in gromacs. Could
anyone help me to figure out this problem?

Thanks in advance.

Best regards

-- 

Yeongkyu Lee

M.S student

Department of Physics

501, Jinjudaero, Jinju, Gyeongnam
,
52828, Korea

Email: monsterpl...@gmail.com

Phone: +82-10-8771-2190
-- 
Gromacs Users mailing list

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[gmx-users] Making Polyamide membrane itp file

[이영규]

Dear gromacs users,

These days, I am working on Polyamide membrane osmosis. And I am struggling
with making a topology file. I've read a paper " *DOI: *
10.1021/acs.jpcb.6b06560 " . The author provides pdb file for the
constructed membrane in supporting information section on the webpage. But
to do simulation, it is necessary to make "itp file. However, I don't know
how to make the file. I read the instruction in "
http://www.gromacs.org/Documentation/How-tos/Polymers;, but still I am
lost. Please give me a hand!!

Thanks in advance!

Sincerely

-- 

Yeongkyu Lee

M.S student

Department of Physics

501, Jinjudaero, Jinju, Gyeongnam
,
52828, Korea

Email: monsterpl...@gmail.com

Phone: +82-10-8771-2190
-- 
Gromacs Users mailing list

* Please search the archive at 
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