[gmx-users] Automated Topology Builder

[Vasiliy Znamenskiy]

Does the type of chemical bond (single, double, triple), built by JSME
Molecular Editor, directly influence on the final result of Automated
Topology Builder (http://compbio.biosci.uq.edu.au/atb/
),
not by number of built protons?
I built a molecule with a some double bond, number of protons is correct,
however finally ATB's "Show structure" option shows this bond as a single
bond, however number of protons there as for a double bond.
Is it an error of visualization only or built topology files have errors?
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Re: [gmx-users] Temperature in Non-equilibrium MD simulation.

[Vasiliy Znamenskiy]

Does the speed of your flows have comparable scale as the  speed of sound?
If very less, don't worry about temperature.

On Wed, Apr 1, 2015 at 6:10 AM, Ho, Tuan A.  wrote:

> Dear all,
>
> As far as I understand GROMACS did NOT exclude the streaming velocity
> (Poisseuille flow) from the temperature calculation and I think it is not
> correct. I was wondering if someone has modified Gromacs code to obtain a
> good thermostat. Please let me know. Thank you very much.
>
> Tuan.
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[gmx-users] ATB

[Vasiliy Znamenskiy]

Dear All

Does the type of chemical bond (single, double, triple), built by JSME
Molecular Editor, directly influence on the final results of Automated
Topology Builder (http://compbio.biosci.uq.edu.au/atb/ ), not by number of
built protons?
I built a molecule with a some double bond, number of protons is correct,
however finally ATB's "Show structure" option shows this bond as a single
bond, however number of protons there as for a double bond.
Is it an error of visualization only or built topology files have errors?

Thank you,
Vasiliy
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[gmx-users] gromacs_win32.zip CPU version: All MS_Windows version: XP/NT/95 Libraries: Static Size: 17633280 FFTW version: 2.1.3 MPI support: no Installation prefix: customizable Comments: This is an

[Vasiliy Znamenskiy]

I hoped that the package (gromacs_win32.zip,
http://www.gromacs.org/Downloads/User_contributions/Gromacs_binaries/i686%2f%2fMS_Windows
), with programs, which are ready to execution, will accelerate my time of
study of the GROMACS  program, but it appeared that I got stuck on a step
GROMPP.
There was an error at execution of the training example.
All my attempts to understand something and to correct, replace also give
mistakes.

Can anybody give me useful advise?
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