[gmx-users] Shear flow with deform option

[Makoto Yoneya]

Dear GROMACS users:

The GROMACS manual says that the off-diagonal elements (of deform option) can 
be used to shear a solid or a liquid.
Then, how should I set the "comm-mode" option (concern for removing center of 
mass translation) to get shear flow with this deform option?
I'd tried "comm-mode=None" (no restriction of the center of mass motion) but it 
looks no difference with "comm-mode=Linear" concern on shear flow.
Also, I'm wondering how the system temperature (from atomic velocities) was 
evaluated if I succeeded to get shear flow with this deform option (mean shear 
flow contribution will be extracted or not).
Sorry if it was FAQ.

Regards,

Makoto Yoneya, Dr.
AIST, Tsukuba
JAPAN
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[gmx-users] GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5

[Makoto Yoneya]

Dear Mark:

 I think you will need to use a 64 bit mingw with GROMACS 5 and up.

Thank you for the comments.
I'd tried MinGW-64 (acturally TDM-GCC-64) and succeeded to build
64bit gromacs-5.0.5 on a windows PC.
However, I need 32bit gromacs-5.0.5 binary for 32bit windows PCs.
Then, I'd tried -m32 option to build 32bit version with TDM-GCC-64
and it failed with many errors.

A solution I'd found was change some lines in the file,
gmxTestLargeFiles.cmake, to somehow re-activate GMX_LARGEFILES option.
Then I could build gromacs-5.0.5 for 32bit windows PCs with TDM-GCC-32
(I'd used it because of newer GCCs than MinGW32).
See
https://staff.aist.go.jp/makoto-yoneya/MDonWINPC/
for the patch and full cmake options.
Hope it helps.

Regards,

Makoto Yoneya, Dr.
AIST, Tsukuba
JAPAN
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[gmx-users] GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5

[Makoto Yoneya]

Dear GROMACS users:

I found that GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5
(e.g. cmake -DGMX_LARGEFILES=OFF bra-bra).
At the end of cmake, it says
CMake Warning:
 Manually-specified variables were not used by the project:
 GMX_LARGEFILES.
Although, there are lines,
include(gmxTestLargeFiles)
 gmx_test_large_files(GMX_LARGEFILES)
in CMakeLists.txt file, this test looks skipped in
actual cmake (no message on this test).

Any info.s on this subject will be welcome!

Regards,

Makoto Yoneya, Dr.
AIST, Tsukuba
JAPAN
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[gmx-users] GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5

[Makoto Yoneya]

Dear Mark and Roland:

Thank you for response.

 Why did you decide to try to set it?

 Why do you ask? What do you try to achieve?

For me, I found it is necessary to compile gromacs with
MinGW32 on 32bit windows PC.
Up to gromacs-4.6.7, it works without any troubles for me
(see https://staff.aist.go.jp/makoto-yoneya/MDonWINPC/ for full
cmake options.)

The reason to try MinGW (not Cygwin) is it runs standalone
in command prompt of windows PC.
I'd been using this gromacs compiled MinGW for short practice class
for primers.
It is much easier than the Cygwin version because we can skip troublesome
Cygwin installation and explanation of some linux commands.

I'm very happy to hear the way to re-activate GMX_LARGEFILES option or
way to compile with MinGW32 without using this.

Regards,

Makoto Yoneya, Dr.
AIST, Tsukuba
JAPAN
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[gmx-users] pdb2gmx compiled with MinGW on WindowsPC

[Makoto Yoneya]

Dear GROMACS users:

This is a self-response for my query in below.

 Does anybody uses gromacs (actually 4.6.7) compiled with MinGW on windows
 PC?
 I'd been using that without any troubles.
 However, quite recently, I firstly tried pdb2gmx (gromacs-4.6.7 compiled
 with MinGW on windows PC) and met the trouble.
 (I'm not bio-related person and I did not use pdb2gmx ever!) Force field
 scan does not work with the pdb2gmx with MinGW.
 I guess it may related to the dirent functions.
 Any other common programs (e.g., grompp, runmd etc.) runs without troubles.
 Any info.s on pdb2gmx compiled with MinGW on windows PC will be welcome!

It seems no one uses gromacs compiles with MinGW.
The problem in above really caused by dirent function on MinGW.
MinGW has dirent.h but it does not work for gromacs.
Then a solution I found was the followings.
In the src/gmxlib/futil.c, change every lines with the structures,

#ifdef HAVE_DIRENT_H
 bra-bra
#elif (defined GMX_NATIVE_WINDOWS)
 bra-bra
#endif

to

#ifdef GMX_NATIVE_WINDOWS
 bra-bra
#elif (defined HAVE_DIRENT_H)
 bara-bra
#endif.

Just the change the order to stop using dirent in MinGW.
Hope it helps someone.

Regards,

Makoto Yoneya, Dr.
AIST, Tsukuba
JAPAN
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[gmx-users] source cord routines for electric fields

[Makoto Yoneya]

Dear David:

Thank a lot for your quick reply.
I'd found the code already includes some time-dependent function.
I'll study how to use it.
Thanks a lot again.

Makoto Yoneya, Dr.
AIST, Tsukuba
JAPAN

On 2014-10-02 08:01, 米谷慎 wrote:
 Dear Gromacs experts:

 I'd like to add the time-dependent function to the electric field
routines
 in GROMACS.
 I could only found the input (reading) codes in src/kernel/readir.c.
 Does anyone know which source cord routines I should modify to add the
 time-dependent functions.

 Thank you for advance.

 Makoto Yoneya, Dr.
 AIST, Tsukuba
 JAPAN

mdlib/sim_util.c
look for function calc_f_el


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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Re: [gmx-users] codes for non-bonded function selection (NBF)

[Makoto Yoneya]

Dear GROMACS experts:

This is a self-reply for my own query on adding new switch from 
Lennard-Jones to Weeks-Chandler-Andersen (WCA) potential.

I'd tried to modify the include/types/enums.h NBFselection line from 
enum { 
 eNBF_NONE, eNBF_LJ, eNBF_BHAM, eNBF_NR 
}; 
to 
enum { 
 eNBF_NONE, eNBF_LJ, eNBF_BHAM,eNBF_WCA, eNBF_NR 
}; 
. i.e., simply add a new selection (eNBF_WCA) and shift eNBF_NR. 
However, only this modification resulted in secgentation error in 
grompp execution. 

The segmentation error was resolved by modifying
src/gmxlib/names.c from
const char *enbf_names[eNBF_NR+1] = {
  , LJ, Buckingham, NULL
to
const char *enbf_names[eNBF_NR+1] = {
  , LJ, Buckingham, WCA, NULL
.

However, switch from LJ to WCA potential  in this way will
require many code modifications and may result in bugs.
Then, I'd changed to switch to WCA by setting
environment variable GMX_NB_GENERIC_WCA since
I anyway needs to set GMX_NB_GENERIC.

If someone want to try the patch to enable WCA potential,
visit to patch place,
http://staff.aist.go.jp/makoto-yoneya/MDonWINPC/
.

Thanks anyway.

Makoto Yoneya, Dr.
AIST, Tsukuba
JAPAN

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