Re: [gmx-users] Can't observe ion separation under the influence of electric field

[Man Hoang Viet]

Hi Live King,

I think the temperature coupling strongly effect on your observation since
the velocity of atoms (ions) will be rescale after every tau-t value. It
means the movement direction of ion under EEF will be mostly canceled for
every tau-t (ps). If you set tau-t to be larger than default value (.i.e
10, 100 or 1000) you can see the effect of EEF on your system.

Viet Man,
University of Pittsburgh School of Pharmacy

>
> Dear David and Harutyun,
>
> Thanks for your reply. Density plots were the first check I did. They show
> a very minor difference. I imagined that the electric field is not
> sufficient, however,  presence of high electric field ( > 1 V or 1000mV)*
> disrupts the membrane and my simulation crashes*. Is there any solution to
> this problem? I will have a look at compel.
>
> On Thu, Feb 13, 2020 at 6:21 PM Harutyun Sahakyan 
> wrote:
>
>> You can use compel and build a double bilayer system to separate ions.
>> However, if you separate positive and negative ions, you will have very
>> high membrane potential, event two ions difference can raise potential
>> about 200 mV. In your case, I suppose 500 mV is not enough to separate
>> all
>> ions in a PBC box.
>>
>> https://www.mpibpc.mpg.de/grubmueller/compel
>>
>>
>>
>> Harutyun Sahakyan
>> Senior Assistant at Laboratory of
>> Computational Modeling of Biological Processes,
>> Institute of Molecular Biology, NAS, Armenia, Yerevan
>> Tel: +374 93 323990
>> h_sahak...@mb.sci.am
>> sahakya...@gmail.com
>>
>> February 13, 2020 2:07 AM, "Live King"  wrote:
>>
>> > Dear all,
>> >
>> > I am running a simple test case with a lipid bilayer (DMPC), water,
>> and
>> > ions (150mM KCL) under the influence of a constant electric field (
>> 300mV,
>> > 500mV, and 700mV). *I expected positive and negative ions to separate
>> in
>> > the presence of an external electric field*. However, I am not
>> observing
>> > such behavior despite running the all-atom simulation for 400ns in any
>> > case. I am using gromacs 2018.2, my mdp file is standard charmm-gui
>> > production with electric field option.
>> >
>> > for example 500mV electric field in Z-direction :
>> > electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 =
>> > 500 mV *
>> >
>> > Are there any settings to run the electric field simulation that I
>> miss?
>> > Any help will be greatly appreciated.
>> >
>> > Thank you,



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Re: [gmx-users] Amber 14SB force-field problem with residue HID

[Man Hoang Viet]

 able to find a few instances of others using the
> command
> via a web search.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On Thu, 19 Sep 2019 at 06:36, m g  wrote:
>
>> Dear Justi,I want to calculate the Tetrahedral Order Parameter (Q) for
>> water in my simulation system. I used "gmx hydorder" command but it is
>> not
>> clear for me. what kinds of flag must be use exactly? how can I set
>> correct
>> number for "-sgang1 and -sgang2" flags? This command is very confusing.
>> how
>> can I get Q?Thanks,Sana
>> --
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> End of gromacs.org_gmx-users Digest, Vol 185, Issue 59
> **
>


-- 
Man Hoang Viet
Institute of Physics,
Polish Academy of Sciences.
Al. Lotnikow 32/46
02-668 Warsaw, Poland.


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Re: [gmx-users] Update Amber force fields, ff12SB abd ff14SB gromacs implementation testing

[Man Hoang Viet]

Hi Justin,

> Date: Mon, 28 Dec 2015 08:18:45 -0500
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Update Amber force fields, ff12SB abd ff14SB
>   gromacs implementation testing
> Message-ID: <568136b5.5090...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/28/15 1:40 AM, Man Hoang Viet wrote:
>> Hi,
>>
>>> Date: Sun, 27 Dec 2015 16:03:50 -0500
>>> From: Justin Lemkul <jalem...@vt.edu>
>>
>>> The energy of the same configuration in both AMBER and GROMACS should
>>> be
>>> the
>>> same if the force field implementation is equivalent.  You don't need
>>> to
>>> run
>>> simulations, extract conformations, etc. to get this.  Take one
>>> coordinate
>>> file,
>>> calculate its energy in each program, and report the result.  The Sorin
>>> group
>>> did a slightly more complex version of this, by testing several
>>> different
>>> coordinate perturbations (the reason for which is explained on their
>>> website),
>>> but the for the purpose of troubleshooting, a single configuration
>>> should
>>> do
>>> initially.  It's really quite straightforward.  If the same coordinates
>>> produce
>>> different energies, there is a fundamental problem in the force field
>>> implementation.  If the problem is shared among Gly and other amino
>>> acids,
>>> this
>>> implies a backbone problem, which is very troubling, but the fact that
>>> you
>>> can't
>>> reproduce the ff99 result means you're likely doing something
>>> incorrectly
>>> in
>>> your assessment.  Be sure you're doing single-point energy calculations
>>> correctly using mdrun -rerun.
>>>
>>> -Justin
>>
>> My simulation for energy calculation is steep minimization with
>> nsteps=0.
>
> This is the wrong way to calculate a single point energy.
>
> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>
> Note the last paragraph.
>
> -Justin
>
>> This simulation gives energy information of the initial structures which
>> are the same in both AMBER and GROMACS simulation.
>> I can't not produce exact conformations as The Sorin done group for
>> testing without their code, however I do test for the initial structures
>> generated by Leap in AMBER by the same way I did for my previous tests.
>> This test result is shown in below table:
>> Error(%) & ff99   & ff99SB  & ff12SB  & ff14SB
>> BOND & 0.001  &  0.001  &  0.001  &  0.001
>> ANGLE& 0.000  &  0.000  &  0.000  &  0.000
>> DIHEDRAL & 0.000  &  0.000  &  0.000  &  0.000
>> 1-4vdW   & 0.000  &  0.000  &  0.000  &  0.000
>> 1-4QQ& 0.000  &  0.000  &  0.000  &  0.000
>> vdW  & 0.000  &  0.000  &  0.000  &  0.000
>> QQ   & 0.002  &  0.002  &  0.002  &  0.002
>> Epot & 0.005  &  0.004  &  0.004  &  0.004
>>
>> In my view, it is not clear what cause the dihedral energy difference.
>> My
>> test assessment, the force field implementations (ff99, ff99SB, ff12SB
>> and
>> ff14SB) and the different  dihedral energy calculations between GROMACS
>> and AMBER are all possible for making the problem. I will try to figure
>> out this issue.

Thank you very much for the information. I have corrected my test as below
commands:
grompp_s  -f eqtest.mdp -p  v.top -c  test.pdb -o  test.tpr
mdrun_s -nt 1 -s test.tpr -rerun test.pdb -g test.log
Then the energy information were taken from test.log

eqtest.mdp:
##
integrator  =  md
emtol   =  100.0
emstep  =  0.005
dt  =  0.01; ps !
nsteps  =  1  ; total 100 ps
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 10
ns_type = grid
rlist   = 1.0
coulombtype = cut-off
rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.0
ewald_rtol  = 1e-5
###

However, the result is still the same as what I reported. Could you please
tell me other way to directly calculate diheral engery by GROMACS from a
give structure (or dihedral)? Till now, I do not think my test assessment
causes the difference of the dihedral energies.


Viet Man,
Postdoctoral Research Scholar,
Department of Physics, NCSU

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Re: [gmx-users] Update Amber force fields, ff12SB abd ff14SB gromacs implementation testing

[Man Hoang Viet]

Hi,

> Date: Fri, 25 Dec 2015 20:24:41 -0500
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Update Amber force fields, ff12SB abd ff14SB
>   gromacs implementation testing
> Message-ID: <567dec59.3040...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/24/15 5:04 AM, Man Hoang Viet wrote:
>> Dear GROMACS users,
>>
>> I have completed the test for the Amber force fields, ff12SB and ff14SB,
>> implementation into GROMACS.
>> The test report is updated at:
>> http://www.gromacs.org/@api/deki/files/252/=ffA2G_test.pdf
>>
>> and the test data set updated at:
>> http://www.gromacs.org/@api/deki/files/253/=FF12SB_FF14SB_GROMACS_TEST.tar.bz2
>>
>
> The dihedral error is rather large, and specific to the protein
> parameters. This
> suggests there is something being calculated somewhat differently.  Can
> you use
> simple single-point energies to identify the source of this problem?
> Errors in
> dihedrals can impact sampling quite a bit.
>
> -Justin

I have just done test for amber99 force field and the result is similar to
other amber force fields (see in below link).
http://www.gromacs.org/@api/deki/files/254/=ffA2G_test.pdf
The table 3 shows the dihedral energy differences of small residues such
as GLY and ALA are significant larger than other ones. I think the smaller
residues the more sampling in the give simulation time (1ns), therefore
the dihedral phase space of the small amino acids are broader than bigger
ones.
Maybe, the sampling conformations is the main reason making my test result
on dihedral energy is a bit different with the one fro Prof. Eric J.
Sorin. (with the same force field amber99).
http://ffamber.cnsm.csulb.edu/ffamber.php
I will try to find out the sources that cause dihedral energy differences
between AMBER and GROAMCS in my test.

Viet Man,
Postdoctoral Research Scholar,
Department of Physics, NCSU.


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Re: [gmx-users] Update Amber force fields, ff12SB abd ff14SB gromacs implementation testing

[Man Hoang Viet]

Hi,

> Date: Sun, 27 Dec 2015 16:03:50 -0500
> From: Justin Lemkul 

> The energy of the same configuration in both AMBER and GROMACS should be
> the
> same if the force field implementation is equivalent.  You don't need to
> run
> simulations, extract conformations, etc. to get this.  Take one coordinate
> file,
> calculate its energy in each program, and report the result.  The Sorin
> group
> did a slightly more complex version of this, by testing several different
> coordinate perturbations (the reason for which is explained on their
> website),
> but the for the purpose of troubleshooting, a single configuration should
> do
> initially.  It's really quite straightforward.  If the same coordinates
> produce
> different energies, there is a fundamental problem in the force field
> implementation.  If the problem is shared among Gly and other amino acids,
> this
> implies a backbone problem, which is very troubling, but the fact that you
> can't
> reproduce the ff99 result means you're likely doing something incorrectly
> in
> your assessment.  Be sure you're doing single-point energy calculations
> correctly using mdrun -rerun.
>
> -Justin

My simulation for energy calculation is steep minimization with nsteps=0.
This simulation gives energy information of the initial structures which
are the same in both AMBER and GROMACS simulation.
I can't not produce exact conformations as The Sorin done group for
testing without their code, however I do test for the initial structures
generated by Leap in AMBER by the same way I did for my previous tests.
This test result is shown in below table:
Error(%) & ff99   & ff99SB  & ff12SB  & ff14SB
BOND & 0.001  &  0.001  &  0.001  &  0.001
ANGLE& 0.000  &  0.000  &  0.000  &  0.000
DIHEDRAL & 0.000  &  0.000  &  0.000  &  0.000
1-4vdW   & 0.000  &  0.000  &  0.000  &  0.000
1-4QQ& 0.000  &  0.000  &  0.000  &  0.000
vdW  & 0.000  &  0.000  &  0.000  &  0.000
QQ   & 0.002  &  0.002  &  0.002  &  0.002
Epot & 0.005  &  0.004  &  0.004  &  0.004

In my view, it is not clear what cause the dihedral energy difference. My
test assessment, the force field implementations (ff99, ff99SB, ff12SB and
ff14SB) and the different  dihedral energy calculations between GROMACS
and AMBER are all possible for making the problem. I will try to figure
out this issue.


Viet Man,
Postdoctoral Reseach Scholar
Department of Physics, NCSU

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[gmx-users] Update Amber force fields, ff12SB abd ff14SB gromacs implementation testing

[Man Hoang Viet]

Dear GROMACS users,

I have completed the test for the Amber force fields, ff12SB and ff14SB,
implementation into GROMACS.
The test report is updated at:
http://www.gromacs.org/@api/deki/files/252/=ffA2G_test.pdf

and the test data set updated at:
http://www.gromacs.org/@api/deki/files/253/=FF12SB_FF14SB_GROMACS_TEST.tar.bz2

Merry X-mas and happy new year!

Bests,
Viet Man

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[gmx-users] amber force fields, ff12SB abd ff14SB gromacs implementation: amino testing

[Man Hoang Viet]

Dear Gromacs users,

I have done the amber force fields, ff12SB and ff14SB implementation test.
This test just do for amino, I will try to do it on nucleic. The test also
performed for amber ff99SB which was already implement and used widely.
Please check:
 http://www.gromacs.org/@api/deki/files/250/=ffA2G_test.pdf for testing
report and
http://www.gromacs.org/@api/deki/files/251/=FF12SB_FF14SB_GROMACS_TEST.tar.bz2
is the testing data set.

I also replaced two new file amber12sb.ff.tar.gz and amber14sb.ff.tar.gz
by the new ones which were correct Makefile.*

Yours sincerely,
Viet Man



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Re: [gmx-users] amber force field ff12SB and ff14SB for gromacs uploaded

[Man Hoang Viet]

ave written some codes (scripts and Fortran) to automatically convert
bonds, angles, dihedrals and compare residues. But adding new atomtypes
and correcting them in residues I have to do by hand.

PS, I am sorry, I forgot changing the forcefield.doc file, but it is not
important :).


> From: Alexey Shvetsov <ale...@omrb.pnpi.spb.ru>
> To: gmx-us...@gromacs.org
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] amber force field ff12SB and ff14SB for
>   gromacs uploaded
> Message-ID: <99d36c6236750208c9b9ccd305836...@omrb.pnpi.spb.ru>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Hi!
>
> Thank you forforcefield conversion! But how you checked that all
energies are same?
>
> PS problems with different ions can be simply fixed with set of defines
>PPS also seems like forcefield.doc in ff directory are wrong. It states
>that it is still amber99sb forcefield
>
> Man Hoang Viet ? 14-12-2015 06:56:
>> Dear gromacs users,
>> The amber force fields, ff12SB abd ff14SB, for gromacs were uploaded.
>>From
>> my side, I may confirm the accuracy of my converting for every atoms,
bonds, angels, impropers and diherals parameters, but it will be much
>> >> better if some ones can double check it (I will provide my codes,
>>strategy
>> and explanation of the converting for gromacs users who really want to
>>do
>> the checking work). Please note that the parameters of ions (such as
>>Na+,
>> Mg+ ...) will be differences in the different water models. Here, the
>>ion
>> parameters are for TIP3P water model. Therefore you will need edit ion
parameters if you wan to use ions in other water models.
>> Yours sincerely,
>> Viet Man
>> Postdoctoral Research Associate,
>> Physics Department, NCSU
>
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov, PhD
> Department of Molecular and Radiation Biophysics
> FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
Leningrad region, Gatchina, Russia
> mailto:alexx...@gmail.com
> mailto:ale...@omrb.pnpi.spb.ru

-- 
Man Hoang Viet
Postdoctoral research associate.
Physics Department, NCSU


















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Re: [gmx-users] amber force field ff12SB and ff14SB for gromacs uploaded

[Man Hoang Viet]

Hi,

> Date: Tue, 15 Dec 2015 13:55:08 -0500
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] amber force field ff12SB and ff14SB for
>   gromacs uploaded
> Message-ID: <5670620c.6040...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 12/15/15 1:52 PM, Man Hoang Viet wrote:

> The concern is less about the method of conversion; these types of
> programs are
> reasonably straightforward to write.  The concern is always that the
> energies
> and forces calculated in one program match the other.  The simplest thing
> to do
> is run some single-point energy evaluations in AMBER and GROMACS.  If they
> match, your conversion is successful.  If they don't, you have a problem
> with
> the integrity of the GROMACS files.  You say above that you "make sure
> that they
> are the same in AMBER and GROMACS" but you don't specify what that means.
> Visual inspection of the contents?  Or actual quantitative assessment?
>
> -Justin
>

Yes, I just try to show to Alexey Shvetsov or some gromas users who want
to do check the conversion. It is too much thing to post for the detail of
residue comparing. I agree with your suggestion about testing. I will try
to do test and report it as soon as possible. Here I really want other
gromacs users do check my conversion and take apart the testing to make
the conversion completely successful. It will give us more freedom in
doing with GROMACS.


> Date: Tue, 15 Dec 2015 20:36:52 +0100
> From: Szil?rd P?ll <pall.szil...@gmail.com>
> To: Discussion list for GROMACS users <gmx-us...@gromacs.org>
> Cc: Discussion list for GROMACS users

> Why is documentation not important, could you elaborate?

I just mean it does not effect on gromacs running. I know it is very
important to authorized information.

>
> Note that the Makefiles are outdated too, I suggest either fixing them or
> removing them.

Thank you for your comment, I fixed it.

> Plus, you seem to have left no contact information in the tarball either
> which (together with the unclear verification process), I'd say, makes the
> FF port risky to use.

I work alone in the conversion that why I wish other users do check and
test the FF together. I hope coming tests will remove the risky and we
will have the new FF in GROMACS.

Viet Man


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[gmx-users] amber force field ff12SB and ff14SB for gromacs uploaded

[Man Hoang Viet]

Dear gromacs users,

The amber force fields, ff12SB abd ff14SB, for gromacs were uploaded. From
my side, I may confirm the accuracy of my converting for every atoms,
bonds, angels, impropers and diherals parameters, but it will be much
better if some ones can double check it (I will provide my codes, strategy
and explanation of the converting for gromacs users who really want to do
the checking work). Please note that the parameters of ions (such as Na+,
Mg+ ...) will be differences in the different water models. Here, the ion
parameters are for TIP3P water model. Therefore you will need edit ion
parameters if you wan to use ions in other water models.

Yours sincerely,

Viet Man
Postdoctoral Research Associate,
Physics Department, NCSU

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Re: [gmx-users] AMBER force fields, ff12SB and ff14SB for GROMACS

[Man Hoang Viet]

> Date: Thu, 10 Dec 2015 18:02:32 -0700
> From: Michael Shirts <mrshi...@gmail.com>
> To: Discussion list for GROMACS users <gmx-us...@gromacs.org>
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] AMBER force fields, ff12SB and ff14SB for
>   GROMACS
> Message-ID:
>   <CA+zJb=idFn0-7ZdQDKcK+0QH8HwyJPBsW=xt-=wsd7nqi-y...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Great!  It's important to have all data validated carefully. Have you
> put together a set of tests, with coverage of all the atom types and
> interaction types, showing that the molecules give the same energies
> in both GROMACS and AMBER?  Validating conversions is quite important
> so that people can trust the results.

I have considered every atoms, atom types, nonbonds and bonds interaction,
atoms in every residues and nucleic acids to make sure they are the same
as in AMBER. If some ones pick up any those things to compare with
original one, I can make sure they will be the same. As you said the test
is very important, but it takes a lot of time and I am working on this. It
will be much better if other gromacs users like you participate the
testing work.

>
> On Thu, Dec 10, 2015 at 4:01 PM, Man Hoang Viet <mhv...@ifpan.edu.pl>
> wrote:
>> Dear GROMACS Admins,
>>
>> I have implemented AMBER force field ff12SB and ff14SB into GROMACS and
>> want to share them with all gromacs users. I have tried to upload it via
>> below link
>> http://www.gromacs.org/Downloads/User_contributions/Force_fields
>> However, I can not do register to upload. Could you please tell me how I
>> can share the amber force fields to gromacs users.
>>
>> Thank you very much.
>>
>> Yours sincerely,
>> --
>> Viet Man,
>>
>> Postdoctoral Research Associate,
>> Physics Department, NCSU
>

Viet Man,
Postdoctoral Research Associate,
Physics Department, NCSU

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[gmx-users] AMBER force fields, ff12SB and ff14SB for GROMACS

[Man Hoang Viet]

Dear GROMACS Admins,

I have implemented AMBER force field ff12SB and ff14SB into GROMACS and
want to share them with all gromacs users. I have tried to upload it via
below link
http://www.gromacs.org/Downloads/User_contributions/Force_fields
However, I can not do register to upload. Could you please tell me how I
can share the amber force fields to gromacs users.

Thank you very much.

Yours sincerely,
-- 
Viet Man,

Postdoctoral Research Associate,
Physics Department, NCSU


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Re: [gmx-users] electric field

[Man Hoang Viet]

Hi,

I can confirm electric field (even laser-pulse form) in GROMACS (all
version from 3.0 to current newest one) work fine. To check it, you may
consider a system containing only an ion (say Na+) in vacuum and set mdp
file as:
###
dt  =  0.0002; ps !
nsteps  =  100  ; total 20 fs

...

Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no
E-x =  1 30 1


After run MD you may check the velocity of the ion and see how it work by
some general motion equations such as Force = -q*E = m*a -->
veleocity=a*t.

Additionally, the option -field of mdrun will give output of electric field.

Good luck!

Viet Man


> Date: Sun, 15 Nov 2015 22:58:34 +0330
> From: Maryam Kowsar 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] electric field
> Message-ID:
>   
> Content-Type: text/plain; charset=UTF-8
>
> Dear users,
>
> I applied electric fields of different magnitudes (less than 1 v/nm since
> higher amounts are avoided) in my system. I have some charged water
> molecules and I expected to see very different results when the magnitude
> is changed, but haven't got that much difference. How can I be sure that
> electric fields worked?
> I found the following link that it changed the code of electric field
> according to the shape of the system:
>  http://www.gromacs.org/Developer_Zone/Programming_Guide/Patching_mdrun
> Can the current implemented code in gromacs be applied for all systems or
> should I change it for different systems?
>
> Thanks!



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Re: [gmx-users] magnetic field - segmentation fault

[Man Hoang Viet]

Hi Maryam Kowsar,

My Name is Man Hoang Viet, you may call me Viet Man (but not Man Hong) :).

I worked on gromacs-4.5.5. But I think it will be the same as (or similar
to) other versions. Try play more and harder with the code, you will get a
lot of things with gromacs. Gromacs is a very flexible and powerful
package.

Have a nice week.

Viet Man



 Dear Man Hong,

 It seems we are looking at the problem from 2 different angles. Well, I am
 going to test it, but I think it's not logical; without T-coupling we
 can't
 rely on the results. However, I wonder why you think it may cause
 problems.
 Velocities should change. I guess I can ask you questions then. Which
 version of gromacs are you working with? Which source codes have you
 modified?
 Thank you!

 On Fri, Jul 24, 2015 at 8:41 AM, Man Hoang Viet mhv...@ifpan.edu.pl
 wrote:



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Re: [gmx-users] magnetic field - segmentation fault

[Man Hoang Viet]

Hi Maryam Kowsar,

I have implemented external magnetic field to GROMACS and tested it. The
code ran well and the test result is consistent with experiment for simple
case (say Na+ in vacuum and without t_coupling). I may guest why your code
got the error. But I am sorry that I can not share my code to anyone now
(but I will do share it to this forum in near future).
However, there is an important issue that MD simulation with t_coupling
always does re-scale velocity of all atoms to keep the given temperature
and it strongly effect on the Lorentz Force of the external magnetic
field. Otherwise, If the t_coupling is not applied, the system temperature
will increase forever. Therefore, I wonder whether we really can estimate
effect of the magnetic field on protein (or other target) in simulation?


On 23 Jul 2015, at 11:52, Maryam Kowsar maryam.kow...@gmail.com wrote:

 Dear users,

 Iam trying to add magnetic field code to gromacs. I think I did all the
 modifications necessary in all source codes but when I use mdrun command
 it
 gives me segmentation fault error while in md.log the magnetic field is
 present. When I change tpx_version the error is gone but in md.log no
 magnetic field is implemented. How can I overcome segmentation fault
 error?  Should tpx_version be changed after adding a code?

 Thanks!

Man Hoang Viet
Institute of Physics,
Polish Academy of Sciences.
Al. Lotnikow 32/46
02-668 Warsaw, Poland.

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[gmx-users] Unit of electric field in gromacs

[Man Hoang Viet]

Dear GROMACS users,

I found a conflicting (may be) about Unit of electric field. In gromacs
manual at page 8, the Unit is around 10^7 V/m = 10^-2 V/nm, while it is
V/nm in output file *_fied.xvg of mdrun. It is a very big difference and
makes me confused. Could you please tell me the correct unit of electric
field in gromacs?

Thank you very much.

Bests,

Viet Man


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Re: [gmx-users] about source code of the old version of GROAMCS (1.0 to 2.0)

[Man Hoang Viet]

 Dear GROMACS team,

 I am looking for source code of the old version (v1.0 to v2.0) of GROMACS,
 which is not available for downloading on GROMACS home page.
 Could you please share them to me?


 I didn't find them on the ftp server in a brief excursion through the
 accumulated junk. However release-2-0 is tagged in the git repo, and the
 initial commit is (I think) release 1.6. If you really need 1.0 for some
 reason, then you should contact the original authors directly.

 Mark

It is enough for me.

Thank you very much again.

Viet Man


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[gmx-users] about source code of the old version of GROAMCS (1.0 to 2.0)

[Man Hoang Viet]

Dear GROMACS team,

I am looking for source code of the old version (v1.0 to v2.0) of GROMACS,
which is not available for downloading on GROMACS home page.
Could you please share them to me?

Thank you very much,

Yours sincerely,

Viet Man

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