Re: [gmx-users] Electric field

[Prithwish Nandi]

Please ignore my message.
I figured it out.
It should be  2*pi*1 = 6.28 for omega to generate a full cycle.



> On 12 Apr 2020, at 14:15, Prithwish Nandi  wrote:
> 
> Hi,
> I am trying to generate an alternating e-field using gromcas input as 
> following:
> 
> electric-field-x = 1.5 1  0  0
> 
> E0= 2 V/nm, omega = 1 cycle/ps
> 
> This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per pico-second.
> 
> I ran this input with mdrun -field option for a sanity check.
> 
> I plotted field.xvg .
> 
> Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps 
> period.
> It is only 1/4 cycle of a cosine wave.
> 
> So, can you please point out what is that I am missing here?
> 
> Thanks,
> 
> PKN\\
> 
> 
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Re: [gmx-users] Electric field or CompEl protocol?

[Alex]

I think CompEl is described in the manual, the options for it are here: 
http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html
I've never used it, so I can't suggest anything, but you can ask on this 
board for specific mdp examples.
The way CompEl works is conceptually simple: it maintains a 
transmembrane ionic concentration gradient by swapping ions across the 
periodic boundary. The result is that on average you get a voltage of 
(kT/q)log(c_above/c_below) across the system. In reality, you get noisy 
results (see Fig. 3 (b) in http://www.mpibpc.mpg.de/grubmueller/compel 
). On the other hand, if you have long simulated times, you can still 
get clean data.


The problem with using a constant field is that it is only physical for 
a system with a nearly constant dielectric throughout. I am guessing 
that is not your case and you have water (epsilon ~80) and a lipid 
membrane (eps ~ 5?). If there was a real voltage across such a box, it 
would almost entirely drop across the membrane (i.e. high field across 
membrane and low field elsewhere). This is why I prefer to use fields 
that are as low as computationally possible.


I would try CompEl at least out of curiosity. In principle, it is a 
solid idea, but I think this algorithm is clunky and how it agrees with 
PBC is unclear to me. If you get clean and reasonable data, please let 
everyone know! :)


Alex


On 5/20/2018 1:16 AM, alex rayevsky wrote:

Dear Alex!

Yes, I thought about all Your reflections and I'm also not sure that CompEl
is well parameterzied for a non-specialist like me and the electric field
is more intuitive for me. However, when I saw the dimension 'V/nm' for the
first time, I thought that something must depend on the length of the  axis
   of application (in my case it is about 12 nm) or the thickness of the
membrane.
These two of 20 articles I've found on the theme befor wrote in gmx
society:
Structural and Functional Effect of an Oscillating Electric Field on the
Dopamine-D3 Receptor: A Molecular Dynamics Simulation Study. ( DOI:
10.1371/journal.pone.0166412 )  and Molecular dynamics of ion transport
through the open conformation of a bacterial voltage-gated sodium channel.
  ( https://doi.org/10.1073/pnas.1214667110). ANd this method works fine, in
general, they've got what they wanted.
But there is no full description of parameterization. what can You say?

Thank You


At the same time compel method is very popular too, here is another mention
of CompEl - http://dx.doi.org/10.1016/j.bpj.2017.02.016


Alex 

Sat, 19 May 2018 17:35:15 -0700


It's more of a philosophical question in, unfortunately. I don't use
CompEl, because I believe it is conceptually clunky, but that's a
matter of opinion that could turn into discussion beyond the scope of
your question. I don't study biomolecules, so I can get away with
applying direct fields. For biomolecules, however, I do suggest at
least looking into CompEl and how it works, and then choosing
appropriate setup sothat you do not slow down your simulation too
much.

That said, 0.4 V/nm does not really correspond to 40 mV in any way. The best
"fake" guess is that the voltage drop across the entire box is its height,
times the value of E-z. It is fake, because your field has nothing to do
with the solution of the Poisson's equation, or the box height. The
consequences of this field do, but the field itself doesn't, if that makes
sense. One other point to be made: water's dielectric breakdown threshold
is around 100 MV/m = 0.1 V/nm. Noone in the community that publishes in
Biophysical Journal seems to care about it, but huge simulated fields can
be incompatible with what's being studied.

My response probably doesn't help much, but this is the situation with all
MD software that relies on Ewald summation.

Alex


On 5/19/2018 5:16 PM, alex rayevsky wrote:

Dear all,

Which protocol, Electric field section or the CompEl, I should use in the
situtation:
1. I built an ion channel by homology, prepared a bilayer membrane, embeded
my protein and run a simulation to relax the system (100 ns)
2. my channel was closed all the time.
3. I want to run four parallel simmulations, starting from the relaxed
state:
a) system under the effect of -80 mV and under +40 mV - the second one
should cause a pore opening;
b) both previous variants with a ligand in the pore;

The voltage sensitive domain of the Nav channel should respond to the
electric stimuli, that is why I thought it is reasonable to apply it to Z
direction and assign electric-field-z = 0.4 0 0 0 for +40mV state, for
example. other parameters should stay intact, I think, because I don't know
if they should be changed...

at the same time I've read several different works when CompEl was
implemented to the membrane-channel systems. The 

Re: [gmx-users] Electric field or CompEl protocol?

[alex rayevsky]

Dear Alex!

Yes, I thought about all Your reflections and I'm also not sure that CompEl
is well parameterzied for a non-specialist like me and the electric field
is more intuitive for me. However, when I saw the dimension 'V/nm' for the
first time, I thought that something must depend on the length of the  axis
  of application (in my case it is about 12 nm) or the thickness of the
membrane.
These two of 20 articles I've found on the theme befor wrote in gmx
society:
Structural and Functional Effect of an Oscillating Electric Field on the
Dopamine-D3 Receptor: A Molecular Dynamics Simulation Study. ( DOI:
10.1371/journal.pone.0166412 )  and Molecular dynamics of ion transport
through the open conformation of a bacterial voltage-gated sodium channel.
 ( https://doi.org/10.1073/pnas.1214667110). ANd this method works fine, in
general, they've got what they wanted.
But there is no full description of parameterization. what can You say?

Thank You


At the same time compel method is very popular too, here is another mention
of CompEl - http://dx.doi.org/10.1016/j.bpj.2017.02.016


Alex 

Sat, 19 May 2018 17:35:15 -0700


It's more of a philosophical question in, unfortunately. I don't use
CompEl, because I believe it is conceptually clunky, but that's a
matter of opinion that could turn into discussion beyond the scope of
your question. I don't study biomolecules, so I can get away with
applying direct fields. For biomolecules, however, I do suggest at
least looking into CompEl and how it works, and then choosing
appropriate setup sothat you do not slow down your simulation too
much.

That said, 0.4 V/nm does not really correspond to 40 mV in any way. The best
"fake" guess is that the voltage drop across the entire box is its height,
times the value of E-z. It is fake, because your field has nothing to do
with the solution of the Poisson's equation, or the box height. The
consequences of this field do, but the field itself doesn't, if that makes
sense. One other point to be made: water's dielectric breakdown threshold
is around 100 MV/m = 0.1 V/nm. Noone in the community that publishes in
Biophysical Journal seems to care about it, but huge simulated fields can
be incompatible with what's being studied.

My response probably doesn't help much, but this is the situation with all
MD software that relies on Ewald summation.

Alex


On 5/19/2018 5:16 PM, alex rayevsky wrote:

Dear all,

Which protocol, Electric field section or the CompEl, I should use in the
situtation:
1. I built an ion channel by homology, prepared a bilayer membrane, embeded
my protein and run a simulation to relax the system (100 ns)
2. my channel was closed all the time.
3. I want to run four parallel simmulations, starting from the relaxed
state:
a) system under the effect of -80 mV and under +40 mV - the second one
should cause a pore opening;
b) both previous variants with a ligand in the pore;

The voltage sensitive domain of the Nav channel should respond to the
electric stimuli, that is why I thought it is reasonable to apply it to Z
direction and assign electric-field-z = 0.4 0 0 0 for +40mV state, for
example. other parameters should stay intact, I think, because I don't know
if they should be changed...

at the same time I've read several different works when CompEl was
implemented to the membrane-channel systems. The end of the
pagehttp://www.mpibpc.mpg.de/grubmueller/compel duplicates a gromacs
manual,
however I didn't find any mention of a voltage handling and what exactly
I'll obtain at the end
Which method is more approrpiate for my task?

Thank You !!





*Nemo me impune lacessit*
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Re: [gmx-users] Electric field or CompEl protocol?

[Alex]

It's more of a philosophical question in, unfortunately. I don't use 
CompEl, because I believe it is conceptually clunky, but that's a matter 
of opinion that could turn into discussion beyond the scope of your 
question. I don't study biomolecules, so I can get away with applying 
direct fields. For biomolecules, however, I do suggest at least looking 
into CompEl and how it works, and then choosing appropriate setup so 
that you do not slow down your simulation too much.


That said, 0.4 V/nm does not really correspond to 40 mV in any way. The 
best "fake" guess is that the voltage drop across the entire box is its 
height, times the value of E-z. It is fake, because your field has 
nothing to do with the solution of the Poisson's equation, or the box 
height. The consequences of this field do, but the field itself doesn't, 
if that makes sense. One other point to be made: water's dielectric 
breakdown threshold is around 100 MV/m = 0.1 V/nm. Noone in the 
community that publishes in Biophysical Journal seems to care about it, 
but huge simulated fields can be incompatible with what's being studied.


My response probably doesn't help much, but this is the situation with 
all MD software that relies on Ewald summation.


Alex


On 5/19/2018 5:16 PM, alex rayevsky wrote:

Dear all,

Which protocol, Electric field section or the CompEl, I should use in the
situtation:
1. I built an ion channel by homology, prepared a bilayer membrane, embeded
my protein and run a simulation to relax the system (100 ns)
2. my channel was closed all the time.
3. I want to run four parallel simmulations, starting from the relaxed
state:
a) system under the effect of -80 mV and under +40 mV - the second one
should cause a pore opening;
b) both previous variants with a ligand in the pore;

The voltage sensitive domain of the Nav channel should respond to the
electric stimuli, that is why I thought it is reasonable to apply it to Z
direction and assign electric-field-z = 0.4 0 0 0 for +40mV state, for
example. other parameters should stay intact, I think, because I don't know
if they should be changed...

at the same time I've read several different works when CompEl was
implemented to the membrane-channel systems. The end of the page
http://www.mpibpc.mpg.de/grubmueller/compel duplicates a gromacs manual,
however I didn't find any mention of a voltage handling and what exactly
I'll obtain at the end
Which method is more approrpiate for my task?

Thank You !!


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Re: [gmx-users] Electric Field

[Ali Ahmed]

Thank you
I'm trying to update it for external magnetic filed applications

On Sun, Feb 18, 2018 at 12:57 PM, Mark Abraham 
wrote:

> Hi,
>
> Suggestion, get the git version of gromacs and use
>
>  git grep -i -G"electric field"
>
> src/gromacs/applied-forces
>
> Mark
>
> On Sun, Feb 18, 2018 at 7:36 PM Ali Ahmed  wrote:
>
> > Dear Mark,
> > I could not find the electric field calculation code. In 2016 version,
> the
> > code was in mdlib/sim_util.cpp but in 2018 version I could not find it.
> > Is it elsewhere? can you tell me, please?
> > Thanks
> >
> > On Fri, Jan 19, 2018 at 12:25 PM, Ali Ahmed  wrote:
> >
> > > Dear Mark,
> > > Thank you. this is good I will study it.
> > >
> > >
> > > On Fri, Jan 19, 2018 at 10:21 AM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >
> > > wrote:
> > >
> > >> Hi,
> > >>
> > >> See section 6.7 of the 2018 reference manual for what is supported.
> > >>
> > >> MArk
> > >>
> > >> On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed 
> wrote:
> > >>
> > >> > Hello GROMACS users
> > >> > I have looked through GROMACS user manual to understand the theory
> > >> behind
> > >> > applying external electric field but I did not find any description.
> > >> Also,
> > >> > I looked at the source code in  sim_util.cpp file but found only the
> > >> > time-dependent electric field.
> > >> > My question does GROMACS consider Lorentz force for applying
> external
> > >> > electric field or using another theory?
> > >> > Thanks
> > >> > Ali
> > >> > --
> > >> > Gromacs Users mailing list
> > >> >
> > >> > * Please search the archive at
> > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> > posting!
> > >> >
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> > >> >
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> > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
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> > >> >
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> > >>
> > >
> > >
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Re: [gmx-users] Electric Field

[Mark Abraham]

Hi,

Suggestion, get the git version of gromacs and use

 git grep -i -G"electric field"

src/gromacs/applied-forces

Mark

On Sun, Feb 18, 2018 at 7:36 PM Ali Ahmed  wrote:

> Dear Mark,
> I could not find the electric field calculation code. In 2016 version, the
> code was in mdlib/sim_util.cpp but in 2018 version I could not find it.
> Is it elsewhere? can you tell me, please?
> Thanks
>
> On Fri, Jan 19, 2018 at 12:25 PM, Ali Ahmed  wrote:
>
> > Dear Mark,
> > Thank you. this is good I will study it.
> >
> >
> > On Fri, Jan 19, 2018 at 10:21 AM, Mark Abraham  >
> > wrote:
> >
> >> Hi,
> >>
> >> See section 6.7 of the 2018 reference manual for what is supported.
> >>
> >> MArk
> >>
> >> On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed  wrote:
> >>
> >> > Hello GROMACS users
> >> > I have looked through GROMACS user manual to understand the theory
> >> behind
> >> > applying external electric field but I did not find any description.
> >> Also,
> >> > I looked at the source code in  sim_util.cpp file but found only the
> >> > time-dependent electric field.
> >> > My question does GROMACS consider Lorentz force for applying external
> >> > electric field or using another theory?
> >> > Thanks
> >> > Ali
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> > posting!
> >> >
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >> > * For (un)subscribe requests visit
> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> > send a mail to gmx-users-requ...@gromacs.org.
> >> >
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
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> >>
> >
> >
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Re: [gmx-users] Electric Field

[Ali Ahmed]

Dear Mark,
I could not find the electric field calculation code. In 2016 version, the
code was in mdlib/sim_util.cpp but in 2018 version I could not find it.
Is it elsewhere? can you tell me, please?
Thanks

On Fri, Jan 19, 2018 at 12:25 PM, Ali Ahmed  wrote:

> Dear Mark,
> Thank you. this is good I will study it.
>
>
> On Fri, Jan 19, 2018 at 10:21 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> See section 6.7 of the 2018 reference manual for what is supported.
>>
>> MArk
>>
>> On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed  wrote:
>>
>> > Hello GROMACS users
>> > I have looked through GROMACS user manual to understand the theory
>> behind
>> > applying external electric field but I did not find any description.
>> Also,
>> > I looked at the source code in  sim_util.cpp file but found only the
>> > time-dependent electric field.
>> > My question does GROMACS consider Lorentz force for applying external
>> > electric field or using another theory?
>> > Thanks
>> > Ali
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] Electric Field

[Ali Ahmed]

Dear Mark,
Thank you. this is good I will study it.


On Fri, Jan 19, 2018 at 10:21 AM, Mark Abraham 
wrote:

> Hi,
>
> See section 6.7 of the 2018 reference manual for what is supported.
>
> MArk
>
> On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed  wrote:
>
> > Hello GROMACS users
> > I have looked through GROMACS user manual to understand the theory behind
> > applying external electric field but I did not find any description.
> Also,
> > I looked at the source code in  sim_util.cpp file but found only the
> > time-dependent electric field.
> > My question does GROMACS consider Lorentz force for applying external
> > electric field or using another theory?
> > Thanks
> > Ali
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Electric Field

[Mark Abraham]

Hi,

See section 6.7 of the 2018 reference manual for what is supported.

MArk

On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed  wrote:

> Hello GROMACS users
> I have looked through GROMACS user manual to understand the theory behind
> applying external electric field but I did not find any description.  Also,
> I looked at the source code in  sim_util.cpp file but found only the
> time-dependent electric field.
> My question does GROMACS consider Lorentz force for applying external
> electric field or using another theory?
> Thanks
> Ali
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Electric field unit

[mah maz]

Seems rational! Thank you very much David.

On Thu, Jan 14, 2016 at 7:20 PM, mah maz  wrote:

> Thank you David but it still seems conflicting to me. V/nm and V/m are 100
> times different! If it is in V/nm then force unit should be wrong!
>
> On Thu, Jan 14, 2016 at 12:20 PM, mah maz  wrote:
>
>> Hi David,
>>
>> In the manual 4.6.7, Page8. It seems logical since the force unit is in
>> KJ/mol.nm. And it can roughly be deduced from ions movements.
>> What is the use of FIELDFAC in src code then?
>>
>> thank you.
>>
>> On Thu, Jan 14, 2016 at 10:54 AM, mah maz  wrote:
>>
>>> Dear users,
>>>
>>> What is the electric field unit in gromacs? In the manual it is KJ/mol.
>>> nm.e but in the source code I encountered V/nm which is about 100 times
>>> KJ/mol.nm.e.
>>>
>>> Thank you.
>>>
>>
>>
>
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Re: [gmx-users] Electric field unit

[mah maz]

Thank you David but it still seems conflicting to me. V/nm and V/m are 100
times different! If it is in V/nm then force unit should be wrong!

On Thu, Jan 14, 2016 at 12:20 PM, mah maz  wrote:

> Hi David,
>
> In the manual 4.6.7, Page8. It seems logical since the force unit is in KJ
> /mol.nm. And it can roughly be deduced from ions movements.
> What is the use of FIELDFAC in src code then?
>
> thank you.
>
> On Thu, Jan 14, 2016 at 10:54 AM, mah maz  wrote:
>
>> Dear users,
>>
>> What is the electric field unit in gromacs? In the manual it is KJ/mol.nm.e
>> but in the source code I encountered V/nm which is about 100 times KJ/mol
>> .nm.e.
>>
>> Thank you.
>>
>
>
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Re: [gmx-users] Electric field unit

[David van der Spoel]

On 14/01/16 08:24, mah maz wrote:

Dear users,

What is the electric field unit in gromacs? In the manual it is KJ/mol.nm.e
but in the source code I encountered V/nm which is about 100 times KJ/mol.nm.e.



V/nm.
Then the manual is wrong, but where did you read that?


Thank you.




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Electric field unit

[David van der Spoel]

On 14/01/16 16:50, mah maz wrote:

Thank you David but it still seems conflicting to me. V/nm and V/m are 100
times different! If it is in V/nm then force unit should be wrong!

Did you check it yourself?

From units.h:

#define E_CHARGE (1.602176565e-19)
#define FARADAY  (E_CHARGE*AVOGADRO)  /* (96000 C/mol)  */
#define FIELDFAC (FARADAY/KILO)   /* ~ 96 C/mol */

From sim_util.cpp
Ext[m] *= Ex[m].a[0]*FIELDFAC;
for (i = start; (i < start+homenr); i++)
{
f[i][m] += charge[i]*Ext[m];
}

In other words, if we specify the field (Ex[m].a[0]) in V/nm we get

(V/nm)*(96 C/mol)
fill in
1 V = 1 J/C
J/(nm C) * (96 C/mol) -> 96 J/mol nm = 0.096 kJ/mol nm
which is the MD force unit.



On Thu, Jan 14, 2016 at 12:20 PM, mah maz  wrote:


Hi David,

In the manual 4.6.7, Page8. It seems logical since the force unit is in KJ
/mol.nm. And it can roughly be deduced from ions movements.
What is the use of FIELDFAC in src code then?

thank you.

On Thu, Jan 14, 2016 at 10:54 AM, mah maz  wrote:


Dear users,

What is the electric field unit in gromacs? In the manual it is KJ/mol.nm.e
but in the source code I encountered V/nm which is about 100 times KJ/mol
.nm.e.

Thank you.







--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] electric field

[Maryam Kowsar]

Thank you Erik and Viet Man!

On Mon, Nov 16, 2015 at 6:24 PM, Man Hoang Viet  wrote:

> 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:
> >    a...@mail.gmail.com>
> > 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] 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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