[gmx-users] Quantification of overcharging

[Soham Sarkar]

Dear All,
   I have a system of two ssDNA of same base sequence. I
started from lower salt concentration to the higher salt concentration,
which immediately shows charge reversal at higher charge concentration. I
want to quantify this overcharging basis on the salt concentration. Please
help me with the detail procedure, how I can show that there is
overcharging at the higher concentration regime but not at the lower
concentration. Thanks in advance.

- Soham

-- 
SOHAM SARKAR
Junior Research Fellow
Department of Chemistry
INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
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Re: [gmx-users] calculating energy between certain groups

[Tasneem Kausar]

First of all define energy groups in mdp file. Then run gmx grompp with
that mdp to generate a new tpr. In gmx mdrun provide reference file (eg
tpr).


On Mon, May 21, 2018 at 7:19 AM, Irem Altan  wrote:

> I tried the following:
>
> mdrun -rerun umbrella0.xtc -np cpu -deffnm umbrella0
>
> and also I can verify from the output file that it didn’t use GPUs.
> However, I still get the same error with gmx enemat:
>
> GROMACS:  gmx enemat, version 2016.3
> Executable:   /opt/gromacs/bin/gmx_mpi
> Data prefix:  /opt/gromacs
> Working dir:  /oasis/scratch/comet/nano3/temp_project/c4_m_4C/rerun
> Command line:
>   gmx_mpi enemat -f umbrella0.edr
>
> Opened umbrella0.edr as single precision energy file
> Will read groupnames from inputfile
> Read 2 groups
> group 0WARNING! could not find group Coul-SR:Protein-Protein (0,0)in
> energy file
> WARNING! could not find group LJ-SR:Protein-Protein (0,0)in energy file
> WARNING! could not find group Coul-SR:Protein-SOL (0,1)in energy file
> WARNING! could not find group LJ-SR:Protein-SOL (0,1)in energy file
> group 1WARNING! could not find group Coul-SR:SOL-SOL (1,1)in energy file
> WARNING! could not find group LJ-SR:SOL-SOL (1,1)in energy file
>
> Will select half-matrix of energies with 0 elements
> Last energy frame read 2000 time 2.000
> Will build energy half-matrix of 2 groups, 0 elements, over 2001 frames
> Segmentation fault
>
> What could be the problem?
>
> Best,
> Irem
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Re: [gmx-users] calculating energy between certain groups

[Irem Altan]

I tried the following:

mdrun -rerun umbrella0.xtc -np cpu -deffnm umbrella0

and also I can verify from the output file that it didn’t use GPUs. However, I 
still get the same error with gmx enemat:

GROMACS:  gmx enemat, version 2016.3
Executable:   /opt/gromacs/bin/gmx_mpi
Data prefix:  /opt/gromacs
Working dir:  /oasis/scratch/comet/nano3/temp_project/c4_m_4C/rerun
Command line:
  gmx_mpi enemat -f umbrella0.edr

Opened umbrella0.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group Coul-SR:Protein-Protein (0,0)in energy file
WARNING! could not find group LJ-SR:Protein-Protein (0,0)in energy file
WARNING! could not find group Coul-SR:Protein-SOL (0,1)in energy file
WARNING! could not find group LJ-SR:Protein-SOL (0,1)in energy file
group 1WARNING! could not find group Coul-SR:SOL-SOL (1,1)in energy file
WARNING! could not find group LJ-SR:SOL-SOL (1,1)in energy file

Will select half-matrix of energies with 0 elements
Last energy frame read 2000 time 2.000
Will build energy half-matrix of 2 groups, 0 elements, over 2001 frames
Segmentation fault

What could be the problem?

Best,
Irem
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Re: [gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?

[Soham Sarkar]

Thanks for clarification..

On Sat, 19 May 2018, 11:11 pm Justin Lemkul,  wrote:

>
>
> On 5/19/18 1:37 PM, Soham Sarkar wrote:
> > Thanks for your reply Justin...
> > But these pressure I provided here are by doing the gmx energy -f
> energy.edr
> > And then selecting the pressure from the list. It only shows these values
> > for respective temperature windows after 1st stage of equillibration..
> What
> > should I do?
> > How do I know what is the actual pressure of my system?
>
> gmx energy prints the average and standard deviation to the screen.
> That's useful.
>
> What you are getting are the "actual pressure" values of the system, but
> what you have to understand is that just looking at those values
> shouldn't lead you to conclude that there's anything wrong.
>
> > Or is there any pressure convergence protocol in REMD?
>
> The system has to have enough time to relax under the new ensemble, but
> that's true of both temperature (which relaxes quickly) and pressure
> (which does not). Most REMD is done with an NVT ensemble to avoid this
> problem (and if you're already using NVT then you should stop worrying
> about the pressure entirely).
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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[gmx-users] Electric field or CompEl protocol?

[alex rayevsky]

 If I find resources for several calculations (the last one continued
for 20 days) I'll try both methods and will share You. It seems I should
find another smaller test system and reproduce the approaches.
Thank You



Sun May 20 09:55:14 CEST 2018
--

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 

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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