Re: [gmx-users] Re: gb_saltconc in implicit water simulations

[Per Larsson]

Hi!

Which results can you not recreate?

Yes - all simulations were run at zero salt concentration. 
Implicitly this means that we did not do anything special to treat the charges. 
The protein has an overall charge of -2, looking at the topology.
In hindsight, we probably should have given this issue more thought, but for 
assessing the correctness of the CHARMM implementation (the parameters) it 
seemed not so important, I'm afraid.

For the sa_algorithm option, this seems weird. If I try to set sa_algorithm = 
Still, I get an error as it is not yet implemented. The only viable options are 
etiher None or Ace-approximation. If you want to mail me your input-files 
off-list, I will have a look after Christmas.

Cheers
/Per


22 dec 2010 kl. 03.23 skrev Rogan Carr:

> Hi Per (and all),
> 
> I am trying to recreate the results of the CHARMM forcefield implementation 
> to better understand how to implement implicit solvent models, but I can't 
> quite recreate your results.  If the Gromacs code doesn't use salt 
> concentrations, does that mean that your simulations were run at zero salt 
> concentration?  Also, how did you deal with the charged residues on the 
> protein?
> 
> Also, sort of on the same topic, no matter what option I choose for 
> sa_algorithm with Gromacs 4.5.3, it always uses sa_algorithm=Still.
> 
> Thanks for your help,
> Rogan
> 
> 
> On Dec 14, 2010, at 12:13 PM, Per Larsson wrote:
> 
>> Hi!
>> 
>> Sorry that I missed this discussion, we recently moved the lab and there 
>> where quite many things to attend to.
>> 
>> When we did the implementation of implicit solvent into Gromacs, one of the 
>> strong points was to see how fast we could make it, to speed up 
>> conformational sampling as much as possible. Adding in the extra 
>> Debye-Huckel term for a non-zero salt-concentration was not a priority at 
>> the time. It might be a bit unfortunate that the option anyway exists in the 
>> mdp-file.
>> I will try and see if I can find the time to put it in, but that will not 
>> happen in the next coming weeks although I agree that it would be very 
>> useful to have :-)
>> 
>> When it comes to the use of explicit ions in an implicit solvent, I hate to 
>> say that I'm not much of an expert, really. Having said that, and someone 
>> else is very welcome to correct me on this point, there does not seem to 
>> exist a wide body of literature about this. In addition to the paper that 
>> Justin pointed to, there is some work done by Michael Feig (eg. 
>> http://www.ncbi.nlm.nih.gov/pubmed/16928023).
>> Also I think that particularly with DNA there are problems with the theory 
>> itself as it does not handle high salt-concentrations very well.
>> 
>> Cheers
>> /Per
>> 
>> 
>> 
>> 14 dec 2010 kl. 20.22 skrev devicerandom:
>> 
>>> On 14/12/10 19:04, Justin A. Lemkul wrote:
> I was going to send a very similar mail -namely, I have a coarse-grain
> system in vacuum where I'd like to simulate a charged polymer. My idea
> was that of adding a single "ghost" counter-ion with zero VdW
> interactions, perhaps keeping it fixed in one corner of the box, but
> I'd like to know how meaningful it is.
> 
 
 "In vacuum" and "implicit solvent" are very different concepts. If you
 are indeed simulating in a vacuum, I would be willing to bet that your
 charged polymer will rapidly associate with your dummy ion simply due to
 attractive Coulombic interactions that are not screened by any
 intervening solvent.
>>> 
>>> Heh, I know very well that -and that is one of the reasons I wanted to know 
>>> how does one cope with that.
>>> 
>>> I mean, if it's a single polymer, perhaps one can naively position restrain 
>>> the ion in a corner of the box, away from the polymer, while the polymer 
>>> stays on its center of mass. But if I want multiple objects in my box, I 
>>> guess it's not going to work.
>>> 
>>> I'd like very much to use implicit solvent as well but I have to see how 
>>> deep is the performance impact on my model -after all, one does coarse 
>>> grain to be raw but *fast* :)
>>> 
 
 In regards to the original post, I have seen this question asked and
 ignored several times already, unfortunately. Most of the literature I
 have read (which primarily uses CHARMM) does not specify how counterions
 are handled, if at all. Maybe there is some intrinsic compensating
 factor in CHARMM that I simply don't know about. I found this:
 
 http://dx.doi.org/10.1002/jcc.20874
 
 But again, it uses CHARMM and fancy modified electrostatic models.
 
 I would really hope that someone who knows about the proper GROMACS
 methodology would comment. This has been a curiosity of mine for some
 time, as well. I have not had a pressing need to try out the implicit
 solvent features, but in the absence of being sure of the methodology, I
 am unlikely to do so.
>>> 
>>> Perhaps the developers of the implicit solvent

Re: [gmx-users] Re: gb_saltconc in implicit water simulations

[Rogan Carr]

Hi Per (and all),

I am trying to recreate the results of the CHARMM forcefield  
implementation to better understand how to implement implicit solvent  
models, but I can't quite recreate your results.  If the Gromacs code  
doesn't use salt concentrations, does that mean that your simulations  
were run at zero salt concentration?  Also, how did you deal with the  
charged residues on the protein?


Also, sort of on the same topic, no matter what option I choose for  
sa_algorithm with Gromacs 4.5.3, it always uses sa_algorithm=Still.


Thanks for your help,
Rogan


On Dec 14, 2010, at 12:13 PM, Per Larsson wrote:


Hi!

Sorry that I missed this discussion, we recently moved the lab and  
there where quite many things to attend to.


When we did the implementation of implicit solvent into Gromacs, one  
of the strong points was to see how fast we could make it, to speed  
up conformational sampling as much as possible. Adding in the extra  
Debye-Huckel term for a non-zero salt-concentration was not a  
priority at the time. It might be a bit unfortunate that the option  
anyway exists in the mdp-file.
I will try and see if I can find the time to put it in, but that  
will not happen in the next coming weeks although I agree that it  
would be very useful to have :-)


When it comes to the use of explicit ions in an implicit solvent, I  
hate to say that I'm not much of an expert, really. Having said  
that, and someone else is very welcome to correct me on this point,  
there does not seem to exist a wide body of literature about this.  
In addition to the paper that Justin pointed to, there is some work  
done by Michael Feig (eg. http://www.ncbi.nlm.nih.gov/pubmed/ 
16928023).
Also I think that particularly with DNA there are problems with the  
theory itself as it does not handle high salt-concentrations very  
well.


Cheers
/Per



14 dec 2010 kl. 20.22 skrev devicerandom:


On 14/12/10 19:04, Justin A. Lemkul wrote:
I was going to send a very similar mail -namely, I have a coarse- 
grain
system in vacuum where I'd like to simulate a charged polymer. My  
idea

was that of adding a single "ghost" counter-ion with zero VdW
interactions, perhaps keeping it fixed in one corner of the box,  
but

I'd like to know how meaningful it is.



"In vacuum" and "implicit solvent" are very different concepts. If  
you
are indeed simulating in a vacuum, I would be willing to bet that  
your
charged polymer will rapidly associate with your dummy ion simply  
due to

attractive Coulombic interactions that are not screened by any
intervening solvent.


Heh, I know very well that -and that is one of the reasons I wanted  
to know how does one cope with that.


I mean, if it's a single polymer, perhaps one can naively position  
restrain the ion in a corner of the box, away from the polymer,  
while the polymer stays on its center of mass. But if I want  
multiple objects in my box, I guess it's not going to work.


I'd like very much to use implicit solvent as well but I have to  
see how deep is the performance impact on my model -after all, one  
does coarse grain to be raw but *fast* :)




In regards to the original post, I have seen this question asked and
ignored several times already, unfortunately. Most of the  
literature I
have read (which primarily uses CHARMM) does not specify how  
counterions

are handled, if at all. Maybe there is some intrinsic compensating
factor in CHARMM that I simply don't know about. I found this:

http://dx.doi.org/10.1002/jcc.20874

But again, it uses CHARMM and fancy modified electrostatic models.

I would really hope that someone who knows about the proper GROMACS
methodology would comment. This has been a curiosity of mine for  
some
time, as well. I have not had a pressing need to try out the  
implicit
solvent features, but in the absence of being sure of the  
methodology, I

am unlikely to do so.


Perhaps the developers of the implicit solvent know about that? I  
hope so...


m.
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Re: [gmx-users] Re: gb_saltconc in implicit water simulations

[Per Larsson]

Hi!

Sorry that I missed this discussion, we recently moved the lab and there where 
quite many things to attend to.

When we did the implementation of implicit solvent into Gromacs, one of the 
strong points was to see how fast we could make it, to speed up conformational 
sampling as much as possible. Adding in the extra Debye-Huckel term for a 
non-zero salt-concentration was not a priority at the time. It might be a bit 
unfortunate that the option anyway exists in the mdp-file. 
I will try and see if I can find the time to put it in, but that will not 
happen in the next coming weeks although I agree that it would be very useful 
to have :-)

When it comes to the use of explicit ions in an implicit solvent, I hate to say 
that I'm not much of an expert, really. Having said that, and someone else is 
very welcome to correct me on this point, there does not seem to exist a wide 
body of literature about this. In addition to the paper that Justin pointed to, 
there is some work done by Michael Feig (eg. 
http://www.ncbi.nlm.nih.gov/pubmed/16928023). 
Also I think that particularly with DNA there are problems with the theory 
itself as it does not handle high salt-concentrations very well.

Cheers
/Per



14 dec 2010 kl. 20.22 skrev devicerandom:

> On 14/12/10 19:04, Justin A. Lemkul wrote:
>>> I was going to send a very similar mail -namely, I have a coarse-grain
>>> system in vacuum where I'd like to simulate a charged polymer. My idea
>>> was that of adding a single "ghost" counter-ion with zero VdW
>>> interactions, perhaps keeping it fixed in one corner of the box, but
>>> I'd like to know how meaningful it is.
>>> 
>> 
>> "In vacuum" and "implicit solvent" are very different concepts. If you
>> are indeed simulating in a vacuum, I would be willing to bet that your
>> charged polymer will rapidly associate with your dummy ion simply due to
>> attractive Coulombic interactions that are not screened by any
>> intervening solvent.
> 
> Heh, I know very well that -and that is one of the reasons I wanted to know 
> how does one cope with that.
> 
> I mean, if it's a single polymer, perhaps one can naively position restrain 
> the ion in a corner of the box, away from the polymer, while the polymer 
> stays on its center of mass. But if I want multiple objects in my box, I 
> guess it's not going to work.
> 
> I'd like very much to use implicit solvent as well but I have to see how deep 
> is the performance impact on my model -after all, one does coarse grain to be 
> raw but *fast* :)
> 
>> 
>> In regards to the original post, I have seen this question asked and
>> ignored several times already, unfortunately. Most of the literature I
>> have read (which primarily uses CHARMM) does not specify how counterions
>> are handled, if at all. Maybe there is some intrinsic compensating
>> factor in CHARMM that I simply don't know about. I found this:
>> 
>> http://dx.doi.org/10.1002/jcc.20874
>> 
>> But again, it uses CHARMM and fancy modified electrostatic models.
>> 
>> I would really hope that someone who knows about the proper GROMACS
>> methodology would comment. This has been a curiosity of mine for some
>> time, as well. I have not had a pressing need to try out the implicit
>> solvent features, but in the absence of being sure of the methodology, I
>> am unlikely to do so.
> 
> Perhaps the developers of the implicit solvent know about that? I hope so...
> 
> m.
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Re: gb_saltconc in implicit water simulations

[devicerandom]

On 14/12/10 19:04, Justin A. Lemkul wrote:

I was going to send a very similar mail -namely, I have a coarse-grain
system in vacuum where I'd like to simulate a charged polymer. My idea
was that of adding a single "ghost" counter-ion with zero VdW
interactions, perhaps keeping it fixed in one corner of the box, but
I'd like to know how meaningful it is.



"In vacuum" and "implicit solvent" are very different concepts. If you
are indeed simulating in a vacuum, I would be willing to bet that your
charged polymer will rapidly associate with your dummy ion simply due to
attractive Coulombic interactions that are not screened by any
intervening solvent.


Heh, I know very well that -and that is one of the reasons I wanted to 
know how does one cope with that.


I mean, if it's a single polymer, perhaps one can naively position 
restrain the ion in a corner of the box, away from the polymer, while 
the polymer stays on its center of mass. But if I want multiple objects 
in my box, I guess it's not going to work.


I'd like very much to use implicit solvent as well but I have to see how 
deep is the performance impact on my model -after all, one does coarse 
grain to be raw but *fast* :)




In regards to the original post, I have seen this question asked and
ignored several times already, unfortunately. Most of the literature I
have read (which primarily uses CHARMM) does not specify how counterions
are handled, if at all. Maybe there is some intrinsic compensating
factor in CHARMM that I simply don't know about. I found this:

http://dx.doi.org/10.1002/jcc.20874

But again, it uses CHARMM and fancy modified electrostatic models.

I would really hope that someone who knows about the proper GROMACS
methodology would comment. This has been a curiosity of mine for some
time, as well. I have not had a pressing need to try out the implicit
solvent features, but in the absence of being sure of the methodology, I
am unlikely to do so.


Perhaps the developers of the implicit solvent know about that? I hope so...

m.
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Re: [gmx-users] Re: gb_saltconc in implicit water simulations

[Justin A. Lemkul]

devicerandom wrote:

On 14/12/10 18:35, Bob Johnson wrote:

Can anyone answer this question or guide me somewhere with helpful
information?
Thanks,
Bob


I was going to send a very similar mail -namely, I have a coarse-grain 
system in vacuum where I'd like to simulate a charged polymer. My idea 
was that of adding a single "ghost" counter-ion with zero VdW 
interactions, perhaps keeping it fixed in one corner of the box, but I'd 
like to know how meaningful it is.




"In vacuum" and "implicit solvent" are very different concepts.  If you are 
indeed simulating in a vacuum, I would be willing to bet that your charged 
polymer will rapidly associate with your dummy ion simply due to attractive 
Coulombic interactions that are not screened by any intervening solvent.


In regards to the original post, I have seen this question asked and ignored 
several times already, unfortunately.  Most of the literature I have read (which 
primarily uses CHARMM) does not specify how counterions are handled, if at all. 
 Maybe there is some intrinsic compensating factor in CHARMM that I simply 
don't know about.  I found this:


http://dx.doi.org/10.1002/jcc.20874

But again, it uses CHARMM and fancy modified electrostatic models.

I would really hope that someone who knows about the proper GROMACS methodology 
would comment.  This has been a curiosity of mine for some time, as well.  I 
have not had a pressing need to try out the implicit solvent features, but in 
the absence of being sure of the methodology, I am unlikely to do so.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: gb_saltconc in implicit water simulations

[devicerandom]

On 14/12/10 18:35, Bob Johnson wrote:

Can anyone answer this question or guide me somewhere with helpful
information?
Thanks,
Bob


I was going to send a very similar mail -namely, I have a coarse-grain 
system in vacuum where I'd like to simulate a charged polymer. My idea 
was that of adding a single "ghost" counter-ion with zero VdW 
interactions, perhaps keeping it fixed in one corner of the box, but I'd 
like to know how meaningful it is.


thanks!
m.



On Thu, Dec 9, 2010 at 4:52 PM, Bob Johnson mailto:bobjohnson1...@gmail.com>> wrote:

Hello everyone,
I am trying to use implicit solvent with a CG DNA model. The model,
however, uses explicit charges, which means that the DNA carries an
overall negative charge. When using implicit solvent with a charged
system in other codes (e.g. Amber), the electrolyte is taken care of
implicitly as well. However, in Gromacs this is currently not
implemented since gb_saltconc is always set to 0. Without any salt,
the DNA duplex is obviously unstable. Are there plans on
implementing implicit counterions so that one can set gb_saltconc to
nonzero values?

It doesn't seem natural to include explicit counterions to
neutralize the system when using implicit solvent. Is there a
typical protocol one follows to neutralize charged systems when
using implicit solvent?
Thanks,
Bob

--
Bob Johnson, PhD
Institute for Computational Molecular Science
Temple University
1900 North 12th Street
Philadelphia, PA 19122
http://astro.temple.edu/~rjohnson 




--
Bob Johnson, PhD
Institute for Computational Molecular Science
Temple University
1900 North 12th Street
Philadelphia, PA 19122
http://astro.temple.edu/~rjohnson



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