Re: [gmx-users] RDF calculation from surface of protein

[ISHRAT JAHAN]

-surf flag is used with -ref flag. Provide the reference file in the -ref
flag.

On Thu, Feb 6, 2020 at 1:52 AM Pandya, Akash 
wrote:

> Hi all,
>
> I am trying to calculate the RDF between the protein surface and the
> centre of mass of my ligand and water molecules. Please find below the
> command I used:
>
> gmx rdf -s proteinLIG.tpr -f proteinLIG.xtc -n index.ndx -o rdf.xvg -bin
> 0.02 -cn number.xvg -surf mol -seltype mol_com
>
>
> I get the following error:
>
>
>
> Inconsistency in user input:
> -surf only works with -ref that consists of atoms
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> I am wondering what this error means? My ref group does contain atoms? Any
> guidance will be much appreciated :)
>
>
> Akash
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-- 
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh
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Re: [gmx-users] rdf calculation for wormlike micelles

[Esra kaçar]

Dear Joe,

Sorry for the confusion. I am working with martini force field and I have
three different molecules in the micelle structure. I want to analyze the
RDF of the constituent molecules with respect to the line that pass through
the center along with its length. As I mention before this line has a
curved structure and I couldn’t figure out how to select that line as a
reference point. I guess a picture would be more helpful to explain my
purpose. It is similar to the Figure 3 in the paper that I gave the link
below:

https://pubs.acs.org/doi/10.1021/acs.langmuir.7b01176

Many thanks,

Esra


2018-03-14 17:51 GMT+03:00 :

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>1. Re: gromacs.org_gmx-users Digest, Vol 167, Issue 73 (Esra ka?ar)
>2. Re: gromacs.org_gmx-users Digest, Vol 167, Issue 73 (Joe Jordan)
>3. Umbrella Sampling - good histogram but no result in   profile
>   (Ben Tam)
>4. Re: Umbrella Sampling - good histogram but no result in
>   profile (Mark Abraham)
>
>
> --
>
> Message: 1
> Date: Wed, 14 Mar 2018 16:28:19 +0300
> From: Esra ka?ar 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue
> 73
> Message-ID:
> 

Re: [gmx-users] rdf calculation for wormlike micelles

[Joe Jordan]

You cannot use a line as the reference. From a brief glance at the paper
you link it seems like maybe you actually want to compute the expectation
value of the micelle backbone, a method known as principle curves which is
a generalization of principle component analysis. At any rate, you should
probably just follow whatever procedure they use in the paper you are
citing.

On Thu, Mar 15, 2018 at 7:48 AM, Esra Kaçar  wrote:

> Dear Joe,
>
> Sorry for the confusion. I am working with martini force field and I have
> three different molecules in the micelle structure. I want to analyze the
> RDF of the constituent molecules with respect to the line that pass through
> the center along with its length. As I mention before this line has a
> curved structure and I couldn’t figure out how to select that line as a
> reference point. I guess a picture would be more helpful to explain my
> purpose. It is similar to the Figure 3 in the paper that I gave the link
> below:
>
> https://pubs.acs.org/doi/10.1021/acs.langmuir.7b01176
>
> Many thanks,
>
> Esra
> --
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Re: [gmx-users] rdf calculation for wormlike micelles

[Esra Kaçar]

Dear Joe,

Sorry for the confusion. I am working with martini force field and I have
three different molecules in the micelle structure. I want to analyze the
RDF of the constituent molecules with respect to the line that pass through
the center along with its length. As I mention before this line has a
curved structure and I couldn’t figure out how to select that line as a
reference point. I guess a picture would be more helpful to explain my
purpose. It is similar to the Figure 3 in the paper that I gave the link
below:

https://pubs.acs.org/doi/10.1021/acs.langmuir.7b01176

Many thanks,

Esra
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Re: [gmx-users] rdf calculation for wormlike micelles

[Joe Jordan]

See here for info on the selection syntax
http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html

On Wed, Mar 14, 2018 at 10:01 AM, Esra Kaçar  wrote:

> Dear all,
>
> I am working on a wormlike micelle that has a curved structure. I want to
> calculate the radial distribution functions of constituent molecules with
> respect to the backbone (the line following the micelle length and
> represents the center of the curved cylindrical structure) of the wormlike
> micelle. Since the structure is curved, I couldn’t find out how to select
> the backbone as a reference point in g_rdf. I am using Gromacs v 5.1.  Any
> suggestions would be appreciated.
>
> Thanks,
>
> Esra
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Re: [gmx-users] RDF calculation.

[Marcelo Depólo]

Well, since you are not interested in the duplex stability, I would not use
-COM. See, during the simulation, the center-of-mass of such a small helix
part can drastically move, leading to a questionable result. Check your
system and make sure that you will not face this situation.

About the PMF, that depends on the ions you are using and the forcefields.
It is already known that some of them are poorly described, so check that
out too.

Hope it can help!
Cheers!

2014-12-27 7:17 GMT-02:00 soumadwip ghosh soumadwipgh...@gmail.com:

 Hi,
 I am studying the dynamics of a double stranded DNA in presence of
 small molecules. I want to study the preferential binding of these
 molecules in the grooves and backbones of the DNA and also calculate the
 feasibility of these binding in terms of calculating the free energy
 change.My question is-

 1. while calculating radial distribution functions say between DNA minor
 groove and choline, should I consider the center-off-mass atom of the minor
 groove by using the -COM option of g_rdf?

 2. Do you think calculation of PMF from g(r) for a specific ion binding
 with the DNA can provide reliable free energy change or do I have to switch
 to umbrella sampling?

 PS: I only want to investigate the small molecule binding, not the
 stability of the DNA duplex as a whole.

 Thanks for your time in advance.

 Soumadwip Ghosh
 Research Fellow
 Indian Institute of Technology Bombay
 India
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Re: [gmx-users] RDF calculation.

[Justin Lemkul]

On 12/27/14 4:17 AM, soumadwip ghosh wrote:

Hi,
 I am studying the dynamics of a double stranded DNA in presence of
small molecules. I want to study the preferential binding of these
molecules in the grooves and backbones of the DNA and also calculate the
feasibility of these binding in terms of calculating the free energy
change.My question is-

1. while calculating radial distribution functions say between DNA minor
groove and choline, should I consider the center-off-mass atom of the minor
groove by using the -COM option of g_rdf?



I'm not sure it's useful.  Choline is a rather flexible molecule, so simply 
considering the COM of the minor groove vs. all atoms of choline is probably 
going to give you a very noisy profile.



2. Do you think calculation of PMF from g(r) for a specific ion binding
with the DNA can provide reliable free energy change or do I have to switch
to umbrella sampling?



This doesn't generally work well for ions, but the quality depends on the force 
field.  Depending on what the ion is, the exchange rate may be impossible to 
observe in an atomistic simulation.  The exchange rates for most common ions can 
range from nanosecond (feasible with MD) to microsecond (not reasonable, even if 
the force field is very accurate).


-Justin


PS: I only want to investigate the small molecule binding, not the
stability of the DNA duplex as a whole.

Thanks for your time in advance.

Soumadwip Ghosh
Research Fellow
Indian Institute of Technology Bombay
India



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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