[gmx-users] Regarding rdf and number of molecules in the FSS of tetramer

[Ashma Khan]

Dear user's
I have calculated the rdf of urea molecules around the peptides for
different concentration of urea and obtained that peak height of first
solvation shell (FSS) decreases with increase in concentration of urea.
After that I have calculated the number of urea molecules in FSS and found
that urea molecules in the FSS increases with concentration of urea. There
is no correlation between the peak height of FSS and number of urea
molecules. Can anybody suggest me ? what is the reason
The command I have used is
gmx rdf -f md.xtc -s md.tpr -o rdf.xvg -selrpos whole_res_com -seltype
whole_res_com
gmx select -f md.xtc -s md.tpr -os number.xvg -select "resname URE and
within 0.5 of group protein" -selrpos whole_res_com -seltype whole_res_com


-- 
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh
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[gmx-users] Regarding RDF

[Ashma Khan]

Dear all,
I have calculated the rdf of urea molecules with different concentrations
along the peptide and obtained the result that in first solvation shell at
0.5 nm g(r) value decreases with increase in concentration but when I
calculated the number of urea molecules by gmx select at 0.5 nm, it
increases with concentration.Is it possible. Anybody can help me why this
is happening . I have used this command for calculating urea molecules and
averaged over the frames.
gmx select -f .xtc -s .tpr  -select 'resname URE and within 0.5 of group
potein' -os .xvg
-- 
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh
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[gmx-users] regarding rdf

[Neha Gupta]

Hi,

I take the following steps to perform rdf calculation for my organic
molecule.

min, min2, eql, eql2 and prd.

In order to check, whether my molecule is intact, I generate .pdb of the
entire system after each step.

Till eql step, my molecule remains intact.

After eql2, the molecule breaks.


I make use of the following code for eql :

integrator   = md
dt   = 0.002 ; 2 fs
nsteps   = 50; 1.0 ns

nstenergy= 200
nstlog   = 2000
nstxout-compressed   = 1

continuation = yes
constraint-algorithm = lincs
constraints  = h-bonds

cutoff-scheme= Verlet

coulombtype  = PME
rcoulomb = 1.0

vdwtype  = Cut-off
rvdw = 1.0
DispCorr = EnerPres

tcoupl   = Nose-Hoover
tc-grps  = LIG  Water
tau-t= 2.0   2.0
ref-t= 298.15   298.15
nhchainlength= 1

pcoupl   = Parrinello-Rahman
tau_p= 2.0
compressibility  = 4.46e-5
ref_p= 1.0


How to fix it?

Thanks,
Neha
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Re: [gmx-users] Regarding RDF, Trajectories

[Mark Abraham]

Hi,

If your simulation is converged with respect to the observable that is the
RDF, then you won't observe a significant change. That's pretty much what
is meant by convergence. And if it isn't converged, then you know your
sampling is not yet ergodic.

Mark

On Wed, Mar 22, 2017 at 7:09 PM Dilip H N  wrote:

> Hello,
> My question is,
> I ran an energy equilibration, followed by nvt, md run. and during analysis
> im plotting RDF form the final trajectories, will the RDF be the same or
> not if i run my simulation for more no. of steps..?? Since the relative
> positions of atoms will be different or not after running for more steps.
> How can i justify it..??
>
> --
> With Best Regards,
>
> DILIP.H.N
> Research Scholar,
> Department of Chemistry, NITK.
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
> --
> Gromacs Users mailing list
>
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> posting!
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[gmx-users] Regarding RDF, Trajectories

[Dilip H N]

Hello,
My question is,
I ran an energy equilibration, followed by nvt, md run. and during analysis
im plotting RDF form the final trajectories, will the RDF be the same or
not if i run my simulation for more no. of steps..?? Since the relative
positions of atoms will be different or not after running for more steps.
How can i justify it..??

-- 
With Best Regards,

DILIP.H.N
Research Scholar,
Department of Chemistry, NITK.



   Sent with Mailtrack

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Re: [gmx-users] Regarding RDF calculations

[Justin Lemkul]

On 2/27/15 2:00 AM, soumadwip ghosh wrote:

Dear users,
   I have a query about some reviews one a paper which I
submitted recently. It deals with the binding of molecular ions with double
stranded DNA segments. My questions are-

1. Is it customary to take into account The centre-of -mass for DNA grooves
or backbones while calculating RDF? Without that being taken into account,
what kind of artifacts are to be seen?



Dealing with RDFs or occupancies around DNA is extremely challenging.  Normal 
RDF lack sensitivity and do not fully describe the behavior of ions around DNA, 
especially given the asymmetry between major and minor grooves.  See, for 
instance, dx.doi.org/10.1021/ja0629460



2. Why is it necessary to show the running co-ordination number up to the
first solvation shell? I have calculated the excess cordination number for
each ions in DNA up to half of the box length using the Kirkwood-Buff
integrals. But I think there is a confusion between running coordination
and the excess coordination number. They state that if a coordination number

3. They have asked about the CHARMM 27 force field being outdated now..How
is this true?



Yes.  There are specific improvements in CHARMM36 for DNA and RNA, with a 
reparametrization of some important backbone torsions in DNA that have 
implications for sampling substates of B-DNA and correct sugar puckering.


-Justin


Please help me out in addressing the reviews. Thanks for your help in
advance.

P.S: I did not take the center-of-mass of molecular ions into account. I
dont think it is wrong for a small molecule..


Regards
Soumadwip Ghosh
Research Fellow
IITB, Mumbai
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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[gmx-users] Regarding RDF calculations

[soumadwip ghosh]

Dear users,
  I have a query about some reviews one a paper which I
submitted recently. It deals with the binding of molecular ions with double
stranded DNA segments. My questions are-

1. Is it customary to take into account The centre-of -mass for DNA grooves
or backbones while calculating RDF? Without that being taken into account,
what kind of artifacts are to be seen?

2. Why is it necessary to show the running co-ordination number up to the
first solvation shell? I have calculated the excess cordination number for
each ions in DNA up to half of the box length using the Kirkwood-Buff
integrals. But I think there is a confusion between running coordination
and the excess coordination number. They state that if a coordination number

3. They have asked about the CHARMM 27 force field being outdated now..How
is this true?

Please help me out in addressing the reviews. Thanks for your help in
advance.

P.S: I did not take the center-of-mass of molecular ions into account. I
dont think it is wrong for a small molecule..


Regards
Soumadwip Ghosh
Research Fellow
IITB, Mumbai
India
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