Re: [gmx-users] residue numbering different

[Jianguo Li]

The first residue number in VMD is 0, not 1.
Jianguo



From: aiswarya pawar 
To: Discussion list for GROMACS users 
Sent: Friday, 16 September 2011 1:21 PM
Subject: [gmx-users] residue numbering different


Hi Users,

When i list the residues in a index file it shows a numbering of residues and 
when open the same protein in VMD and check the residue numbering its 
different. i want to visualise the protein in VMD and select a residue number 
from VMD and use in gromacs ie want to make an index file in gromacs so how 
would go about.

Thanks

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Re: [gmx-users] residue numbering different

[Mark Abraham]

On 16/09/2011 3:21 PM, aiswarya pawar wrote:

Hi Users,

When i list the residues in a index file it shows a numbering of 
residues and when open the same protein in VMD and check the residue 
numbering its different. i want to visualise the protein in VMD and 
select a residue number from VMD and use in gromacs ie want to make an 
index file in gromacs so how would go about.


Try genconf -renumber

Mark
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[gmx-users] residue numbering different

[aiswarya pawar]

Hi Users,

When i list the residues in a index file it shows a numbering of residues
and when open the same protein in VMD and check the residue numbering its
different. i want to visualise the protein in VMD and select a residue
number from VMD and use in gromacs ie want to make an index file in gromacs
so how would go about.

Thanks
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Re: [gmx-users] radial distribution function

[Tsjerk Wassenaar]

Hey,

This is just exactly what you'd expect for polymer chains in a
solution (suspension?). From the closest neighbours the fine
structure, the discrete distribution of carbon atoms, is still seen,
but for those further away it's blurred. Dallas' excercise should be a
fine way to show that more explicitly.

Cheers,

Tsjerk

On Fri, Sep 16, 2011 at 12:26 AM, Dallas Warren
 wrote:
> Load up some frames into VMD and start measuring the distances shown by the
> peaks in your RDF, link them with what you actually see in there (using
> something like a transparent representation of the carbon atom(s) using VDW
> then set the sphere scale so that it matches the correct radius, may be an
> easier way to do this, but this would make it easy to see).  Appears it may
> be something real, so just check the coordinate file and see where they are
> actually coming from.
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
>
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of Moeed
> Sent: Friday, 16 September 2011 12:55 AM
> To: jalem...@vt.edu; Discussion list for GROMACS users
> Subject: Re: [gmx-users] radial distribution function
>
>
>
> Hello again,
>
> I tried comparing RDF plots generated by sampling from 4 to 5 ns run and a
> longer run from 4 to 30 ns to see whether the small jumps on the plot are
> due to insufficient sampling. Attached is the new plot showing that two RDF
> curves are almost identical. I only wanted to let you know and please
> comment on the attached plot if you have any ideas. Thank you. :)
>
> Moeed
>
> On Sat, Sep 10, 2011 at 10:00 AM, Moeed  wrote:
>
> Thank you for your input. I am going to run for another 15 ns to see if the
> little jumps vanish.
>
> Best,
>
>
>
> On Fri, Sep 9, 2011 at 9:16 PM, Justin A. Lemkul  wrote:
>
> lina wrote:
>
>
>
> On Sat, Sep 10, 2011 at 3:35 AM, Moeed  > wrote:
>
>    Dear users,
>
>    I have created radial distribution function plot for Carbon atoms in
>    a system containing polymer chains. I see some little jumps between
>    first and second peak.
>    I need your help to comment on how this behavior can be justified
>    (or if the plot is wrong).
>
>    g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx
>    Thank you in advance.
>
>
> I think your figure is fine.
>
>
>
> I think, based on information given in subsequent messages, that there is
> insufficient data collection to assess whether this RDF plot is as
> meaningful as it could be.  There is nothing glaringly wrong, but the
> roughness is due to insufficient sampling.
>
>
>
> You just need how to proper interpret your figures, truly understand what
> the "radial distribution" means.
>
>
>
>
> I think it inappropriate to suggest that the OP does not understand the
> concept behind the figure; some guidance, perhaps is necessary, but nothing
> more.
>
> -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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>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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RE: [gmx-users] radial distribution function

[Dallas Warren]

Load up some frames into VMD and start measuring the distances shown by the 
peaks in your RDF, link them with what you actually see in there (using 
something like a transparent representation of the carbon atom(s) using VDW 
then set the sphere scale so that it matches the correct radius, may be an 
easier way to do this, but this would make it easy to see).  Appears it may be 
something real, so just check the coordinate file and see where they are 
actually coming from.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Moeed
Sent: Friday, 16 September 2011 12:55 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] radial distribution function

Hello again,

I tried comparing RDF plots generated by sampling from 4 to 5 ns run and a 
longer run from 4 to 30 ns to see whether the small jumps on the plot are due 
to insufficient sampling. Attached is the new plot showing that two RDF curves 
are almost identical. I only wanted to let you know and please comment on the 
attached plot if you have any ideas. Thank you. :)

Moeed
On Sat, Sep 10, 2011 at 10:00 AM, Moeed 
mailto:lecie...@googlemail.com>> wrote:
Thank you for your input. I am going to run for another 15 ns to see if the 
little jumps vanish.

Best,

On Fri, Sep 9, 2011 at 9:16 PM, Justin A. Lemkul 
mailto:jalem...@vt.edu>> wrote:


lina wrote:



On Sat, Sep 10, 2011 at 3:35 AM, Moeed 
mailto:lecie...@googlemail.com> 
>> wrote:

   Dear users,

   I have created radial distribution function plot for Carbon atoms in
   a system containing polymer chains. I see some little jumps between
   first and second peak.
   I need your help to comment on how this behavior can be justified
   (or if the plot is wrong).

   g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx -b xxx
   Thank you in advance.


I think your figure is fine.

I think, based on information given in subsequent messages, that there is 
insufficient data collection to assess whether this RDF plot is as meaningful 
as it could be.  There is nothing glaringly wrong, but the roughness is due to 
insufficient sampling.


You just need how to proper interpret your figures, truly understand what the 
"radial distribution" means.


I think it inappropriate to suggest that the OP does not understand the concept 
behind the figure; some guidance, perhaps is necessary, but nothing more.


-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: g_sas of ligands

[Tsjerk Wassenaar]

Hey,

The protein-buried hydrophobic area will only be considered if you use
a combined group comprising ligands and protein to calculate the
surface (and ligands only for output). If you use ligand only as group
for calculation and for output, you'll only get the area buried
between ligands.

Hope it helps,

Tsjerk

On Fri, Sep 9, 2011 at 3:03 PM, Justin A. Lemkul  wrote:
>
>
> Steven Neumann wrote:
>>
>> Was my question not clear or noone can help me? I am wondering whether
>> calculations of ligand hydrophobic SAS (decrease during the simualtion) can
>> be result of binding to protein?
>
> Presumably it's due to both aggregation and binding to the protein, if, in
> fact both phenomena occur.  The extent of each effect will vary with time
> and you may have to analyze each ligand separately (i.e. do 30 calculations)
> to gather the detail you need.  In the absence of seeing the commands used
> to calculate the quantities you did, it's hard to comment further on any of
> the other points.
>
> -Justin
>
>>  On Fri, Sep 9, 2011 at 8:23 AM, Steven Neumann > > wrote:
>>
>>    Dear Gromacs Users,
>>         I am calculating SAS using g_sas of ligands in my system: protein,
>>    30 ligands in water. The hydrophobic SAS of ligands decrease and
>>    reach stable value. Hydrophilic remains stable over the simulation
>>    time. I am wondering whether it  (the decrease o hydrophobic) is
>>    because of binding to protein or aggregations of my small molecules
>>    (They do aggregate) or both? I mean: how is it caculated? Is binding
>>    to protein included in the decrease of the hydrophobic SAS of
>>    lignads or it is impossible and  aggregation will be the one thing?
>>         Thank you,
>>
>
> --
> 
>
> 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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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] V(R) around protein

[Tsjerk Wassenaar]

Hey Mark, Nihal,

On Tue, Sep 13, 2011 at 2:06 AM, Mark Abraham  wrote:
> On 13/09/2011 9:47 AM, E. Nihal Korkmaz wrote:
>
> And I don't think g_sas would do what i want. It calculates the volume of
> the protein itself. I am interested in the V of space at a distance R from
> the surface of the protein, excluding the volume of the protein. In other
> words, i need the surface accessible volume as a function of distance from
> the surface of the protein.
>
> So do two calculations with different probe radii.

That won't work. A probe with infinite radius will give the convex
volume of the peptide, not the volume that is desired. You could
change the atomic radii to get the volume. There is also another way,
which is not completely trivial. Yet it lies along the lines of a tool
I have, which could be modified to suit the need. If you're
interested, you can contact me off list for more information.

Cheers,

Tsjerk



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] simulation with amber10 and gromacs 4.5.1

[Tsjerk Wassenaar]

Hey vrk.

You should carefully compare all run parameters that were active in either
program. Sending the parameter files to the list might raise some useful
suggestions.

Cheers,

Tsjerk

On Sep 14, 2011 3:53 PM, "Justin A. Lemkul"  wrote:

vijayaraj ramadoss wrote: > > Hello Users, > > Previous I have done
simulation of small protein us...
Did you run replicates of each system, or are you basing your observations
on a single trajectory?  You need to compare properly sampled systems.  A
single trajectory is generally not enough to make reliable conclusions.

-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] Counting non-bonding interaction

[Justin A. Lemkul]

Chih-Ying Lin wrote:



Hi
Is there any function counting non-bonding interaction with Gromacs ?



You got a response to this question already:

http://lists.gromacs.org/pipermail/gmx-users/2011-September/064299.html

Please be more specific.

-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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[gmx-users] Counting non-bonding interaction

[Chih-Ying Lin]

Hi
Is there any function counting non-bonding interaction with Gromacs ?

Thanks
Lin
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Re: [gmx-users] Free energy sampling using G_bar

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Hello all,

I am finished running a free energy calculation using g_bar and i
followed Justin Lemkuls tutorial and I am in the process of analyzing
inorder to determine if I had adequate sampling.  I have read the
'BAR' paper by Bennett but there are still some concerns whether I
have enough sampling (see attached).   I see in the tutorial that the
sampling goes up to very large sample numbers, some greater than
30,000 where mine only make it to about 300.  This 'samples' refers to


Sampling in the tutorial is excessive; I believe I state that in discussing the 
free energy output settings.



how many times a certain energy level was experienced?  Does this mean


Yes.  The output histograms show the distribution of energy values in 
neighboring windows.



my system should be left for longer times?  My lines don't line as as
closely as the Methane Decoupling tutorial do.  Also, for other


The histograms look fine to me.  Lots of overlap.


solvents that I used, some are giving me a warning for violating the
2nd law of thermodynamics and i noticed its because on one of the
output lines, the entropy decreases a small bit, and some are giving
me a free energy with a std deviation of at most 1.7 kJ/mol.   Does
this all mean my sampling is not enough?



Perhaps in this instance, yes, but not all of the sampling.  You may have to 
sample a bit more in the window that's causing problems, but likely not all of 
them.  I don't know whether uneven sampling (i.e. more points in one window 
relative to others) is a problem for BAR.


-Justin


Thanks for your help.

--
Best regards,
Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com



--


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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[gmx-users] Free energy sampling using G_bar

[Fabian Casteblanco]

Hello all,

I am finished running a free energy calculation using g_bar and i
followed Justin Lemkuls tutorial and I am in the process of analyzing
inorder to determine if I had adequate sampling.  I have read the
'BAR' paper by Bennett but there are still some concerns whether I
have enough sampling (see attached).   I see in the tutorial that the
sampling goes up to very large sample numbers, some greater than
30,000 where mine only make it to about 300.  This 'samples' refers to
how many times a certain energy level was experienced?  Does this mean
my system should be left for longer times?  My lines don't line as as
closely as the Methane Decoupling tutorial do.  Also, for other
solvents that I used, some are giving me a warning for violating the
2nd law of thermodynamics and i noticed its because on one of the
output lines, the entropy decreases a small bit, and some are giving
me a free energy with a std deviation of at most 1.7 kJ/mol.   Does
this all mean my sampling is not enough?

Thanks for your help.

--
Best regards,
Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com


H2.agr.tar.gz
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Re: [gmx-users] radial distribution function

[Moeed]

Hello again,

I tried comparing RDF plots generated by sampling from 4 to 5 ns run and a
longer run from 4 to 30 ns to see whether the small jumps on the plot are
due to insufficient sampling. Attached is the new plot showing that two RDF
curves are almost identical. I only wanted to let you know and please
comment on the attached plot if you have any ideas. Thank you. :)

Moeed

On Sat, Sep 10, 2011 at 10:00 AM, Moeed  wrote:

> Thank you for your input. I am going to run for another 15 ns to see if the
> little jumps vanish.
>
> Best,
>
>
> On Fri, Sep 9, 2011 at 9:16 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> lina wrote:
>>
>>
>>>
>>> On Sat, Sep 10, 2011 at 3:35 AM, Moeed >> lecielll@googlemail.**com >> wrote:
>>>
>>>Dear users,
>>>
>>>I have created radial distribution function plot for Carbon atoms in
>>>a system containing polymer chains. I see some little jumps between
>>>first and second peak.
>>>I need your help to comment on how this behavior can be justified
>>>(or if the plot is wrong).
>>>
>>>g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx
>>>Thank you in advance.
>>>
>>>
>>> I think your figure is fine.
>>>
>>
>>
>> I think, based on information given in subsequent messages, that there is
>> insufficient data collection to assess whether this RDF plot is as
>> meaningful as it could be.  There is nothing glaringly wrong, but the
>> roughness is due to insufficient sampling.
>>
>>
>>
>>> You just need how to proper interpret your figures, truly understand what
>>> the "radial distribution" means.
>>>
>>>
>>
>> I think it inappropriate to suggest that the OP does not understand the
>> concept behind the figure; some guidance, perhaps is necessary, but nothing
>> more.
>>
>>
>> -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
>>
>> ==**==
>> --
>> 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/Searchbefore
>>  posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>
>
<>-- 
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Re: [gmx-users] Re: amb2gmx.pl to convert GLYCAM topology

[Alan]

Thanks Yun,

Have a look at http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx so
you may have tips of how to improve you check. One thing I recorded that
makes diff is that amber input files have 6 decimals of precision and
PDB/GRO only 3.

Not knowing exactly what you did, but it sounds that 0.05% (for total pot
energy?) is OK.

Alan



On 15 September 2011 06:18, Yun Shi  wrote:

> Hi Alan,
>
> For example, in the Glycam_06g.dat file, you can find:
> 
> OH-CG-CG-OS   1   -1.10  0.0-1
> 
>
> So this dihedral parameter has a force constant of -1.10, and this is what
> I mean by "GLYCAM force field assigns negative force constants to some
> dihedrals".
>
> I did try the GMX45 approach, and using the conversion factor 4.184, I got
> a difference of about 0.05%.  I am not sure if this is caused not setting
> step size in the sander minimization.
>
> Regards,
> Yun
>
>
>
>
>
>
>
> Date: Tue, 13 Sep 2011 12:03:10 +0100
> From: Alan 
> Subject: Re: [gmx-users] Re: amb2gmx.pl to convert GLYCAM topology
> To: Discussion list for GROMACS users 
> Message-ID:
> >
> Content-Type: text/plain; charset="utf-8"
>
>
> Hi Yun,
>
> Have you read http://ambermd.org/formats.html?
>
> In particular, this note:
>
> """
> NOTE: *the atom numbers in the following arrays that describe bonds,
> angles,
> and dihedrals are coordinate array indexes for runtime speed. The true atom
> number equals the absolute value of the number divided by three, plus one.
> In the case of the dihedrals, if the fourth atom is negative, this implies
> that the dihedral is an improper. If the third atom is negative, this
> implies that the end group interations are to be ignored. End group
> interactions are ignored, for example, in dihedrals of various ring systems
> (to prevent double counting of 1-4 interactions) and in multiterm
> dihedrals.
> *
> """
>
> I may be failing to understand what you mean by "GLYCAM force field assigns
> negative force constants to some dihedrals".
>
> Anyway, since GMX 4.5 can go without RB convertions, you can do this:
>
> acpype -x disac.inpcrd -p disac.prmtop --gmx45
>
> If you have sander, you can do just one step of EM and compare against one
> step EM with GMX. Do the proper conversions and Energies diff should be <
> 0.001%.
>
> Cheers,
>
> Alan
>
> On 12 September 2011 21:21, Yun Shi  wrote:
>
> > Hi all,
> >
> > I am not a CS person, but I did find something in acpype.py as
> >
> > .
> > if phase in [0, 180]:
> > properDihedralsGmx45.append([
>
>> item[0].atoms, phaseRaw,
>> > kPhi, period])
>> > if not self.gmx45:
>> > if kPhi > 0: V[period] = 2 * kPhi * cal
>> > if period == 1:
>> > C[0] += 0.5 * V[period]
>> > if phase == 0:
>> > C[1] -= 0.5 * V[period]
>> > else:
>> > C[1] += 0.5 * V[period]
>> > elif period == 2:
>> > ..
>> >
>> > kPhi here seems to be the dihedral force constant, and it seems if kPhi
>> <
>> > 0, no value will be assigned to C[0], C[1], C[2] ...
>> >
>> > I wonder if the negative dihedral force constants problem could be
>> solved
>> > by changing 'kPhi > 0' to 'kPhi != 0' for acpype?
>> >
>> > Thanks,
>> >
>> > Yun
>> >
>> > --
>> > 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!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>>
>>
>>
>> --
>> Alan Wilter SOUSA da SILVA, DSc
>> Bioinformatician, UniProt - PANDA, EMBL-EBI
>> CB10 1SD, Hinxton, Cambridge, UK
>> +44 1223 49 4588
>> -- next part --
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110913/f9bc31d1/attachment-0001.html
>>
>> --
>>
>> Message: 5
>> Date: Tue, 13 Sep 2011 16:46:44 +0530
>> From: om prakash 
>> Subject: [gmx-users] Unsubscribe me Please
>>
>> To: gmx-users@gromacs.org
>> Message-ID:
>>> t9y...@mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Unsubscribe me Please
>> --
>> Om Prakash Sharma
>> Ph.D Scholar & DIT JRF
>> Centre for Bioinformatics
>> Pondicherry University
>> Pondicherry-605014
>> -- next part --
>
>
> --
> 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!
> Please don't post (un)subscribe requests to the list. Use the
> 

[gmx-users] regarding energy run and g_lie

[גדעון לפידות]

בתאריך 15 בספטמבר 2011 12:58, מאת גדעון לפידות :

> Hello GMX users,
>
> I have a couple of questions regrading energy run and g_lie:
> 1. I am interested in calculating the estimated binding energy between pip2
> and a protein using the lie method.
> 2. I have run the protein ligand  complex for 40 ns with counter-ions,
> npt ensemble and PME
> 3. In order to calculate the ligand -sol Eqq and Elj I have run the ligand
> for 10 ns , also adding counter ions.
> 4. The resulting energies from the solvated ligand were around -3000 KJ
> of electrostatic energy and about +200 KJ of lj energy.
>
> So what I am asking is first, is it fair to assume that the positive LJ
> value of the ligand solvent energy is due to the high electrostatics energy
> between ligand and sol?
> And secondly, since the sol-lig elec. energy is much higher than lig-prot
> elec. energy doing simple lie calculation provides a positive binding
> energy, which obviously contradicts the biology. So is the whole calculation
> not valid or can I do some tweaking with lie formula (for instance change
> the alpha and beta parameters) to try and reproduce experimental data.
>
> Thanks,
>
> Gideon
>
> and second
>
>
> 2011/9/14 
>
> Send gmx-users mailing list submissions to
>>gmx-users@gromacs.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>> or, via email, send a message with subject or body 'help' to
>>gmx-users-requ...@gromacs.org
>>
>> You can reach the person managing the list at
>>gmx-users-ow...@gromacs.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of gmx-users digest..."
>>
>>
>> Today's Topics:
>>
>>   1. Re: installation of FFTW (Mark Abraham)
>>   2. Potential energy problem (madhumita das)
>>   3. Re: Potential energy problem (Mark Abraham)
>>
>>
>> --
>>
>> Message: 1
>> Date: Wed, 14 Sep 2011 15:28:30 +1000
>> From: Mark Abraham 
>> Subject: Re: [gmx-users] installation of FFTW
>> To: Discussion list for GROMACS users 
>> Message-ID: <4e703b7e.7020...@anu.edu.au>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> On 14/09/2011 3:24 PM, ITHAYARAJA wrote:
>> >
>> > Hi
>> >
>> > I am working with RHEL 6 beta, I unable to install the FFTW package
>> > while installation I found the following error,
>>
>> There is no error reported in what you have shown.
>>
>> >
>> >
>> > make[3]: Leaving directory `/home/Ithayaraja/Desktop/
>> > fftw-3.3.1-beta1/tools'
>> > make[2]: Leaving directory
>> > `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/tools'
>> > Making all in m4
>> > make[2]: Entering directory
>> `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4'
>> > make[2]: Nothing to be done for `all'.
>> > make[2]: Leaving directory
>> `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4'
>> > make[1]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1'
>> >
>> >
>> > can you help me to find out where i did wrong?
>>
>> Not without knowing your configure line, knowing that you have followed
>> the instructions on the GROMACS webpage, seeing what the actual error
>> message was, and knowing why you're trying to use a beta of a version of
>> FFTW that is a few years out of date. :)
>>
>> Mark
>>
>>
>> --
>>
>> Message: 2
>> Date: Wed, 14 Sep 2011 12:59:42 +0530
>> From: madhumita das 
>> Subject: [gmx-users] Potential energy problem
>> To: gmx-users@gromacs.org
>> Message-ID:
>>> y_yz808...@mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi Gromacs users,
>>
>> I am doing the protein lipid system packing step and thus shrinking and
>> minimizing the system alternately but after first minimization rest of all
>> minimization steps show E pot=nan and no minimization step occurs in the
>> em.log file. How to get rid of this problem? Please help.
>>
>>
>> Yours faithfully,
>>
>> Madhumita Das.
>> -- next part --
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110914/470889d8/attachment-0001.html
>>
>> --
>>
>> Message: 3
>> Date: Wed, 14 Sep 2011 17:48:52 +1000
>> From: Mark Abraham 
>> Subject: Re: [gmx-users] Potential energy problem
>> To: Discussion list for GROMACS users 
>> Message-ID: <4e705c64.1020...@anu.edu.au>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> On 14/09/2011 5:29 PM, madhumita das wrote:
>> > Hi Gromacs users,
>> >
>> > I am doing the protein lipid system packing step and thus shrinking
>> > and minimizing the system alternately but after first minimization
>> > rest of all minimization steps show E pot=nan and no minimization step
>> > occurs in the em.log file. How to get rid of this problem? Please help.
>>
>> It is likely that your system is
>> http://www.gromacs.org/Documentation/Terminology/Blowi

[gmx-users] Re: gmx-users Digest, Vol 89, Issue 83

[גדעון לפידות]

Hello GMX users,

I have a couple of questions regrading energy run and g_lie:
1. I am interested in calculating the estimated binding energy between pip2
and a protein using the lie method.
2. I have run the protein ligand  complex for 40 ns with counter-ions,
npt ensemble and PME
3. In order to calculate the ligand -sol Eqq and Elj I have run the ligand
for 10 ns , also adding counter ions.
4. The resulting energies from the solvated ligand were around -3000 KJ
of electrostatic energy and about +200 KJ of lj energy.

So what I am asking is first, is it fair to assume that the positive LJ
value of the ligand solvent energy is due to the high electrostatics energy
between ligand and sol?
And secondly, since the sol-lig elec. energy is much higher than lig-prot
elec. energy doing simple lie calculation provides a positive binding
energy, which obviously contradicts the biology. So is the whole calculation
not valid or can I do some tweaking with lie formula (for instance change
the alpha and beta parameters) to try and reproduce experimental data.

Thanks,

Gideon

and second


2011/9/14 

> Send gmx-users mailing list submissions to
>gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>gmx-users-requ...@gromacs.org
>
> You can reach the person managing the list at
>gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>   1. Re: installation of FFTW (Mark Abraham)
>   2. Potential energy problem (madhumita das)
>   3. Re: Potential energy problem (Mark Abraham)
>
>
> --
>
> Message: 1
> Date: Wed, 14 Sep 2011 15:28:30 +1000
> From: Mark Abraham 
> Subject: Re: [gmx-users] installation of FFTW
> To: Discussion list for GROMACS users 
> Message-ID: <4e703b7e.7020...@anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 14/09/2011 3:24 PM, ITHAYARAJA wrote:
> >
> > Hi
> >
> > I am working with RHEL 6 beta, I unable to install the FFTW package
> > while installation I found the following error,
>
> There is no error reported in what you have shown.
>
> >
> >
> > make[3]: Leaving directory `/home/Ithayaraja/Desktop/
> > fftw-3.3.1-beta1/tools'
> > make[2]: Leaving directory
> > `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/tools'
> > Making all in m4
> > make[2]: Entering directory
> `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4'
> > make[2]: Nothing to be done for `all'.
> > make[2]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4'
> > make[1]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1'
> >
> >
> > can you help me to find out where i did wrong?
>
> Not without knowing your configure line, knowing that you have followed
> the instructions on the GROMACS webpage, seeing what the actual error
> message was, and knowing why you're trying to use a beta of a version of
> FFTW that is a few years out of date. :)
>
> Mark
>
>
> --
>
> Message: 2
> Date: Wed, 14 Sep 2011 12:59:42 +0530
> From: madhumita das 
> Subject: [gmx-users] Potential energy problem
> To: gmx-users@gromacs.org
> Message-ID:
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Gromacs users,
>
> I am doing the protein lipid system packing step and thus shrinking and
> minimizing the system alternately but after first minimization rest of all
> minimization steps show E pot=nan and no minimization step occurs in the
> em.log file. How to get rid of this problem? Please help.
>
>
> Yours faithfully,
>
> Madhumita Das.
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110914/470889d8/attachment-0001.html
>
> --
>
> Message: 3
> Date: Wed, 14 Sep 2011 17:48:52 +1000
> From: Mark Abraham 
> Subject: Re: [gmx-users] Potential energy problem
> To: Discussion list for GROMACS users 
> Message-ID: <4e705c64.1020...@anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 14/09/2011 5:29 PM, madhumita das wrote:
> > Hi Gromacs users,
> >
> > I am doing the protein lipid system packing step and thus shrinking
> > and minimizing the system alternately but after first minimization
> > rest of all minimization steps show E pot=nan and no minimization step
> > occurs in the em.log file. How to get rid of this problem? Please help.
>
> It is likely that your system is
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> Mark
>
>
> --
>
> --
> gmx-users mailing list
> gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Se