date:20150403

Hi,

There's nothing in GROMACS that specifically supports reweighting
replica-exchange simulations.

Mark
On 03/04/2015 10:03 am, "NISHA Prakash"  wrote:

> Hi,
>
> Can somebody please help with WHAM reweighting scheme for REMD analysis.
> The command "gmx wham" works for Umbrella sampling simulation but I couldnt
> find a way out for T-REMD.
> There are similar questions which have been posted here but unfortunately,
> I haven't found answers for the same.
> WHAM for REMD has been well documented for AMBER but I couldnt find any
> help for Gromacs.
> I am a novice in the field and help is appreciated.
>
> Thanks!
>
> Nisha
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Re: [gmx-users] Regarding groups making by make_ndx

Yes, you can combine groups in make_ndx, probably with '&&' or something.
Check out its built-in help.

Mark
On 03/04/2015 10:49 am, "neha chaudhary"  wrote:

> Hello Sir,
>
> I want to make a new group that contain 2-3 amino acid residues present in
> protein. But when I am running nvt simulation with this new group error
> message like multiple t-coupling groups in (1 and 3). So, I am using
> "splitres" option in make_ndx module of gromacs to separate number of
> residues in protein. Is there any way to combine these separated residues
> to make a new group .
>
> Best Regards,
>
> *Neha*
>
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himachal Pradesh,
> --
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Re: [gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie

2015-04-03 Thread NISHA Prakash

Hi Mark,

Thanks for your quick response.
Can you please suggest a way out?
As you pointed out previously, I have 18 ensembles and I would like to
study the conformational changes, the interactions between the protein and
the ligand and finally, I would like to extract the stable conformation
from the simulation data.
How do I go about analysing the REMD results.
Your tutorial was indeed very helpful but apart from that, I couldn't find
much information in that area.

Thanks again,
Nisha

On Fri, Apr 3, 2015 at 2:38 PM, Mark Abraham 
wrote:

> Hi,
>
> There's nothing in GROMACS that specifically supports reweighting
> replica-exchange simulations.
>
> Mark
> On 03/04/2015 10:03 am, "NISHA Prakash"  wrote:
>
> > Hi,
> >
> > Can somebody please help with WHAM reweighting scheme for REMD analysis.
> > The command "gmx wham" works for Umbrella sampling simulation but I
> couldnt
> > find a way out for T-REMD.
> > There are similar questions which have been posted here but
> unfortunately,
> > I haven't found answers for the same.
> > WHAM for REMD has been well documented for AMBER but I couldnt find any
> > help for Gromacs.
> > I am a novice in the field and help is appreciated.
> >
> > Thanks!
> >
> > Nisha
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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Re: [gmx-users] DSSP with gmx 5.0.4

On 03/04/2015 7:36 am, "RJ"  wrote:
>
> Dear gmx users,
>
>
> I tried DSSP of both binary and .exe by renaming it as dssp
(dssp-2.0.4-linux-amd64 & dssp-2.0.4-win32.exe from
ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/) and placed in
usr/local/bin/dssp.

Don't try to install a Windows program. Remove everything and then use only
the Linux version that matches your system.

>
> set the excusable too (  "which dssp" /usr/local/bin/dssp).
>
>
> Both of them gives  same error as follows;
> I also given a permission for dssp file "chmod 777 dssp" but still the
error doesnt go. I use all new version but cant fix it? Any help plz.

That command can only work if you are in the same directory, and as root.
You didn't specify anything about that, so probably the dash binary has the
wrong permissions. Inspect them with ls -l.

Mark

>
> gmx do_dssp -f prd_noPBC.xtc -s prd.tpr -sc scount.xvg -o ss.xpm -dt 10
-ver 2
>
>
> Selected 5: 'MainChain'
> There are 1446 residues in your selected group
> dssp cmd='/usr/local/bin/dssp -i ddiyE5RC -o ddPnxMzu > /dev/null 2>
/dev/null'
> Reading frame   0 time0.000
> Back Off! I just backed up ddiyE5RC to ./#ddiyE5RC.1#
>
>
> ---
> Program gmx, VERSION 5.0.4
> Source code file:
/home/raju/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670
>
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
option.
> ---
> Program gmx, VERSION 5.0.4
> Source code file:
/home/raju/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670
>
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
option.
>
>
>
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Re: [gmx-users] GMX-compatible DNA coordinates

Hi,

Googling things like "gromacs DNA structure" is a good bet. There are no
fully standardised naming schemes or workflows, so you will likely not have
something do everything for you.

Mark
On 03/04/2015 7:03 am, "Alex"  wrote:

>  I'm fully aware that this is a forum for discussing Gromacs, but there's
> a bit of a frustrating situation that involves using it.
>
> I need a linear ssDNA chain, sequence of my choosing, anything that will
> work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields
> for it, everything as is. You suggested AMBER in the past, so AMBER it is.
>
>
> ChemOffice produced a PDB with incompatible atom types. make-na server (
> http://structure.usc.edu/make-na/server.html) also produced something
> pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a
> usable topology out of the box with an established potential implemented in
> Gromacs? Anything that will not involve manual modification of PDBs or
> writing text-processing scripts will make me very happy.
>
>
> I will really appreciate any suggestions.
>
>
> Thank you,
>
>
> Alex
>
>
>
>
> --
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[gmx-users] G_rmsf, reference structure

2015-04-03 Thread Eerden, van, F.J.

Dears,

I have calculated the RMSF from a protein trajectory in Gromacs 4.5.5.

My question is how the RMSF is calculated:
A)
1) fitting of the trajectory to the tpr file supplied by -s
2) calculating the averaged atom coordinates over time (x~)
3) calculating the deviation from the averaged structure (x-x~), for each
time frame
4) averaging over all time frames 

OR
B)
1) fitting of the trajectory to the tpr file supplied by -s
2) calculating the deviation from the TPR structure (x-x*), for each time
frame
3) averaging over all time frames 

This question has already popped up multiple times in the mailing list:
https://www.mail-archive.com/gmx-users@gromacs.org/msg25391.html
and
http://comments.gmane.org/gmane.science.biology.gromacs.user/38359

The problem is that there are multiple answers given:
In the first one, it is argued that method A is used
in the second mailing list, Marc Abraham states that method B is being
used, while Tsjerk mentions method A.

I tried to resolve this by looking into thee source code,
and although to me it seems that it is option, B, I do not trust my Gromacs
code reading capabilities that well ;)

Happy Easter!

Floris
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Re: [gmx-users] G_rmsf, reference structure

Hi Floris,

By default it's A. There is an option for doing B. But B makes no sense.

Cheers,

Tsjerk
On Apr 3, 2015 1:10 PM, "Eerden, van, F.J."  wrote:

> Dears,
>
> I have calculated the RMSF from a protein trajectory in Gromacs 4.5.5.
>
> My question is how the RMSF is calculated:
> A)
> 1) fitting of the trajectory to the tpr file supplied by -s
> 2) calculating the averaged atom coordinates over time (x~)
> 3) calculating the deviation from the averaged structure (x-x~), for each
> time frame
> 4) averaging over all time frames 
>
> OR
> B)
> 1) fitting of the trajectory to the tpr file supplied by -s
> 2) calculating the deviation from the TPR structure (x-x*), for each time
> frame
> 3) averaging over all time frames 
>
> This question has already popped up multiple times in the mailing list:
> https://www.mail-archive.com/gmx-users@gromacs.org/msg25391.html
> and
> http://comments.gmane.org/gmane.science.biology.gromacs.user/38359
>
> The problem is that there are multiple answers given:
> In the first one, it is argued that method A is used
> in the second mailing list, Marc Abraham states that method B is being
> used, while Tsjerk mentions method A.
>
> I tried to resolve this by looking into thee source code,
> and although to me it seems that it is option, B, I do not trust my Gromacs
> code reading capabilities that well ;)
>
> Happy Easter!
>
> Floris
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Re: [gmx-users] GMX-compatible DNA coordinates

Mark,

Not to troll, but why did you assume that I didn't do my due diligence before posting here?
Because, you see, you could have left that second part of your reply (which only confirms the legitimacy of my initial question), and it would make it less insulting.

Alex

Hi,
Googling things like "gromacs DNA structure" is a good bet. There are no fully standardised naming schemes or workflows, so you will likely not have something do everything for you.
Mark
On 03/04/2015 7:03 am, "Alex" wrote:

I'm fully aware that this is a forum for discussing Gromacs, but there's a bit of a frustrating situation that involves using it.
I need a linear ssDNA chain, sequence of my choosing, anything that will work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields for it, everything as is. You suggested AMBER in the past, so AMBER it is.

ChemOffice produced a PDB with incompatible atom types. make-na server (http://structure.usc.edu/make-na/server.html) also produced something pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a usable topology out of the box with an established potential implemented in Gromacs? Anything that will not involve manual modification of PDBs or writing text-processing scripts will make me very happy.

I will really appreciate any suggestions.

Thank you,

Alex

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Alex mailto:nedoma...@gmail.com

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Re: [gmx-users] GMX-compatible DNA coordinates

Hi Alex,

You've solved the issue of getting a DNA structure, but now you're facing a
problem of getting Gromacs to prune it. That has to do with the naming
scheme mainly. Your best bet is using sed to do name substitution. Probably
google will give some good hints about such substitutions in PDB files.

Cheers,

Tsjerk
On Apr 3, 2015 3:40 PM, "Alex"  wrote:

>  Mark,
>
>
> Not to troll, but why did you assume that I didn't do my due diligence
> before posting here?
>
> Because, you see, you could have left that second part of your reply
> (which only confirms the legitimacy of my initial question), and it would
> make it less insulting.
>
>
> Alex
>
>
>
>   >
>
> Hi,
>
> Googling things like "gromacs DNA structure" is a good bet. There are no
> fully standardised naming schemes or workflows, so you will likely not have
> something do everything for you.
>
> Mark
>
> On 03/04/2015 7:03 am, "Alex"  wrote:
>
>
> I'm fully aware that this is a forum for discussing Gromacs, but there's a
> bit of a frustrating situation that involves using it.
>
> I need a linear ssDNA chain, sequence of my choosing, anything that will
> work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields
> for it, everything as is. You suggested AMBER in the past, so AMBER it is.
>
>
> ChemOffice produced a PDB with incompatible atom types. make-na server (
> http://structure.usc.edu/make-na/server.html) also produced something
> pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a
> usable topology out of the box with an established potential implemented in
> Gromacs? Anything that will not involve manual modification of PDBs or
> writing text-processing scripts will make me very happy.
>
>
> I will really appreciate any suggestions.
>
>
> Thank you,
>
>
> Alex
>
>
>
>
> --
>
> Gromacs Users mailing list
>
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
>
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>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
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>
>
>
>
>
> --
>
> Best regards,
>
>  Alexmailto:nedoma...@gmail.com
> 
>
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Re: [gmx-users] GMX-compatible DNA coordinates

Hi,

I tried that search myself and found some things that looked potentially
useful to you, so I suggested that search. Either you might find something
useful there, or the dialogue could progress about what you need. Requiring
perfect input for pdb2gmx is a fairly stringent expectation.

Mark
On 03/04/2015 3:40 pm, "Alex"  wrote:

>  Mark,
>
>
> Not to troll, but why did you assume that I didn't do my due diligence
> before posting here?
>
> Because, you see, you could have left that second part of your reply
> (which only confirms the legitimacy of my initial question), and it would
> make it less insulting.
>
>
> Alex
>
>
>
>   >
>
> Hi,
>
> Googling things like "gromacs DNA structure" is a good bet. There are no
> fully standardised naming schemes or workflows, so you will likely not have
> something do everything for you.
>
> Mark
>
> On 03/04/2015 7:03 am, "Alex"  wrote:
>
>
> I'm fully aware that this is a forum for discussing Gromacs, but there's a
> bit of a frustrating situation that involves using it.
>
> I need a linear ssDNA chain, sequence of my choosing, anything that will
> work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields
> for it, everything as is. You suggested AMBER in the past, so AMBER it is.
>
>
> ChemOffice produced a PDB with incompatible atom types. make-na server (
> http://structure.usc.edu/make-na/server.html) also produced something
> pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a
> usable topology out of the box with an established potential implemented in
> Gromacs? Anything that will not involve manual modification of PDBs or
> writing text-processing scripts will make me very happy.
>
>
> I will really appreciate any suggestions.
>
>
> Thank you,
>
>
> Alex
>
>
>
>
> --
>
> Gromacs Users mailing list
>
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
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>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
>
>
> --
>
> Best regards,
>
>  Alexmailto:nedoma...@gmail.com
> 
>
> --
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Re: [gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie

Hi,

You seem to be essentially asking for your experiment to be designed for
you, after an arbitrary simulation is complete. You should think about what
and how to observe before you simulate, e.g. from what others have done for
similar systems.

Consideration of reweighting is secondary. Generally, the only difference
with REMD simulations is that you cannot assume that the set of frames from
an ensemble are from a contiguous trajectory.

Mark
On 03/04/2015 11:21 am, "NISHA Prakash"  wrote:

> Hi Mark,
>
> Thanks for your quick response.
> Can you please suggest a way out?
> As you pointed out previously, I have 18 ensembles and I would like to
> study the conformational changes, the interactions between the protein and
> the ligand and finally, I would like to extract the stable conformation
> from the simulation data.
> How do I go about analysing the REMD results.
> Your tutorial was indeed very helpful but apart from that, I couldn't find
> much information in that area.
>
> Thanks again,
> Nisha
>
> On Fri, Apr 3, 2015 at 2:38 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > There's nothing in GROMACS that specifically supports reweighting
> > replica-exchange simulations.
> >
> > Mark
> > On 03/04/2015 10:03 am, "NISHA Prakash"  wrote:
> >
> > > Hi,
> > >
> > > Can somebody please help with WHAM reweighting scheme for REMD
> analysis.
> > > The command "gmx wham" works for Umbrella sampling simulation but I
> > couldnt
> > > find a way out for T-REMD.
> > > There are similar questions which have been posted here but
> > unfortunately,
> > > I haven't found answers for the same.
> > > WHAM for REMD has been well documented for AMBER but I couldnt find any
> > > help for Gromacs.
> > > I am a novice in the field and help is appreciated.
> > >
> > > Thanks!
> > >
> > > Nisha
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] GMX-compatible DNA coordinates

On 03/04/2015 5:53 pm, "Mark Abraham"  wrote:
>
> Hi,
>
> I tried that search myself and found some things that looked potentially
useful to you, so I suggested that search. Either you might find something
useful there, or the dialogue could progress about what you need. Requiring
perfect input for pdb2gmx is a fairly stringent expectation.

i.e. The use of sed or similar tools is normal, as Tsjerk says also. There
are too many options, and nobody has built the Babel fish of MD input!

Mark

> Mark
>
> On 03/04/2015 3:40 pm, "Alex"  wrote:
>>
>> Mark,
>>
>>
>> Not to troll, but why did you assume that I didn't do my due diligence
before posting here?
>>
>> Because, you see, you could have left that second part of your reply
(which only confirms the legitimacy of my initial question), and it would
make it less insulting.
>>
>>
>> Alex
>>
>>
>>
>> >
>>
>> Hi,
>>
>> Googling things like "gromacs DNA structure" is a good bet. There are no
fully standardised naming schemes or workflows, so you will likely not have
something do everything for you.
>>
>> Mark
>>
>> On 03/04/2015 7:03 am, "Alex"  wrote:
>>
>>
>> I'm fully aware that this is a forum for discussing Gromacs, but there's
a bit of a frustrating situation that involves using it.
>>
>> I need a linear ssDNA chain, sequence of my choosing, anything that will
work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields
for it, everything as is. You suggested AMBER in the past, so AMBER it is.
>>
>>
>> ChemOffice produced a PDB with incompatible atom types. make-na server (
http://structure.usc.edu/make-na/server.html) also produced something
pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a
usable topology out of the box with an established potential implemented in
Gromacs? Anything that will not involve manual modification of PDBs or
writing text-processing scripts will make me very happy.
>>
>>
>> I will really appreciate any suggestions.
>>
>>
>> Thank you,
>>
>>
>> Alex
>>
>>
>>
>>
>> --
>>
>> Gromacs Users mailing list
>>
>>
>> * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
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>>
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>>
>>
>>
>> --
>>
>> Best regards,
>>
>>  Alexmailto:nedoma...@gmail.com
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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Re: [gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie

2015-04-03 Thread NISHA Prakash

Hi Mark,

All I want to know is the first step that I have to take in analyzing the
trajectories. By way of mentioning what I want to do was to essentially
list out my aim only to make my question clear.
With REMD results, I want to know whether analyzing individual ensemble is
the way to go or look at the ensembles together, this is because I would
like to bring out a comparison between the simulations with protein bound
to three different ligands.

I hope I have made myself clear.

Thanks again,

Nisha



On Fri, Apr 3, 2015 at 9:33 PM, Mark Abraham 
wrote:

> Hi,
>
> You seem to be essentially asking for your experiment to be designed for
> you, after an arbitrary simulation is complete. You should think about what
> and how to observe before you simulate, e.g. from what others have done for
> similar systems.
>
> Consideration of reweighting is secondary. Generally, the only difference
> with REMD simulations is that you cannot assume that the set of frames from
> an ensemble are from a contiguous trajectory.
>
> Mark
> On 03/04/2015 11:21 am, "NISHA Prakash"  wrote:
>
> > Hi Mark,
> >
> > Thanks for your quick response.
> > Can you please suggest a way out?
> > As you pointed out previously, I have 18 ensembles and I would like to
> > study the conformational changes, the interactions between the protein
> and
> > the ligand and finally, I would like to extract the stable conformation
> > from the simulation data.
> > How do I go about analysing the REMD results.
> > Your tutorial was indeed very helpful but apart from that, I couldn't
> find
> > much information in that area.
> >
> > Thanks again,
> > Nisha
> >
> > On Fri, Apr 3, 2015 at 2:38 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > There's nothing in GROMACS that specifically supports reweighting
> > > replica-exchange simulations.
> > >
> > > Mark
> > > On 03/04/2015 10:03 am, "NISHA Prakash" 
> wrote:
> > >
> > > > Hi,
> > > >
> > > > Can somebody please help with WHAM reweighting scheme for REMD
> > analysis.
> > > > The command "gmx wham" works for Umbrella sampling simulation but I
> > > couldnt
> > > > find a way out for T-REMD.
> > > > There are similar questions which have been posted here but
> > > unfortunately,
> > > > I haven't found answers for the same.
> > > > WHAM for REMD has been well documented for AMBER but I couldnt find
> any
> > > > help for Gromacs.
> > > > I am a novice in the field and help is appreciated.
> > > >
> > > > Thanks!
> > > >
> > > > Nisha
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
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> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
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> > >
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> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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> > >
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Re: [gmx-users] GMX-compatible DNA coordinates

2015-04-03 Thread Mauricio Esguerra Neira

Alex,


You can use X3DNA to produce any nucleic acid geometry you’d like and
gromacs pdb2gmx will understand it.

For example, to create a single-strand of 16 DNA bases you only need a file
with the corresponding rigid-body base-step parameters such as the
ssdna.par file shown below:

  16 # bases
   0 # ***local step parameters***
#  Shift Slide Rise  Tilt  Roll  Twist
T  0.000 0.000 0.000 0.000 0.000 0.000
A  0.280-0.664 3.201 2.499-2.89532.486
C -0.314-0.644 2.640 8.643 2.63128.956
C  0.424-0.849 3.240 1.756 1.69033.400
A  1.519-0.396 3.077 4.184 6.15239.140
A  0.412-0.670 2.797 6.57711.30926.608
C -0.183-2.185 2.859 6.133 5.12617.125
A  0.423-1.477 6.195   -18.545   -26.69136.074
C  1.216-0.879 3.063 5.417 8.46635.858
A -9.111-4.794-5.43374.82943.216   -56.814
C  3.440 0.344 3.176 3.03612.62142.046
A -9.111-4.794-5.43374.82943.216   -56.814
C  3.440 0.344 3.176 3.03612.62142.046
A  1.478 0.681 3.05613.088 0.20844.226
A -0.358-0.777 3.494-2.803-4.53433.162
A -0.264-0.272 2.833 9.637 1.45730.508



With such a file at hand all you have to do is issue the following two
commands to 3DNA.

x3dna_utils cp_std -d BDNA

Which copies a standard BDNA backbone scaffold in the folder you’re at, and
then:

rebuild -atomic ssdna.par ssdna.pdb

This will generate the file ssdna.pdb which you can find at:

http://wikisend.com/download/614970/ssdna.pdb

It works with:

pdb2gmx -f ssdna.pdb -o start.pdb -p topol.top -i posre.itp -ff
charmm27 -water tip3p

In principle the online version of 3DNA, w3dna, would also work for
generating nucleic acid models of any desired sequence. But sadly the X3DNA
version working in the backend of the webserver is awfully outdated and
uses the old convention of simply A, G, T, C, instead of DA, DG, DT, DC, to
name the nucleotide residues.


Hope this helps,


Mauricio



+++
 Mauricio Esguerra Neira, Ph.D.
 Post-Doctoral Fellow
 Hugo Gutiérrez de Terán P.I.
 Department of Cell and Molecular Biology
 Uppsala University
 Phone Number: (+46)073-678-5334
 mesguerra.org
 mauricio.esgue...@icm.uu.se
+++
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Re: [gmx-users] GMX-compatible DNA coordinates





Gentlemen,

Building a script to rename the atom is obviously an option. I was just wondering if I missed something, e.g. a VMD plugin that could do it quickly. As far as google searching, I have done that, and I have found some things (like the make-NA server, or this: http://smog-server.org/cgi-bin/GenTopGro.pl). This is still not quite what I was aiming for. Hence, my initial question. I didn't mean to be snippy, but I did try searching, believe me. On the other hand, I assume that you are much better versed in the problem at hand, so then maybe you'd be able to appreciate info I simply ignored. Obviously, I welcome anything you can suggest. If this boils down to me writing a renaming script, so be it. :)

Thanks,

Alex





>



On 03/04/2015 5:53 pm, "Mark Abraham"  wrote:
>
> Hi,
>
> I tried that search myself and found some things that looked potentially useful to you, so I suggested that search. Either you might find something useful there, or the dialogue could progress about what you need. Requiring perfect input for pdb2gmx is a fairly stringent expectation.
i.e. The use of sed or similar tools is normal, as Tsjerk says also. There are too many options, and nobody has built the Babel fish of MD input! 
Mark
> Mark
>
> On 03/04/2015 3:40 pm, "Alex"  wrote:
>>
>> Mark,
>>
>>
>> Not to troll, but why did you assume that I didn't do my due diligence before posting here? 
>>
>> Because, you see, you could have left that second part of your reply (which only confirms the legitimacy of my initial question), and it would make it less insulting.
>>
>>
>> Alex
>>
>>
>>
>> >
>>
>> Hi,
>>
>> Googling things like "gromacs DNA structure" is a good bet. There are no fully standardised naming schemes or workflows, so you will likely not have something do everything for you.
>>
>> Mark
>>
>> On 03/04/2015 7:03 am, "Alex"  wrote:
>>
>>
>> I'm fully aware that this is a forum for discussing Gromacs, but there's a bit of a frustrating situation that involves using it.
>>
>> I need a linear ssDNA chain, sequence of my choosing, anything that will work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields for it, everything as is. You suggested AMBER in the past, so AMBER it is.
>>
>>
>> ChemOffice produced a PDB with incompatible atom types. make-na server (http://structure.usc.edu/make-na/server.html) also produced something pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a usable topology out of the box with an established potential implemented in Gromacs? Anything that will not involve manual modification of PDBs or writing text-processing scripts will make me very happy.
>>
>>
>> I will really appreciate any suggestions.
>>
>>
>> Thank you,
>>
>>
>> Alex
>>
>>
>>
>>
>> --
>>
>> Gromacs Users mailing list
>>
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>> * For (un)subscribe requests visit
>>
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>>
>>
>>
>> -- 
>>
>> Best regards,
>>
>>  Alex                            mailto:nedoma...@gmail.com
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
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-- 
Best regards,
 Alex                            mailto:nedoma...@gmail.com



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Re: [gmx-users] GMX-compatible DNA coordinates

Mauricio,

That is very useful, thanks a lot. I'll try it in a bit.

Alex


MEN> Alex,


MEN> You can use X3DNA to produce any nucleic acid geometry you’d like and
MEN> gromacs pdb2gmx will understand it.

MEN> For example, to create a single-strand of 16 DNA bases you only need a file
MEN> with the corresponding rigid-body base-step parameters such as the
MEN> ssdna.par file shown below:

MEN>   16 # bases
MEN>0 # ***local step parameters***
MEN> #  Shift Slide Rise  Tilt  Roll  Twist
MEN> T  0.000 0.000 0.000 0.000 0.000 0.000
MEN> A  0.280-0.664 3.201 2.499-2.89532.486
MEN> C -0.314-0.644 2.640 8.643 2.63128.956
MEN> C  0.424-0.849 3.240 1.756 1.69033.400
MEN> A  1.519-0.396 3.077 4.184 6.15239.140
MEN> A  0.412-0.670 2.797 6.57711.30926.608
MEN> C -0.183-2.185 2.859 6.133 5.12617.125
MEN> A  0.423-1.477 6.195   -18.545   -26.69136.074
MEN> C  1.216-0.879 3.063 5.417 8.46635.858
MEN> A -9.111-4.794-5.43374.82943.216   -56.814
MEN> C  3.440 0.344 3.176 3.03612.62142.046
MEN> A -9.111-4.794-5.43374.82943.216   -56.814
MEN> C  3.440 0.344 3.176 3.03612.62142.046
MEN> A  1.478 0.681 3.05613.088 0.20844.226
MEN> A -0.358-0.777 3.494-2.803-4.53433.162
MEN> A -0.264-0.272 2.833 9.637 1.45730.508



MEN> With such a file at hand all you have to do is issue the following two
MEN> commands to 3DNA.

MEN> x3dna_utils cp_std -d BDNA

MEN> Which copies a standard BDNA backbone scaffold in the folder you’re at, and
MEN> then:

MEN> rebuild -atomic ssdna.par ssdna.pdb

MEN> This will generate the file ssdna.pdb which you can find at:

MEN> http://wikisend.com/download/614970/ssdna.pdb

MEN> It works with:

MEN> pdb2gmx -f ssdna.pdb -o start.pdb -p topol.top -i posre.itp -ff
MEN> charmm27 -water tip3p

MEN> In principle the online version of 3DNA, w3dna, would also work for
MEN> generating nucleic acid models of any desired sequence. But sadly the X3DNA
MEN> version working in the backend of the webserver is awfully outdated and
MEN> uses the old convention of simply A, G, T, C, instead of DA, DG, DT, DC, to
MEN> name the nucleotide residues.


MEN> Hope this helps,


MEN> Mauricio



MEN> +++
MEN>  Mauricio Esguerra Neira, Ph.D.
MEN>  Post-Doctoral Fellow
MEN>  Hugo Gutiérrez de Terán P.I.
MEN>  Department of Cell and Molecular Biology
MEN>  Uppsala University
MEN>  Phone Number: (+46)073-678-5334
MEN>  mesguerra.org
MEN>  mauricio.esgue...@icm.uu.se
MEN> +++



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Re: [gmx-users] GMX-compatible DNA coordinates

Hi Alex,

Writing a sed oneliner is not the same as writing a renaming script. I
commonly use them to process PDB files in some way and it's surprising how
much you can do without scripting.

Cheers,

Tsjerk
On Apr 3, 2015 7:13 PM, "Alex"  wrote:

>  Gentlemen,
>
>
> Building a script to rename the atom is obviously an option. I was just
> wondering if I missed something, e.g. a VMD plugin that could do it
> quickly. As far as google searching, I have done that, and I have found
> some things (like the make-NA server, or this:
> http://smog-server.org/cgi-bin/GenTopGro.pl). This is still not quite
> what I was aiming for. Hence, my initial question. I didn't mean to be
> snippy, but I did try searching, believe me. On the other hand, I assume
> that you are much better versed in the problem at hand, so then maybe you'd
> be able to appreciate info I simply ignored. Obviously, I welcome anything
> you can suggest. If this boils down to me writing a renaming script, so be
> it. :)
>
>
> Thanks,
>
>
> Alex
>
>
>
>   >
>
>
> On 03/04/2015 5:53 pm, "Mark Abraham"  wrote:
>
> >
>
> > Hi,
>
> >
>
> > I tried that search myself and found some things that looked potentially
> useful to you, so I suggested that search. Either you might find something
> useful there, or the dialogue could progress about what you need. Requiring
> perfect input for pdb2gmx is a fairly stringent expectation.
>
> i.e. The use of sed or similar tools is normal, as Tsjerk says also. There
> are too many options, and nobody has built the Babel fish of MD input!
>
> Mark
>
> > Mark
>
> >
>
> > On 03/04/2015 3:40 pm, "Alex"  wrote:
>
> >>
>
> >> Mark,
>
> >>
>
> >>
>
> >> Not to troll, but why did you assume that I didn't do my due diligence
> before posting here?
>
> >>
>
> >> Because, you see, you could have left that second part of your reply
> (which only confirms the legitimacy of my initial question), and it would
> make it less insulting.
>
> >>
>
> >>
>
> >> Alex
>
> >>
>
> >>
>
> >>
>
> >> >
>
> >>
>
> >> Hi,
>
> >>
>
> >> Googling things like "gromacs DNA structure" is a good bet. There are
> no fully standardised naming schemes or workflows, so you will likely not
> have something do everything for you.
>
> >>
>
> >> Mark
>
> >>
>
> >> On 03/04/2015 7:03 am, "Alex"  wrote:
>
> >>
>
> >>
>
> >> I'm fully aware that this is a forum for discussing Gromacs, but
> there's a bit of a frustrating situation that involves using it.
>
> >>
>
> >> I need a linear ssDNA chain, sequence of my choosing, anything that
> will work with, say, AMBER99SB-ILDN. Not trying to find any funny
> forcefields for it, everything as is. You suggested AMBER in the past, so
> AMBER it is.
>
> >>
>
> >>
>
> >> ChemOffice produced a PDB with incompatible atom types. make-na server (
> http://structure.usc.edu/make-na/server.html) also produced something
> pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a
> usable topology out of the box with an established potential implemented in
> Gromacs? Anything that will not involve manual modification of PDBs or
> writing text-processing scripts will make me very happy.
>
> >>
>
> >>
>
> >> I will really appreciate any suggestions.
>
> >>
>
> >>
>
> >> Thank you,
>
> >>
>
> >>
>
> >> Alex
>
> >>
>
> >>
>
> >>
>
> >>
>
> >> --
>
> >>
>
> >> Gromacs Users mailing list
>
> >>
>
> >>
>
> >> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> >>
>
> >>
>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> >>
>
> >>
>
> >> * For (un)subscribe requests visit
>
> >>
>
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>
> >> --
>
> >>
>
> >> Best regards,
>
> >>
>
> >>  Alexmailto:nedoma...@gmail.com
>
> >>
>
> >>
>
> >> --
>
> >> Gromacs Users mailing list
>
> >>
>
> >> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> >>
>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> >>
>
> >> * For (un)subscribe requests visit
>
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
>
>
> --
>
> Best regards,
>
>  Alexmailto:nedoma...@gmail.com
> 
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] GMX-compatible DNA coordinates

Hi Tsjerk,

You're right. It's just that the last time I used a sed or awk script of my own composition was in college, which is ~13 years ago. :))
So, this is still an undertaking for someone like me. But yes, what you said is well taken. Lack of knowledge/desire to rename atoms in text files shouldn't hinder research.
I do think that having a person such as yourself of Justin on my team to implement what I have in mind would speed things up tremendously, but noone seems to be interested, hint-hint. ;)

Thanks,

Alex

>

Hi Alex,
Writing a sed oneliner is not the same as writing a renaming script. I commonly use them to process PDB files in some way and it's surprising how much you can do without scripting.
Cheers,
Tsjerk
On Apr 3, 2015 7:13 PM, "Alex"  wrote:

Gentlemen,

Building a script to rename the atom is obviously an option. I was just wondering if I missed something, e.g. a VMD plugin that could do it quickly. As far as google searching, I have done that, and I have found some things (like the make-NA server, or this: http://smog-server.org/cgi-bin/GenTopGro.pl). This is still not quite what I was aiming for. Hence, my initial question. I didn't mean to be snippy, but I did try searching, believe me. On the other hand, I assume that you are much better versed in the problem at hand, so then maybe you'd be able to appreciate info I simply ignored. Obviously, I welcome anything you can suggest. If this boils down to me writing a renaming script, so be it. :)

Thanks,

Alex

>

On 03/04/2015 5:53 pm, "Mark Abraham"  wrote:
>
> Hi,
>
> I tried that search myself and found some things that looked potentially useful to you, so I suggested that search. Either you might find something useful there, or the dialogue could progress about what you need. Requiring perfect input for pdb2gmx is a fairly stringent expectation.
i.e. The use of sed or similar tools is normal, as Tsjerk says also. There are too many options, and nobody has built the Babel fish of MD input! 
Mark
> Mark
>
> On 03/04/2015 3:40 pm, "Alex"  wrote:
>>
>> Mark,
>>
>>
>> Not to troll, but why did you assume that I didn't do my due diligence before posting here? 
>>
>> Because, you see, you could have left that second part of your reply (which only confirms the legitimacy of my initial question), and it would make it less insulting.
>>
>>
>> Alex
>>
>>
>>
>> >
>>
>> Hi,
>>
>> Googling things like "gromacs DNA structure" is a good bet. There are no fully standardised naming schemes or workflows, so you will likely not have something do everything for you.
>>
>> Mark
>>
>> On 03/04/2015 7:03 am, "Alex"  wrote:
>>
>>
>> I'm fully aware that this is a forum for discussing Gromacs, but there's a bit of a frustrating situation that involves using it.
>>
>> I need a linear ssDNA chain, sequence of my choosing, anything that will work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields for it, everything as is. You suggested AMBER in the past, so AMBER it is.
>>
>>
>> ChemOffice produced a PDB with incompatible atom types. make-na server (http://structure.usc.edu/make-na/server.html) also produced something pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a usable topology out of the box with an established potential implemented in Gromacs? Anything that will not involve manual modification of PDBs or writing text-processing scripts will make me very happy.
>>
>>
>> I will really appreciate any suggestions.
>>
>>
>> Thank you,
>>
>>
>> Alex
>>
>>
>>
>>
>> --
>>
>> Gromacs Users mailing list
>>
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>> * For (un)subscribe requests visit
>>
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>>
>>
>>
>> -- 
>>
>> Best regards,
>>
>>  Alex                            mailto:nedoma...@gmail.com
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.

-- 
Best regards,
 Alex                            mailto:nedoma...@gmail.com

--
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-- 
Best regards,
 Alex

[gmx-users] the study of concentration effect in gromacs

2015-04-03 Thread elham tazikeh

Dear All
i know for increasing ions in gromacs, we have to using GENION tool
but i dont know how increase or change * the protein* or drug concentration
in gromacs.
i ll really apriciate for any response
-- 
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] GMX-compatible DNA coordinates

Hi Alex,

I've done it before, but I can't do it from the top of my head without
seeing the input and checking what Gromacs wants. It's not hard work, it's
not a lot of work, but it is work, and more than we'll usually consider
doing for answering a post on the mailing list. On the other hand, you can
always try to raise interest in a collaboration, which is a completely
different matter :)

Cheers,

Tsjerk


On Fri, Apr 3, 2015 at 8:21 PM, Alex  wrote:

>  Hi Tsjerk,
>
>
> You're right. It's just that the last time I used a sed or awk script of
> my own composition was in college, which is ~13 years ago. :))
>
> So, this is still an undertaking for someone like me. But yes, what you
> said is well taken. Lack of knowledge/desire to rename atoms in text files
> shouldn't hinder research.
>
> I do think that having a person such as yourself of Justin on my team to
> implement what I have in mind would speed things up tremendously, but noone
> seems to be interested, hint-hint. ;)
>
>
> Thanks,
>
>
> Alex
>
>
>
>   >
>
> Hi Alex,
>
> Writing a sed oneliner is not the same as writing a renaming script. I
> commonly use them to process PDB files in some way and it's surprising how
> much you can do without scripting.
>
> Cheers,
>
> Tsjerk
>
> On Apr 3, 2015 7:13 PM, "Alex"  wrote:
>
>
> Gentlemen,
>
>
> Building a script to rename the atom is obviously an option. I was just
> wondering if I missed something, e.g. a VMD plugin that could do it
> quickly. As far as google searching, I have done that, and I have found
> some things (like the make-NA server, or this:
> http://smog-server.org/cgi-bin/GenTopGro.pl). This is still not quite
> what I was aiming for. Hence, my initial question. I didn't mean to be
> snippy, but I did try searching, believe me. On the other hand, I assume
> that you are much better versed in the problem at hand, so then maybe you'd
> be able to appreciate info I simply ignored. Obviously, I welcome anything
> you can suggest. If this boils down to me writing a renaming script, so be
> it. :)
>
>
> Thanks,
>
>
> Alex
>
>
>
>   >
>
>
> On 03/04/2015 5:53 pm, "Mark Abraham"  wrote:
>
> >
>
> > Hi,
>
> >
>
> > I tried that search myself and found some things that looked potentially
> useful to you, so I suggested that search. Either you might find something
> useful there, or the dialogue could progress about what you need. Requiring
> perfect input for pdb2gmx is a fairly stringent expectation.
>
> i.e. The use of sed or similar tools is normal, as Tsjerk says also. There
> are too many options, and nobody has built the Babel fish of MD input!
>
> Mark
>
> > Mark
>
> >
>
> > On 03/04/2015 3:40 pm, "Alex"  wrote:
>
> >>
>
> >> Mark,
>
> >>
>
> >>
>
> >> Not to troll, but why did you assume that I didn't do my due diligence
> before posting here?
>
> >>
>
> >> Because, you see, you could have left that second part of your reply
> (which only confirms the legitimacy of my initial question), and it would
> make it less insulting.
>
> >>
>
> >>
>
> >> Alex
>
> >>
>
> >>
>
> >>
>
> >> >
>
> >>
>
> >> Hi,
>
> >>
>
> >> Googling things like "gromacs DNA structure" is a good bet. There are
> no fully standardised naming schemes or workflows, so you will likely not
> have something do everything for you.
>
> >>
>
> >> Mark
>
> >>
>
> >> On 03/04/2015 7:03 am, "Alex"  wrote:
>
> >>
>
> >>
>
> >> I'm fully aware that this is a forum for discussing Gromacs, but
> there's a bit of a frustrating situation that involves using it.
>
> >>
>
> >> I need a linear ssDNA chain, sequence of my choosing, anything that
> will work with, say, AMBER99SB-ILDN. Not trying to find any funny
> forcefields for it, everything as is. You suggested AMBER in the past, so
> AMBER it is.
>
> >>
>
> >>
>
> >> ChemOffice produced a PDB with incompatible atom types. make-na server (
> http://structure.usc.edu/make-na/server.html) also produced something
> pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a
> usable topology out of the box with an established potential implemented in
> Gromacs? Anything that will not involve manual modification of PDBs or
> writing text-processing scripts will make me very happy.
>
> >>
>
> >>
>
> >> I will really appreciate any suggestions.
>
> >>
>
> >>
>
> >> Thank you,
>
> >>
>
> >>
>
> >> Alex
>
> >>
>
> >>
>
> >>
>
> >>
>
> >> --
>
> >>
>
> >> Gromacs Users mailing list
>
> >>
>
> >>
>
> >> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> >>
>
> >>
>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> >>
>
> >>
>
> >> * For (un)subscribe requests visit
>
> >>
>
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>
> >> --
>
> >>
>
> >> Best regards,
>
> >>
>
> >>  Alexmailto:nedoma...@gmail.com
>
> >>
>
> >>
>
> >> --
>
> >> Gromacs Users mailing lis

Re: [gmx-users] the study of concentration effect in gromacs

Hi Elham,

You can increase the protein concentration by using a smaller box, or by
putting two or more proteins in a box together. With drugs, you can raise
the concentration by adding more, using the insert option of genbox.

Cheers,

Tsjerk

On Fri, Apr 3, 2015 at 9:13 PM, elham tazikeh 
wrote:

> Dear All
> i know for increasing ions in gromacs, we have to using GENION tool
> but i dont know how increase or change * the protein* or drug concentration
> in gromacs.
> i ll really apriciate for any response
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>

-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] GMX-compatible DNA coordinates