[gmx-users] Manual installation of new analysis tool

[Venkat Reddy]

Dear all,
I have got  an analysis tool for analyzing membrane density from Dr.Luca
monticelli. I have followed the installation instructions as given.

1) First thing is to load GROMACS
   $ *source /usr/local/gromacs/bin/GMXRC*
2) Enter the source directory of the program then make
   $ cd g_mydensity
   $ make
According to the instructions, it should create an executable "*g_mydensity*"
but I am getting the following errors

*cc `pkg-config --libs libgmx`  g_mydensity.o matrix.o distances.o
dist_mode.o grid_mode.o   -o g_mydensity*
*g_mydensity.o: In function `gmx_log2':*
*g_mydensity.c:(.text+0xa8): undefined reference to `log'*
*g_mydensity.o: In function `gmx_invsqrt':*
*g_mydensity.c:(.text+0xf2): undefined reference to `gmx_invsqrt_exptab'*
*g_mydensity.c:(.text+0x101): undefined reference to `gmx_invsqrt_fracttab'*
*g_mydensity.o: In function `matrix_convert':*
*g_mydensity.c:(.text+0x381): undefined reference to `cos'*
*g_mydensity.c:(.text+0x3ad): undefined reference to `sin'*
*g_mydensity.c:(.text+0x3da): undefined reference to `cos'*
*g_mydensity.c:(.text+0x403): undefined reference to `cos'*
*g_mydensity.c:(.text+0x416): undefined reference to `cos'*
*g_mydensity.c:(.text+0x429): undefined reference to `cos'*
*g_mydensity.c:(.text+0x447): undefined reference to `sin'*
*g_mydensity.c:(.text+0x4ad): undefined reference to `sqrt'*
*g_mydensity.o: In function `get_electrons':*
*g_mydensity.c:(.text+0x527): undefined reference to `ffopen'*
*g_mydensity.c:(.text+0x564): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0x5b6): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0x600): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0x62e): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0x68d): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0x6eb): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0x74f): undefined reference to `ffclose'*
*g_mydensity.o: In function `center_coords':*
*g_mydensity.c:(.text+0x88f): undefined reference to `calc_box_center'*
*g_mydensity.o: In function `calc_electron_density':*
*g_mydensity.c:(.text+0x945): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0x973): undefined reference to `read_first_x'*
*g_mydensity.c:(.text+0x9a0): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0xa38): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0xa81): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0xac1): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0xaf6): undefined reference to `gmx_rmpbc_init'*
*g_mydensity.c:(.text+0xb18): undefined reference to `set_pbc'*
*g_mydensity.c:(.text+0xb38): undefined reference to `gmx_rmpbc'*
*g_mydensity.c:(.text+0xe0b): undefined reference to `read_next_x'*
*g_mydensity.c:(.text+0xe1e): undefined reference to `gmx_rmpbc_done'*
*g_mydensity.c:(.text+0xe29): undefined reference to `close_trj'*
*g_mydensity.c:(.text+0xecc): undefined reference to `save_free'*
*g_mydensity.o: In function `calc_density':*
*g_mydensity.c:(.text+0xf32): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0xf60): undefined reference to `read_first_x'*
*g_mydensity.c:(.text+0xf8d): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0x101c): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0x1065): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0x10a5): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0x10da): undefined reference to `gmx_rmpbc_init'*
*g_mydensity.c:(.text+0x10fc): undefined reference to `set_pbc'*
*g_mydensity.c:(.text+0x111c): undefined reference to `gmx_rmpbc'*
*g_mydensity.c:(.text+0x143a): undefined reference to `read_next_x'*
*g_mydensity.c:(.text+0x144d): undefined reference to `gmx_rmpbc_done'*
*g_mydensity.c:(.text+0x146e): undefined reference to `close_trj'*
*g_mydensity.c:(.text+0x1511): undefined reference to `save_free'*
*g_mydensity.o: In function `plot_density':*
*g_mydensity.c:(.text+0x159c): undefined reference to `xvgropen'*
*g_mydensity.c:(.text+0x15bf): undefined reference to `xvgr_legend'*
*g_mydensity.c:(.text+0x16ea): undefined reference to `ffclose'*
*g_mydensity.o: In function `gmx_mydensity':*
*g_mydensity.c:(.text+0x18bd): undefined reference to `CopyRight'*
*g_mydensity.c:(.text+0x1923): undefined reference to `parse_common_args'*
*g_mydensity.c:(.text+0x19a0): undefined reference to `ftp2fn'*
*g_mydensity.c:(.text+0x19af): undefined reference to `read_top'*
*g_mydensity.c:(.text+0x1a84): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0x1ab4): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0x1ae4): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0x1b0b): undefined reference to `ftp2fn_null'*
*g_mydensity.c:(.text+0x1b39): undefined reference to `get_index'*
*g_mydensity.c:(.text+0x1b67): undefined reference to `ftp2fn'*
*g_mydensity.c:(.text+0x1be1): undefined reference to `ftp2fn'*
*g_mydensity.c:(.text+0x1c6a): undefined reference

Re: [gmx-users] plots in gromacs

[tarak karmakar]

Hi,

Steps to get a plot in jpeg, png etc. format are

xmgrace plot.xvg -free

go to the print setup option
choose any option as jpeg, png etc. present in a specific box
then click the print option at the left. It'll export the image file in
jpeg or png format. Now you can use these images everywhere u want ...:)

regards
Tarak


On Wed, Apr 24, 2013 at 5:20 AM, Dallas Warren wrote:

> The .xvg file is a text data file, it is not a graph.
>
> That means you can use whatever your favourite graphing software is to
> plot the data: xmgrace, gnuplot, MS Excel, Sigma Plot etc.
>
> If you are using Excel, which it appears you are, then you simple import
> the data file into your spreadsheet (with the appropriate filtering
> options).
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Discovery Biology
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> > -Original Message-
> > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> > boun...@gromacs.org] On Behalf Of vansh
> > Sent: Tuesday, 23 April 2013 5:33 PM
> > To: gmx-users@gromacs.org
> > Subject: [gmx-users] plots in gromacs
> >
> > as i am very new to it.. can anyone suggest me how to change the graph
> > format
> > obtained in gromacs (.xvg) into office 7 based system???
> >
> >
> > tyhanks  in advance
> >
> >
> >
> > -
> > thanks in advance :)
> > --
> > View this message in context: http://gromacs.5086.x6.nabble.com/plots-
> > in-gromacs-tp5007561.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>



-- 
*Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809 *
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Re: [gmx-users] how to build the loop of protein model

[tarak karmakar]

Hi,

For the first part of your problem, I would suggest to visit this online
server where you can model your loop, http://falc-loop.seoklab.org/  . It
utilizes homology modeling kind of analogy to add the loop.

Time span within which a disordered loop gets converted to alpha-helix is
not so precise and thus can not be truly predicted. Run for a few tens of
ns and see whether any change is happening to that loop region. 2fs time
step can be used provided you have to use proper constraints.

Regards,
Tarak


On Wed, Apr 24, 2013 at 8:19 AM, aixintiankong wrote:

> Dear,
>In my system ,the loop is  part of the active pocket  of the protein.
> when the ligand is absent, the loop is disordered and if the ligand is
> present , the loop can transform into helix.
>In order to simulate the disordered loop transform into helix , i
> should build a model thant the ligand is in the disoreded loop site. In my
> system, there is a NAD+ cofactor in the active site and interact with the
> ligand.when the ligand and cofactor NAD+ coexist, the disordered loop can
> transform into helix.
>In the PDB(protein date base) i find the complex with the liand,NAD+
> and the  state of the loop is helix. i also  find a protein structure
> without the liand, NAD+ and the state of the loop is disordered. The
>  sequences similarity of the two structure is 100% and sturctue the the
>  RMSD bettwen the two protein is 0.275 .
> i don't know how to build a model that  the protein, NAD+ and ligand
> coexsit,but the loop of protein is disordered. can i use the Homology
> modeling ,docking or just use pymol extract the NAD+ and ligand from the
> complex and the put them into the protein with the disoreded loop ? And
> then to make a MD.
>In order to make the disordered into the helix using gromacs, how long
> should i run the MD and what is  the value of dt , 0.001 or 0.002?
>thank you very much!
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
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>



-- 
*Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809 *
-- 
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[gmx-users] how to build the loop of protein model

[aixintiankong]

Dear,
   In my system ,the loop is  part of the active pocket  of the protein. when 
the ligand is absent, the loop is disordered and if the ligand is present , the 
loop can transform into helix.
   In order to simulate the disordered loop transform into helix , i should 
build a model thant the ligand is in the disoreded loop site. In my system, 
there is a NAD+ cofactor in the active site and interact with the ligand.when 
the ligand and cofactor NAD+ coexist, the disordered loop can transform into 
helix.
   In the PDB(protein date base) i find the complex with the liand,NAD+ and the 
 state of the loop is helix. i also  find a protein structure without the 
liand, NAD+ and the state of the loop is disordered. The  sequences similarity 
of the two structure is 100% and sturctue the the  RMSD bettwen the two protein 
is 0.275 .
i don't know how to build a model that  the protein, NAD+ and ligand 
coexsit,but the loop of protein is disordered. can i use the Homology modeling 
,docking or just use pymol extract the NAD+ and ligand from the complex and the 
put them into the protein with the disoreded loop ? And then to make a MD.
   In order to make the disordered into the helix using gromacs, how long 
should i run the MD and what is  the value of dt , 0.001 or 0.002?
   thank you very much!
-- 
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

Dear Justin/Mark,

I have asked this question previously in the forum, I got some reply from
other members. It will be more useful if you can provide you expert
comments on the same. I am planning to run REMD for a peptide (406 atoms )+
solvent system (27639). The temperature range I selected is from 300 to
500. I want to select appropriate temp. for 56 replicas (as I have 56
processors available). I used the t-remd calculator for temp. generation.
It provided some 200 temp. values. Here are my questions :
1. Is it possible to select equally spaced temp. values from those values ??
2. I checked that reducing the no. of water mol. decreases the temp.
values. What if I reduce the no. of water mol., will if affect the
simulation ??



On Tue, Apr 23, 2013 at 11:15 PM, massimo sandal wrote:

> In general, the smaller is your system, the less temperatures you will need
> (and you'll have better performance).
>
> Notice however that implicit solvent, while surely a possibility worth
> considering, is not usually considered to be very good -take care that if
> you write a paper from implicit solvent results, reviewers might not be
> happy. There is a chance that the results coming out of your simulation
> might be nonsense. Discuss this choice with your supervisor and/or with
> expert colleagues who know about limitations of implicit solvent. You need
> to be able to justify your choice scientifically -for example testing it
> with a known,similar system and observing that implicit solvent reproduces
> the behaviour of that system in explicit solvent well.
>
> About reducing the box size, by all means try it, but always make sure it
> is large enough to avoid that the periodic copies of your molecule see each
> other. See
>
> http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water#Box_Preparationand
> be sure to understand it.
>
>
> 2013/4/23 bharat gupta 
>
> > Thanks a lot for your prompt responses. By using implicit solvent , I am
> > getting on 9 temperature values. I think this should work , I will try it
> > out. Also, i checked that when the no. of water molecules are reduced ,
> the
> > no. of temp. values are also reduced. If I reduce the no. of water
> > molecules or reduce the size of box , will it help. As of now I am using
> > octahedron box.
> >
> >
> > On Tue, Apr 23, 2013 at 10:43 PM, massimo sandal  > >wrote:
> >
> > > It depends on what you want to do. Possible it is certainly possible,
> but
> > > you can't be guaranteed to observe the conformational changes you
> desire
> > to
> > > observe. Again, it does not depend only on the REMD, but also on the
> > length
> > > of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also
> > depends
> > > on your system itself -and this you cannot know without trying.
> > >
> > > If you want to improve sampling beyond what standard REMD can do, to
> > > exploit your computational resources at the best, you can look into
> other
> > > approaches like solute tempering (
> > > http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics (
> > > http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to
> > study
> > > *well* this kind of things, talk with experts in these techniques,  and
> > > remember that there is no guarantee any of them will bring the result
> you
> > > want. Good luck! :)
> > >
> > >
> > >
> > >
> > > 2013/4/23 bharat gupta 
> > >
> > > > So, my final question is whether is possible to do REMD for my
> system,
> > > > using the computational resource that I have.
> > > >
> > > >
> > > > On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal <
> > deviceran...@gmail.com
> > > > >wrote:
> > > >
> > > > > Who knows? It depends on the size of your peptide, on the energy
> > > > landscape,
> > > > > on how long is the run you plan to do. I would bet on "no",
> however.
> > > > >
> > > > >
> > > > > 2013/4/23 bharat gupta 
> > > > >
> > > > > > But if I choose a smaller temperature range , would it be
> possible
> > to
> > > > > > observe any folding event ??
> > > > > >
> > > > > >
> > > > > > On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal <
> > > > deviceran...@gmail.com
> > > > > > >wrote:
> > > > > >
> > > > > > > Thanks, now it's clearer.
> > > > > > >
> > > > > > > > Now, how can I temp. from these, so that the replicas can
> > > exchange
> > > > > ...
> > > > > > >
> > > > > > > You can't, I would say. The system you have requires so many
> > > replicas
> > > > > to
> > > > > > > exchange properly from the two temperature extremes you set up.
> > As
> > > > you
> > > > > > have
> > > > > > > seen, if you pick up temperatures in that range randomly, they
> > > can't
> > > > > > > exchange anymore. They are too far away.
> > > > > > >
> > > > > > > I would choose a smaller temperature range. There is little
> else
> > > you
> > > > > can
> > > > > > > do, I think.
> > > > > > >
> > > > > > >
> > > > > > > 2013/4/23 bharat gupta 
> > > > > > >
> > > > > > > > Sorry for that, I explain it again. Actually

RE: [gmx-users] plots in gromacs

[Dallas Warren]

The .xvg file is a text data file, it is not a graph.

That means you can use whatever your favourite graphing software is to plot the 
data: xmgrace, gnuplot, MS Excel, Sigma Plot etc.

If you are using Excel, which it appears you are, then you simple import the 
data file into your spreadsheet (with the appropriate filtering options).

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 


> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of vansh
> Sent: Tuesday, 23 April 2013 5:33 PM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] plots in gromacs
> 
> as i am very new to it.. can anyone suggest me how to change the graph
> format
> obtained in gromacs (.xvg) into office 7 based system???
> 
> 
> tyhanks  in advance
> 
> 
> 
> -
> thanks in advance :)
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/plots-
> in-gromacs-tp5007561.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> 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
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[gmx-users] Energetics of ion and subatrate binding sites

[ram bio]

Dear Gromacs Users,

I have simulated a protein with different ions and same substrate bound to
it in POPC lipid bilayer using Groamcs 4.5.4. The ion binding and substrate
binding sites are coupled. After Md simulation we see a reorganization of
these sites. Now, we are trying to calculate the energetics of these ion
and substrate binding sites. Could any one please suggest  ideas or methods
to do the same in Gromacs package? Please let me know.

Thanks

Pramod
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[gmx-users] port to Gromacs of recent CHARMM FF changes (C37)

[Guilherme Menegon Arantes]

Dear GMX user,

Are you aware of a GROMACS topology implementation of the recent 
dihedral corrections to CHARMM22/CMAP given by RB Best et al., JCTC, 
2012, 8, 3257-3273?

If this has already been done, would you be kind enough to send me the
updated files?

Best regards,

Guilherme

--

Prof. Dr. Guilherme Menegon Arantes

Instituto de Química
Universidade de São Paulo
Av. Prof. Lineu Prestes, 748
São Paulo  05508-000
Brasil
Fone: 55-11-30913848
http://gaznevada.iq.usp.br/
___

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Re: [gmx-users] Re: protein-ligand interactions in charmm force field

[Justin Lemkul]

On 4/23/13 10:18 AM, James Starlight wrote:

Justin,


as the example I have 2 systems consisted of receptor completed with 2
different ligands.

After 100ns of production run I've realized that both of that ligands has
the same degree of conformational dynamics on internal degrees of freedom (
the same RMSD as the measure of internal mobility of that compounds). But
the main difference was in the mobility of the smaller agonist molecule
(movement inside the ligand-binding pocket   in comparison to the bulkier
antagonist. So as consequence I've obtained  higher value of the MSD in
case of smaller ligand. Could the MSD be representative measure of such
whole-body motion of the ligand ? What advantages have the calculation of
the diffusion coefficient ( which could be calculated from MSD )?



Maybe.  What other studies have examined similar properties, and what did they 
measure?



2) How I could visualize such ligand mobility ? For example for dynamics on
internal degrees of freedom Principal components analysis could give best
representation of conformational mobility.
In case when I want to explore diffusional-behavior I should obtain
representation of some confrontational volume (the surface within
ligand-binding cavity  accessible for the ligand). What Gromac's tools
could be useful for that?



Chapter 8 of the manual.  There may or may not be an existing Gromacs tool that 
will do the things you want.  The only way to find out is to go looking.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] specbonds are not taken by gromos force field?

[Justin Lemkul]

On 4/23/13 9:36 AM, 라지브간디 wrote:

Dear Justin,


Sorry for the confusion.


What I was trying to explain is " pdb2gmx output of topol.top file shows the 
detection of heme (FE) bound with histidine (NE2) atom but missing to mention the 
gromacs bond, angle, dihedral type code.


Which clearly means that pdb2gmx to not able detect the gromacs bond type code 
to assign their parameters...


I have checked the parameter of this heme-his and its found like this :


bond


#define gb_340.198   0.6400e+06
; NR  -   FE120


angle

#define ga_17   115.00   50.00; NR(heme)  -  FE  - NR 10
#define ga_34   125.00  375.00; FE  - NR  - CR1 (5-ring)
dihedral#define gd_38 0.0000.0  4; -NR-FE-   0.0

Could you tell how do make pdb2gmx to assign this parameter ? Thanks in advance.



If there is a problem with pdb2gmx (i.e. a bug), then you'll have to modify the 
code.  Otherwise, just modify the topology by hand to include the information 
that is missing.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] which tool returns vectors?

[Justin Lemkul]

On 4/23/13 9:27 AM, Steven Neumann wrote:

Dear Users,

Does any one know which command is capable to return the vector of a
specified group of 2 atoms (e.g. C=O in protein) over the simulation time?



Not directly, but you can probably use g_traj and post-process the coordinate 
information.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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: protein-ligand interactions in charmm force field

[James Starlight]

Justin,


as the example I have 2 systems consisted of receptor completed with 2
different ligands.

After 100ns of production run I've realized that both of that ligands has
the same degree of conformational dynamics on internal degrees of freedom (
the same RMSD as the measure of internal mobility of that compounds). But
the main difference was in the mobility of the smaller agonist molecule
(movement inside the ligand-binding pocket   in comparison to the bulkier
antagonist. So as consequence I've obtained  higher value of the MSD in
case of smaller ligand. Could the MSD be representative measure of such
whole-body motion of the ligand ? What advantages have the calculation of
the diffusion coefficient ( which could be calculated from MSD )?

2) How I could visualize such ligand mobility ? For example for dynamics on
internal degrees of freedom Principal components analysis could give best
representation of conformational mobility.
In case when I want to explore diffusional-behavior I should obtain
representation of some confrontational volume (the surface within
ligand-binding cavity  accessible for the ligand). What Gromac's tools
could be useful for that?


James


2013/2/7 Justin Lemkul 

>
>
> On 2/7/13 5:15 AM, James Starlight wrote:
>
>> Justin,
>>
>> Thanks again for suggestion. I've found that g_mindist is exactly what
>> I need. I'm not quite sure how I could use that tools to find all
>> possible interactions between my ligand and several polar residues
>> defined in the ndx file ( I have no problem only when I examined
>> manually each possible interaction separately). Finally I'm not quite
>>
>
> There's no way to do automated screening for these types of things.
>  You'll have to choose groups of interest and make corresponding index
> groups for analysis.
>
>
>  sure about number of contacts calculated by g_mindist. E.g I've
>> examined it for my ligand ( having 3 polar atoms and large hydrophobic
>> ring)  and 1 serine residue ( 1 polar side chain group ). As the
>> ouitput I've obtain 60 maximum contact number (and 10- minimum). Why
>> maximum number was so big ?
>>
>>
> Sounds about right if you're using the whole serine residue, or even just
> its side chain.  The number of contacts (if memory serves, but do check the
> code!) is at most N^2, where N is the total number of atoms in both of the
> chosen groups.
>
>
>  Some another question- I want to find a way to esstimate average
>> mobility of my ligands in the ligand binding pocket.
>> For example I have 2 different complexes of my protein with 2
>> different ligands- one of that liugand is big and occupy big spacy
>> whithin protein interiour ( so that ligand is less mobile). On the
>> contrary the second ligand is samller and flexible so it muast be more
>> mobile within protein and it seen visually during visualisation of the
>> md trajectory. But how it could be estimated in some values ?
>>
>>
> You can define mobility in a lot of ways - RMSF, diffusion constant, RMSD,
> etc.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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] Fwd: Selecting the temperature distribution

[massimo sandal]

In general, the smaller is your system, the less temperatures you will need
(and you'll have better performance).

Notice however that implicit solvent, while surely a possibility worth
considering, is not usually considered to be very good -take care that if
you write a paper from implicit solvent results, reviewers might not be
happy. There is a chance that the results coming out of your simulation
might be nonsense. Discuss this choice with your supervisor and/or with
expert colleagues who know about limitations of implicit solvent. You need
to be able to justify your choice scientifically -for example testing it
with a known,similar system and observing that implicit solvent reproduces
the behaviour of that system in explicit solvent well.

About reducing the box size, by all means try it, but always make sure it
is large enough to avoid that the periodic copies of your molecule see each
other. See
http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water#Box_Preparationand
be sure to understand it.


2013/4/23 bharat gupta 

> Thanks a lot for your prompt responses. By using implicit solvent , I am
> getting on 9 temperature values. I think this should work , I will try it
> out. Also, i checked that when the no. of water molecules are reduced , the
> no. of temp. values are also reduced. If I reduce the no. of water
> molecules or reduce the size of box , will it help. As of now I am using
> octahedron box.
>
>
> On Tue, Apr 23, 2013 at 10:43 PM, massimo sandal  >wrote:
>
> > It depends on what you want to do. Possible it is certainly possible, but
> > you can't be guaranteed to observe the conformational changes you desire
> to
> > observe. Again, it does not depend only on the REMD, but also on the
> length
> > of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also
> depends
> > on your system itself -and this you cannot know without trying.
> >
> > If you want to improve sampling beyond what standard REMD can do, to
> > exploit your computational resources at the best, you can look into other
> > approaches like solute tempering (
> > http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics (
> > http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to
> study
> > *well* this kind of things, talk with experts in these techniques,  and
> > remember that there is no guarantee any of them will bring the result you
> > want. Good luck! :)
> >
> >
> >
> >
> > 2013/4/23 bharat gupta 
> >
> > > So, my final question is whether is possible to do REMD for my system,
> > > using the computational resource that I have.
> > >
> > >
> > > On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal <
> deviceran...@gmail.com
> > > >wrote:
> > >
> > > > Who knows? It depends on the size of your peptide, on the energy
> > > landscape,
> > > > on how long is the run you plan to do. I would bet on "no", however.
> > > >
> > > >
> > > > 2013/4/23 bharat gupta 
> > > >
> > > > > But if I choose a smaller temperature range , would it be possible
> to
> > > > > observe any folding event ??
> > > > >
> > > > >
> > > > > On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal <
> > > deviceran...@gmail.com
> > > > > >wrote:
> > > > >
> > > > > > Thanks, now it's clearer.
> > > > > >
> > > > > > > Now, how can I temp. from these, so that the replicas can
> > exchange
> > > > ...
> > > > > >
> > > > > > You can't, I would say. The system you have requires so many
> > replicas
> > > > to
> > > > > > exchange properly from the two temperature extremes you set up.
> As
> > > you
> > > > > have
> > > > > > seen, if you pick up temperatures in that range randomly, they
> > can't
> > > > > > exchange anymore. They are too far away.
> > > > > >
> > > > > > I would choose a smaller temperature range. There is little else
> > you
> > > > can
> > > > > > do, I think.
> > > > > >
> > > > > >
> > > > > > 2013/4/23 bharat gupta 
> > > > > >
> > > > > > > Sorry for that, I explain it again. Actually, I used the this
> > link
> > > to
> > > > > > > generate a temp. distribution. But I can do REMD for 56
> replicas
> > > > only,
> > > > > > as I
> > > > > > > have 56 processors available. The t-remd calculator provides
> 220
> > > > > > > temperature values :
> > > > > > >
> > > > > > > 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14,
> > > > 308.17,
> > > > > > > 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50,
> > > > 317.56,
> > > > > > > 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10,
> > > > 327.18,
> > > > > > > 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93,
> > > > 337.04,
> > > > > > > 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00,
> > > > 347.13,
> > > > > > > 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31,
> > > > 357.47,
> > > > > > > 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86,
> > > > 368.05,
> > > > > > > 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68,
> > > > 378.90

Re: [gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

Thanks a lot for your prompt responses. By using implicit solvent , I am
getting on 9 temperature values. I think this should work , I will try it
out. Also, i checked that when the no. of water molecules are reduced , the
no. of temp. values are also reduced. If I reduce the no. of water
molecules or reduce the size of box , will it help. As of now I am using
octahedron box.


On Tue, Apr 23, 2013 at 10:43 PM, massimo sandal wrote:

> It depends on what you want to do. Possible it is certainly possible, but
> you can't be guaranteed to observe the conformational changes you desire to
> observe. Again, it does not depend only on the REMD, but also on the length
> of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also depends
> on your system itself -and this you cannot know without trying.
>
> If you want to improve sampling beyond what standard REMD can do, to
> exploit your computational resources at the best, you can look into other
> approaches like solute tempering (
> http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics (
> http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to study
> *well* this kind of things, talk with experts in these techniques,  and
> remember that there is no guarantee any of them will bring the result you
> want. Good luck! :)
>
>
>
>
> 2013/4/23 bharat gupta 
>
> > So, my final question is whether is possible to do REMD for my system,
> > using the computational resource that I have.
> >
> >
> > On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal  > >wrote:
> >
> > > Who knows? It depends on the size of your peptide, on the energy
> > landscape,
> > > on how long is the run you plan to do. I would bet on "no", however.
> > >
> > >
> > > 2013/4/23 bharat gupta 
> > >
> > > > But if I choose a smaller temperature range , would it be possible to
> > > > observe any folding event ??
> > > >
> > > >
> > > > On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal <
> > deviceran...@gmail.com
> > > > >wrote:
> > > >
> > > > > Thanks, now it's clearer.
> > > > >
> > > > > > Now, how can I temp. from these, so that the replicas can
> exchange
> > > ...
> > > > >
> > > > > You can't, I would say. The system you have requires so many
> replicas
> > > to
> > > > > exchange properly from the two temperature extremes you set up. As
> > you
> > > > have
> > > > > seen, if you pick up temperatures in that range randomly, they
> can't
> > > > > exchange anymore. They are too far away.
> > > > >
> > > > > I would choose a smaller temperature range. There is little else
> you
> > > can
> > > > > do, I think.
> > > > >
> > > > >
> > > > > 2013/4/23 bharat gupta 
> > > > >
> > > > > > Sorry for that, I explain it again. Actually, I used the this
> link
> > to
> > > > > > generate a temp. distribution. But I can do REMD for 56 replicas
> > > only,
> > > > > as I
> > > > > > have 56 processors available. The t-remd calculator provides 220
> > > > > > temperature values :
> > > > > >
> > > > > > 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14,
> > > 308.17,
> > > > > > 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50,
> > > 317.56,
> > > > > > 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10,
> > > 327.18,
> > > > > > 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93,
> > > 337.04,
> > > > > > 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00,
> > > 347.13,
> > > > > > 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31,
> > > 357.47,
> > > > > > 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86,
> > > 368.05,
> > > > > > 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68,
> > > 378.90,
> > > > > > 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75,
> > > 390.00,
> > > > > > 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10,
> > > 401.38,
> > > > > > 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74,
> > > 413.05,
> > > > > > 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68,
> > > 425.03,
> > > > > > 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89,
> > > 437.26,
> > > > > > 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38,
> > > 449.79,
> > > > > > 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18,
> > > 462.63,
> > > > > > 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32,
> > > 475.80,
> > > > > > 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76,
> > > 489.27,
> > > > > > 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52,
> > > 503.07,
> > > > > > 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65,
> > > 517.24,
> > > > > > 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10,
> > > 531.73,
> > > > > > 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90,
> > > 546.56,
> > > > > > 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06,
> > > 561.76,
> > > > > > 563.48, 565.19, 566.92, 568.6

Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

In general, look in the literature what other people have done on similar
systems, and try to go from there.


2013/4/23 massimo sandal 

> It depends on what you want to do. Possible it is certainly possible, but
> you can't be guaranteed to observe the conformational changes you desire to
> observe. Again, it does not depend only on the REMD, but also on the length
> of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also depends
> on your system itself -and this you cannot know without trying.
>
> If you want to improve sampling beyond what standard REMD can do, to
> exploit your computational resources at the best, you can look into other
> approaches like solute tempering (
> http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics (
> http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to
> study *well* this kind of things, talk with experts in these techniques,
> and remember that there is no guarantee any of them will bring the result
> you want. Good luck! :)
>
>
>
>
> 2013/4/23 bharat gupta 
>
>> So, my final question is whether is possible to do REMD for my system,
>> using the computational resource that I have.
>>
>>
>> On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal > >wrote:
>>
>> > Who knows? It depends on the size of your peptide, on the energy
>> landscape,
>> > on how long is the run you plan to do. I would bet on "no", however.
>> >
>> >
>> > 2013/4/23 bharat gupta 
>> >
>> > > But if I choose a smaller temperature range , would it be possible to
>> > > observe any folding event ??
>> > >
>> > >
>> > > On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal <
>> deviceran...@gmail.com
>> > > >wrote:
>> > >
>> > > > Thanks, now it's clearer.
>> > > >
>> > > > > Now, how can I temp. from these, so that the replicas can exchange
>> > ...
>> > > >
>> > > > You can't, I would say. The system you have requires so many
>> replicas
>> > to
>> > > > exchange properly from the two temperature extremes you set up. As
>> you
>> > > have
>> > > > seen, if you pick up temperatures in that range randomly, they can't
>> > > > exchange anymore. They are too far away.
>> > > >
>> > > > I would choose a smaller temperature range. There is little else you
>> > can
>> > > > do, I think.
>> > > >
>> > > >
>> > > > 2013/4/23 bharat gupta 
>> > > >
>> > > > > Sorry for that, I explain it again. Actually, I used the this
>> link to
>> > > > > generate a temp. distribution. But I can do REMD for 56 replicas
>> > only,
>> > > > as I
>> > > > > have 56 processors available. The t-remd calculator provides 220
>> > > > > temperature values :
>> > > > >
>> > > > > 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14,
>> > 308.17,
>> > > > > 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50,
>> > 317.56,
>> > > > > 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10,
>> > 327.18,
>> > > > > 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93,
>> > 337.04,
>> > > > > 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00,
>> > 347.13,
>> > > > > 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31,
>> > 357.47,
>> > > > > 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86,
>> > 368.05,
>> > > > > 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68,
>> > 378.90,
>> > > > > 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75,
>> > 390.00,
>> > > > > 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10,
>> > 401.38,
>> > > > > 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74,
>> > 413.05,
>> > > > > 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68,
>> > 425.03,
>> > > > > 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89,
>> > 437.26,
>> > > > > 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38,
>> > 449.79,
>> > > > > 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18,
>> > 462.63,
>> > > > > 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32,
>> > 475.80,
>> > > > > 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76,
>> > 489.27,
>> > > > > 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52,
>> > 503.07,
>> > > > > 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65,
>> > 517.24,
>> > > > > 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10,
>> > 531.73,
>> > > > > 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90,
>> > 546.56,
>> > > > > 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06,
>> > 561.76,
>> > > > > 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60,
>> > 577.47,
>> > > > > 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65,
>> > 593.44,
>> > > > > 595.24, 597.04, 598.85, 600.66
>> > > > >
>> > > > >
>> > > > > Now, how can I temp. from these, so that the replicas can exchange
>> > ...
>> > > > >
>> > > > >
>> > > > > On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal <
>> > > deviceran...@gmail.com
>> 

Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

It depends on what you want to do. Possible it is certainly possible, but
you can't be guaranteed to observe the conformational changes you desire to
observe. Again, it does not depend only on the REMD, but also on the length
of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also depends
on your system itself -and this you cannot know without trying.

If you want to improve sampling beyond what standard REMD can do, to
exploit your computational resources at the best, you can look into other
approaches like solute tempering (
http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics (
http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to study
*well* this kind of things, talk with experts in these techniques,  and
remember that there is no guarantee any of them will bring the result you
want. Good luck! :)




2013/4/23 bharat gupta 

> So, my final question is whether is possible to do REMD for my system,
> using the computational resource that I have.
>
>
> On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal  >wrote:
>
> > Who knows? It depends on the size of your peptide, on the energy
> landscape,
> > on how long is the run you plan to do. I would bet on "no", however.
> >
> >
> > 2013/4/23 bharat gupta 
> >
> > > But if I choose a smaller temperature range , would it be possible to
> > > observe any folding event ??
> > >
> > >
> > > On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal <
> deviceran...@gmail.com
> > > >wrote:
> > >
> > > > Thanks, now it's clearer.
> > > >
> > > > > Now, how can I temp. from these, so that the replicas can exchange
> > ...
> > > >
> > > > You can't, I would say. The system you have requires so many replicas
> > to
> > > > exchange properly from the two temperature extremes you set up. As
> you
> > > have
> > > > seen, if you pick up temperatures in that range randomly, they can't
> > > > exchange anymore. They are too far away.
> > > >
> > > > I would choose a smaller temperature range. There is little else you
> > can
> > > > do, I think.
> > > >
> > > >
> > > > 2013/4/23 bharat gupta 
> > > >
> > > > > Sorry for that, I explain it again. Actually, I used the this link
> to
> > > > > generate a temp. distribution. But I can do REMD for 56 replicas
> > only,
> > > > as I
> > > > > have 56 processors available. The t-remd calculator provides 220
> > > > > temperature values :
> > > > >
> > > > > 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14,
> > 308.17,
> > > > > 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50,
> > 317.56,
> > > > > 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10,
> > 327.18,
> > > > > 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93,
> > 337.04,
> > > > > 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00,
> > 347.13,
> > > > > 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31,
> > 357.47,
> > > > > 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86,
> > 368.05,
> > > > > 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68,
> > 378.90,
> > > > > 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75,
> > 390.00,
> > > > > 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10,
> > 401.38,
> > > > > 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74,
> > 413.05,
> > > > > 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68,
> > 425.03,
> > > > > 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89,
> > 437.26,
> > > > > 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38,
> > 449.79,
> > > > > 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18,
> > 462.63,
> > > > > 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32,
> > 475.80,
> > > > > 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76,
> > 489.27,
> > > > > 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52,
> > 503.07,
> > > > > 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65,
> > 517.24,
> > > > > 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10,
> > 531.73,
> > > > > 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90,
> > 546.56,
> > > > > 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06,
> > 561.76,
> > > > > 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60,
> > 577.47,
> > > > > 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65,
> > 593.44,
> > > > > 595.24, 597.04, 598.85, 600.66
> > > > >
> > > > >
> > > > > Now, how can I temp. from these, so that the replicas can exchange
> > ...
> > > > >
> > > > >
> > > > > On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal <
> > > deviceran...@gmail.com
> > > > > >wrote:
> > > > >
> > > > > > I don't understand your question. If you got the temperature
> > > > > distribution,
> > > > > > what else do you need?
> > > > > >
> > > > > >
> > > > > > 2013/4/23 bharat gupta 
> > > > > >
> > > > > > > I have got the temperature distributio

[gmx-users] specbonds are not taken by gromos force field?

[라지브간디]

Dear Justin,


Sorry for the confusion.


What I was trying to explain is " pdb2gmx output of topol.top file shows the 
detection of heme (FE) bound with histidine (NE2) atom but missing to mention 
the gromacs bond, angle, dihedral type code.


Which clearly means that pdb2gmx to not able detect the gromacs bond type code 
to assign their parameters...


I have checked the parameter of this heme-his and its found like this :


bond


#define gb_340.198   0.6400e+06
; NR  -   FE120


angle

#define ga_17   115.00   50.00; NR(heme)  -  FE  - NR 10
#define ga_34   125.00  375.00; FE  - NR  - CR1 (5-ring)
dihedral#define gd_38 0.0000.0  4; -NR-FE-   0.0

Could you tell how do make pdb2gmx to assign this parameter ? Thanks in advance.






Can you please provide an exact example of what the issue is? Your question 
conflicts itself - first you say the parameters are not looked up in 
ffbonded.itp, but then you say the parameters are there. There are frequent 
reports of issues with heme in Gromos96 force fields, but none ever seem to get 
resolved, usually due to lack of information. 

-Justin 


On 4/19/13 10:45 AM, ��� wrote: 
> Hello gromacs. 
> 
> 
> I wanna simulate the heme contain proteins which has bond FE-NE2 from HIS as 
> it already found in specbond section. 
> 
> 
> When i use pdb2gmx, I could see the links of these but in topology file but 
> not parameter information which detects from ffbonded.itp. 
> 
> 
> I also checked the ffbonded.itp file and found that it has default parameter 
> information for heme links with his, which also described in specbond column. 
> 
> 
> What can be done to pdb2gmx to detect these bond parameter from ffbonded.itp 
> file? 
> 
> 


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Re: [gmx-users] Interaction across PBC

[Steven Neumann]

Thanks a lot

Steven


On Tue, Apr 23, 2013 at 2:18 PM, Justin Lemkul  wrote:

>
>
> On 4/23/13 9:15 AM, Steven Neumann wrote:
>
>> Shall I specify one index group for two regions or 2 seprate? g_mindist
>> asks just for one group.
>>
>>
> If it only takes one, then you can only give it one.
>
>
>  would twice as cutoff would be sufficent to assess they do not interact?
>>
>>
> Probably, maybe less, but that depends on the cutoff itself.  Water
> ordering can persist for up to 2.0 nm or so.
>
> -Justin
>
>
>> On Tue, Apr 23, 2013 at 1:54 PM, Steven Neumann > >wrote:
>>
>>  Thank you.
>>>
>>> Steven
>>>
>>>
>>> On Tue, Apr 23, 2013 at 1:23 PM, Justin Lemkul  wrote:
>>>
>>>

 On 4/23/13 6:37 AM, Steven Neumann wrote:

  Dear Gmx users,
>
>
> My protien has got some strong acidic and strong basic parts. I fold
> and
> unfold my protein with different temperaturss. I bserved high affinity
> of
> those regions towards each other, they are very close to each other
> over
> the simulation.
>
> How can I possibly check whether my two regions do not interact across
> the
> boundary conditions with such high affinity?
>
>
>  g_mindist -pi with a suitable index group.

 -Justin

 --
 ====


 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
 >

 ====

 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 http://lists.gromacs.org/mailman/listinfo/gmx-users>
 >
 * Please search the archive at http://www.gromacs.org/**
 Support/Mailing_Lists/Search>>> Mailing_Lists/Search>before
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 >


>>>
>>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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[gmx-users] which tool returns vectors?

[Steven Neumann]

Dear Users,

Does any one know which command is capable to return the vector of a
specified group of 2 atoms (e.g. C=O in protein) over the simulation time?

Steven
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

So, my final question is whether is possible to do REMD for my system,
using the computational resource that I have.


On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal wrote:

> Who knows? It depends on the size of your peptide, on the energy landscape,
> on how long is the run you plan to do. I would bet on "no", however.
>
>
> 2013/4/23 bharat gupta 
>
> > But if I choose a smaller temperature range , would it be possible to
> > observe any folding event ??
> >
> >
> > On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal  > >wrote:
> >
> > > Thanks, now it's clearer.
> > >
> > > > Now, how can I temp. from these, so that the replicas can exchange
> ...
> > >
> > > You can't, I would say. The system you have requires so many replicas
> to
> > > exchange properly from the two temperature extremes you set up. As you
> > have
> > > seen, if you pick up temperatures in that range randomly, they can't
> > > exchange anymore. They are too far away.
> > >
> > > I would choose a smaller temperature range. There is little else you
> can
> > > do, I think.
> > >
> > >
> > > 2013/4/23 bharat gupta 
> > >
> > > > Sorry for that, I explain it again. Actually, I used the this link to
> > > > generate a temp. distribution. But I can do REMD for 56 replicas
> only,
> > > as I
> > > > have 56 processors available. The t-remd calculator provides 220
> > > > temperature values :
> > > >
> > > > 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14,
> 308.17,
> > > > 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50,
> 317.56,
> > > > 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10,
> 327.18,
> > > > 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93,
> 337.04,
> > > > 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00,
> 347.13,
> > > > 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31,
> 357.47,
> > > > 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86,
> 368.05,
> > > > 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68,
> 378.90,
> > > > 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75,
> 390.00,
> > > > 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10,
> 401.38,
> > > > 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74,
> 413.05,
> > > > 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68,
> 425.03,
> > > > 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89,
> 437.26,
> > > > 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38,
> 449.79,
> > > > 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18,
> 462.63,
> > > > 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32,
> 475.80,
> > > > 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76,
> 489.27,
> > > > 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52,
> 503.07,
> > > > 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65,
> 517.24,
> > > > 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10,
> 531.73,
> > > > 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90,
> 546.56,
> > > > 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06,
> 561.76,
> > > > 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60,
> 577.47,
> > > > 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65,
> 593.44,
> > > > 595.24, 597.04, 598.85, 600.66
> > > >
> > > >
> > > > Now, how can I temp. from these, so that the replicas can exchange
> ...
> > > >
> > > >
> > > > On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal <
> > deviceran...@gmail.com
> > > > >wrote:
> > > >
> > > > > I don't understand your question. If you got the temperature
> > > > distribution,
> > > > > what else do you need?
> > > > >
> > > > >
> > > > > 2013/4/23 bharat gupta 
> > > > >
> > > > > > I have got the temperature distribution from the same link, but
> how
> > > to
> > > > > > select evenly spaced temperatures for 56 replicas, I need to know
> > > that
> > > > > >
> > > > > >
> > > > > > On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal <
> > > > deviceran...@gmail.com
> > > > > > >wrote:
> > > > > >
> > > > > > > Look here: http://folding.bmc.uu.se/remd/
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > 2013/4/23 bharat gupta 
> > > > > > >
> > > > > > > > Dear gmx users,
> > > > > > > >
> > > > > > > > I am planning to run REMD for a peptide (406 atoms )+ solvent
> > > > system
> > > > > > > > (27639). The temperature range I selected is from 300 to
> 500. I
> > > > want
> > > > > to
> > > > > > > > select appropriate temp. for 56 replicas. I randomly chose
> some
> > > > temp
> > > > > > > > distribution and the exchange probabilities was 0.0. I know
> > that
> > > we
> > > > > can
> > > > > > > use
> > > > > > > > the formula  Ti=T0*ek*i, but what is the value for i and K
> here
> > > ??
> > > > > > > >
> > > > > > > > 
> > > > > > > > BHARAT
> > > > > > > > --
> > > > > > > > gmx-users mailing listgmx-users@gromacs.org
> > > 

Re: [gmx-users] Interaction across PBC

[Justin Lemkul]

On 4/23/13 9:15 AM, Steven Neumann wrote:

Shall I specify one index group for two regions or 2 seprate? g_mindist
asks just for one group.



If it only takes one, then you can only give it one.


would twice as cutoff would be sufficent to assess they do not interact?



Probably, maybe less, but that depends on the cutoff itself.  Water ordering can 
persist for up to 2.0 nm or so.


-Justin



On Tue, Apr 23, 2013 at 1:54 PM, Steven Neumann wrote:


Thank you.

Steven


On Tue, Apr 23, 2013 at 1:23 PM, Justin Lemkul  wrote:




On 4/23/13 6:37 AM, Steven Neumann wrote:


Dear Gmx users,


My protien has got some strong acidic and strong basic parts. I fold and
unfold my protein with different temperaturss. I bserved high affinity of
those regions towards each other, they are very close to each other over
the simulation.

How can I possibly check whether my two regions do not interact across
the
boundary conditions with such high affinity?



g_mindist -pi with a suitable index group.

-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
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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--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Interaction across PBC

[Steven Neumann]

Shall I specify one index group for two regions or 2 seprate? g_mindist
asks just for one group.

would twice as cutoff would be sufficent to assess they do not interact?


On Tue, Apr 23, 2013 at 1:54 PM, Steven Neumann wrote:

> Thank you.
>
> Steven
>
>
> On Tue, Apr 23, 2013 at 1:23 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 4/23/13 6:37 AM, Steven Neumann wrote:
>>
>>> Dear Gmx users,
>>>
>>>
>>> My protien has got some strong acidic and strong basic parts. I fold and
>>> unfold my protein with different temperaturss. I bserved high affinity of
>>> those regions towards each other, they are very close to each other over
>>> the simulation.
>>>
>>> How can I possibly check whether my two regions do not interact across
>>> the
>>> boundary conditions with such high affinity?
>>>
>>>
>> g_mindist -pi with a suitable index group.
>>
>> -Justin
>>
>> --
>> ==**==
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> 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!
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

Who knows? It depends on the size of your peptide, on the energy landscape,
on how long is the run you plan to do. I would bet on "no", however.


2013/4/23 bharat gupta 

> But if I choose a smaller temperature range , would it be possible to
> observe any folding event ??
>
>
> On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal  >wrote:
>
> > Thanks, now it's clearer.
> >
> > > Now, how can I temp. from these, so that the replicas can exchange ...
> >
> > You can't, I would say. The system you have requires so many replicas to
> > exchange properly from the two temperature extremes you set up. As you
> have
> > seen, if you pick up temperatures in that range randomly, they can't
> > exchange anymore. They are too far away.
> >
> > I would choose a smaller temperature range. There is little else you can
> > do, I think.
> >
> >
> > 2013/4/23 bharat gupta 
> >
> > > Sorry for that, I explain it again. Actually, I used the this link to
> > > generate a temp. distribution. But I can do REMD for 56 replicas only,
> > as I
> > > have 56 processors available. The t-remd calculator provides 220
> > > temperature values :
> > >
> > > 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14, 308.17,
> > > 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50, 317.56,
> > > 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10, 327.18,
> > > 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93, 337.04,
> > > 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00, 347.13,
> > > 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31, 357.47,
> > > 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86, 368.05,
> > > 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68, 378.90,
> > > 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75, 390.00,
> > > 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10, 401.38,
> > > 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74, 413.05,
> > > 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68, 425.03,
> > > 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89, 437.26,
> > > 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38, 449.79,
> > > 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18, 462.63,
> > > 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32, 475.80,
> > > 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76, 489.27,
> > > 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52, 503.07,
> > > 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65, 517.24,
> > > 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10, 531.73,
> > > 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90, 546.56,
> > > 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06, 561.76,
> > > 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60, 577.47,
> > > 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65, 593.44,
> > > 595.24, 597.04, 598.85, 600.66
> > >
> > >
> > > Now, how can I temp. from these, so that the replicas can exchange ...
> > >
> > >
> > > On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal <
> deviceran...@gmail.com
> > > >wrote:
> > >
> > > > I don't understand your question. If you got the temperature
> > > distribution,
> > > > what else do you need?
> > > >
> > > >
> > > > 2013/4/23 bharat gupta 
> > > >
> > > > > I have got the temperature distribution from the same link, but how
> > to
> > > > > select evenly spaced temperatures for 56 replicas, I need to know
> > that
> > > > >
> > > > >
> > > > > On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal <
> > > deviceran...@gmail.com
> > > > > >wrote:
> > > > >
> > > > > > Look here: http://folding.bmc.uu.se/remd/
> > > > > >
> > > > > >
> > > > > >
> > > > > > 2013/4/23 bharat gupta 
> > > > > >
> > > > > > > Dear gmx users,
> > > > > > >
> > > > > > > I am planning to run REMD for a peptide (406 atoms )+ solvent
> > > system
> > > > > > > (27639). The temperature range I selected is from 300 to 500. I
> > > want
> > > > to
> > > > > > > select appropriate temp. for 56 replicas. I randomly chose some
> > > temp
> > > > > > > distribution and the exchange probabilities was 0.0. I know
> that
> > we
> > > > can
> > > > > > use
> > > > > > > the formula  Ti=T0*ek*i, but what is the value for i and K here
> > ??
> > > > > > >
> > > > > > > 
> > > > > > > BHARAT
> > > > > > > --
> > > > > > > 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
> > > > > > >
> > > > > > --
> > > > > > 

Re: [gmx-users] Differences between 4.5.5 and 4.6.2-dev?

[Stefan Kesselheim]

Dear Berk, dear mailing list,

On Apr 23, 2013, at 2:18 PM, Berk Hess  wrote:

> The PME settings you mention won't make any difference.

Thanks for clarification. I was expecting that but they somehow were the best 
candidates in my view.

> I don't see anything that can explain the differnce.
> But are you sure that the difference is statistically relevant?
> How did you determine sigma?
> There could be long time correlations in your system.

I would be very surprised to find long time correlations as the equilibrium 
distribution of ions is (almost) flat. In the stationary state the motion of 
the water will be very slow (I did check that) and "friction time" thus 
velocity autocorrelation decay time caused by water/ion friction is very short. 
And that should be identical for both systems.

About statistics: The 128 ions of both species move virtually independently and 
thus the standard error of the travelled distances is a good measure for the 
statistical accuracy. But I also made independent runs, also with different ion 
numbers, and really did a careful statistical analysis of the data. (E.g.: I 
simulated with different numbers of ions and fitted a of polynomial orders to 
the conductance. Then performed a chi^2 test to decide which is necessary, and 
that seemed OK. I do trust my error bars. My profs in my undergrads were 
exceptionally picky about them.)

> Have you check the temperature? You could be putting a lot of energy into the 
> system.
> To simplify things, you might want to set rvdw=0.9 which removes integration 
> errors
> due to the twin-range cut-off, makes your simulations faster and will have 
> little effect
> on your results.

The temperature is 300.6, target temperature was 300. That should be fine. I 
did check weaker fields and weaker thermostat coupling. Everything stayed 
optimally consistent, within 4.5.5, however incompatible with 4.6.2.
I'm rerunning with cutoffs=1.4 now. I should get results by tomorrow. 

Thanks a lot for your help. I'll tell my news tomorrow and meanwhile I have a 
thesis to write :-).
Cheers
Stefan
> 
> Cheers,
> 
> Berk
> 
> 
>> From: kes...@icp.uni-stuttgart.de
>> Date: Tue, 23 Apr 2013 10:20:50 +0200
>> To: gmx-users@gromacs.org
>> Subject: [gmx-users] Differences between 4.5.5 and 4.6.2-dev?
>> 
>> Dear Gromacs users,
>> a short disclaimer first: I'm new to using GROMACS and new to doing 
>> atomistic resolution modelling. If I'm doing anything very wrong, I'd be 
>> very happy to hear.
>> 
>> I'm trying to simulate ion current in a nanopore. My nanopore consists of LJ 
>> particles positioned on the surface of a cylinder, that is closed with 
>> itself over PBC, thus my system is quasi-infinite. The pore is filled with 
>> SPC/E water and (in this particular simulation) 128 NA+ and CL- ions where 
>> I'm using the gromos53a6 ion parameters. An electric field is applied in the 
>> periodic direction. The current is then the sum of the distances traveled by 
>> all ions in a production run divided by the length of the box times +- 1 
>> (depending on the ion species), divided by the simulation time.
>> 
>> I noticed now the following:
>> With GROMACS 4.5.5 and 4.6.2 I obtained different values for the currents; 
>> the NA ions travel faster in 4.6.2 while the Cl ions travel faster in 4.5.5. 
>> The difference is about 20% in both cases and it is statistically 
>> significant (5 or more sigma).
>> 
>> I'm using PME for electrostatics as later a DNA molecule will be added, and 
>> the long range nature of electrostatics will most likely be quite important. 
>> I am using a twin range cutoff scheme with
>> rlist = 0.9
>> rcoulomb = 0.9
>> rvdw = 1.4
>> and
>> ewald_rtol = 1e-05
>> and the default fourier_spacing (which should be 1.2 nm).
>> According to g_pme_error this choice is not particularly smart (I will do 
>> better, I promise) but however should not explain any differences between 
>> the two versions.
>> 
>> Comparing the gmxdump output of both tprs i noticed the following 
>> differences:
>> 4.6.2 | 4.5.5
>> verlet-buffer-drift = 0.005 | verlet-buffer-drift = 0
>> fourierspacing = 0.12 | fourierspacing = 0
>> dihre-fc = 0 | dihre-fc = 1000
>> 
>> These parameters are my top candidates to explain differences, but I have 
>> attached the rest of the production run mdp below.
>> 
>> My 4.5.5 version was the official one compiled on our local supercomputer 
>> (by the admins) and my 4.6.2 version is from the git repository, branch 
>> release-4.6, last commit 873b98540a47a5727e69342117ab71f8c8b75072. No GPU 
>> usage involved. 4.5.5 with "usual" mpi, 4.6.2 with thread-mpi.
>> 
>> Can anybody think of an explanation? My hope would be that some default 
>> behaviour has changed between the versions.
>> My short-term strategy is rerunning with a single cutoff of 1.4, an optimal 
>> choice of ewald_rtol (tuned with g_pme_error) and hope that the differences 
>> disappear. This however will take a while.
>

Re: [gmx-users] Interaction across PBC

[Steven Neumann]

Thank you.

Steven


On Tue, Apr 23, 2013 at 1:23 PM, Justin Lemkul  wrote:

>
>
> On 4/23/13 6:37 AM, Steven Neumann wrote:
>
>> Dear Gmx users,
>>
>>
>> My protien has got some strong acidic and strong basic parts. I fold and
>> unfold my protein with different temperaturss. I bserved high affinity of
>> those regions towards each other, they are very close to each other over
>> the simulation.
>>
>> How can I possibly check whether my two regions do not interact across the
>> boundary conditions with such high affinity?
>>
>>
> g_mindist -pi with a suitable index group.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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] Problem with the simulation of C2160 (fullerene)

[Justin Lemkul]

On 4/23/13 1:31 AM, jhon michael espinosa duran wrote:

Hi guys

I have a problem with the MD simulation of C2160 (Fullerene)
with doxorubicin molecules inside. I have a OPLS force field
for C60 that I am using for C2160, and for Doxorubicin, I generate
the force field using PRODRG.
The problem is that PRODRG is based on Gromacs so the two structures
are based on different force fields.



Make sure you get the nomenclature right here - it is not based on "Gromacs," 
the parameters it gives you are based on Gromos96 43A1.  The fact of the matter 
is those parameters are very poor and require manual refinement (see 
http://pubs.acs.org/doi/abs/10.1021/ci100335w).



What can I do to fix the problem?
I can change the drug if it is necessary, any drug avaliable in OPLS?



You need to choose a force field that can adequately describe all species.  You 
can't mix and match.  Most drugs and small molecules are not built in to 
existing force fields, which are generally only designed for proteins, nucleic 
acids, and some lipids.  Common cofactors typically exist in most force fields, 
but not many other molecules unless someone has published parameters for them.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Interaction across PBC

[Justin Lemkul]

On 4/23/13 6:37 AM, Steven Neumann wrote:

Dear Gmx users,


My protien has got some strong acidic and strong basic parts. I fold and
unfold my protein with different temperaturss. I bserved high affinity of
those regions towards each other, they are very close to each other over
the simulation.

How can I possibly check whether my two regions do not interact across the
boundary conditions with such high affinity?



g_mindist -pi with a suitable index group.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Fwd: Selecting the temperature distribution

[bharat gupta]

But if I choose a smaller temperature range , would it be possible to
observe any folding event ??


On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal wrote:

> Thanks, now it's clearer.
>
> > Now, how can I temp. from these, so that the replicas can exchange ...
>
> You can't, I would say. The system you have requires so many replicas to
> exchange properly from the two temperature extremes you set up. As you have
> seen, if you pick up temperatures in that range randomly, they can't
> exchange anymore. They are too far away.
>
> I would choose a smaller temperature range. There is little else you can
> do, I think.
>
>
> 2013/4/23 bharat gupta 
>
> > Sorry for that, I explain it again. Actually, I used the this link to
> > generate a temp. distribution. But I can do REMD for 56 replicas only,
> as I
> > have 56 processors available. The t-remd calculator provides 220
> > temperature values :
> >
> > 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14, 308.17,
> > 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50, 317.56,
> > 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10, 327.18,
> > 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93, 337.04,
> > 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00, 347.13,
> > 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31, 357.47,
> > 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86, 368.05,
> > 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68, 378.90,
> > 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75, 390.00,
> > 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10, 401.38,
> > 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74, 413.05,
> > 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68, 425.03,
> > 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89, 437.26,
> > 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38, 449.79,
> > 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18, 462.63,
> > 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32, 475.80,
> > 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76, 489.27,
> > 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52, 503.07,
> > 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65, 517.24,
> > 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10, 531.73,
> > 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90, 546.56,
> > 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06, 561.76,
> > 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60, 577.47,
> > 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65, 593.44,
> > 595.24, 597.04, 598.85, 600.66
> >
> >
> > Now, how can I temp. from these, so that the replicas can exchange ...
> >
> >
> > On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal  > >wrote:
> >
> > > I don't understand your question. If you got the temperature
> > distribution,
> > > what else do you need?
> > >
> > >
> > > 2013/4/23 bharat gupta 
> > >
> > > > I have got the temperature distribution from the same link, but how
> to
> > > > select evenly spaced temperatures for 56 replicas, I need to know
> that
> > > >
> > > >
> > > > On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal <
> > deviceran...@gmail.com
> > > > >wrote:
> > > >
> > > > > Look here: http://folding.bmc.uu.se/remd/
> > > > >
> > > > >
> > > > >
> > > > > 2013/4/23 bharat gupta 
> > > > >
> > > > > > Dear gmx users,
> > > > > >
> > > > > > I am planning to run REMD for a peptide (406 atoms )+ solvent
> > system
> > > > > > (27639). The temperature range I selected is from 300 to 500. I
> > want
> > > to
> > > > > > select appropriate temp. for 56 replicas. I randomly chose some
> > temp
> > > > > > distribution and the exchange probabilities was 0.0. I know that
> we
> > > can
> > > > > use
> > > > > > the formula  Ti=T0*ek*i, but what is the value for i and K here
> ??
> > > > > >
> > > > > > 
> > > > > > BHARAT
> > > > > > --
> > > > > > 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
> > > > > >
> > > > > --
> > > > > 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/Suppo

RE: [gmx-users] Differences between 4.5.5 and 4.6.2-dev?

[Berk Hess]

Hi,

The PME settings you mention won't make any difference.

I don't see anything that can explain the differnce.
But are you sure that the difference is statistically relevant?
How did you determine sigma?
There could be long time correlations in your system.

Have you check the temperature? You could be putting a lot of energy into the 
system.
To simplify things, you might want to set rvdw=0.9 which removes integration 
errors
due to the twin-range cut-off, makes your simulations faster and will have 
little effect
on your results.

Cheers,

Berk


> From: kes...@icp.uni-stuttgart.de
> Date: Tue, 23 Apr 2013 10:20:50 +0200
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Differences between 4.5.5 and 4.6.2-dev?
>
> Dear Gromacs users,
> a short disclaimer first: I'm new to using GROMACS and new to doing atomistic 
> resolution modelling. If I'm doing anything very wrong, I'd be very happy to 
> hear.
>
> I'm trying to simulate ion current in a nanopore. My nanopore consists of LJ 
> particles positioned on the surface of a cylinder, that is closed with itself 
> over PBC, thus my system is quasi-infinite. The pore is filled with SPC/E 
> water and (in this particular simulation) 128 NA+ and CL- ions where I'm 
> using the gromos53a6 ion parameters. An electric field is applied in the 
> periodic direction. The current is then the sum of the distances traveled by 
> all ions in a production run divided by the length of the box times +- 1 
> (depending on the ion species), divided by the simulation time.
>
> I noticed now the following:
> With GROMACS 4.5.5 and 4.6.2 I obtained different values for the currents; 
> the NA ions travel faster in 4.6.2 while the Cl ions travel faster in 4.5.5. 
> The difference is about 20% in both cases and it is statistically significant 
> (5 or more sigma).
>
> I'm using PME for electrostatics as later a DNA molecule will be added, and 
> the long range nature of electrostatics will most likely be quite important. 
> I am using a twin range cutoff scheme with
> rlist = 0.9
> rcoulomb = 0.9
> rvdw = 1.4
> and
> ewald_rtol = 1e-05
> and the default fourier_spacing (which should be 1.2 nm).
> According to g_pme_error this choice is not particularly smart (I will do 
> better, I promise) but however should not explain any differences between the 
> two versions.
>
> Comparing the gmxdump output of both tprs i noticed the following differences:
> 4.6.2 | 4.5.5
> verlet-buffer-drift = 0.005 | verlet-buffer-drift = 0
> fourierspacing = 0.12 | fourierspacing = 0
> dihre-fc = 0 | dihre-fc = 1000
>
> These parameters are my top candidates to explain differences, but I have 
> attached the rest of the production run mdp below.
>
> My 4.5.5 version was the official one compiled on our local supercomputer (by 
> the admins) and my 4.6.2 version is from the git repository, branch 
> release-4.6, last commit 873b98540a47a5727e69342117ab71f8c8b75072. No GPU 
> usage involved. 4.5.5 with "usual" mpi, 4.6.2 with thread-mpi.
>
> Can anybody think of an explanation? My hope would be that some default 
> behaviour has changed between the versions.
> My short-term strategy is rerunning with a single cutoff of 1.4, an optimal 
> choice of ewald_rtol (tuned with g_pme_error) and hope that the differences 
> disappear. This however will take a while.
> Cheers and thanks in advance
> Stefan Kesselheim
>
>
> Here is the rest of my mdp file.
>
> define = -DPOSRES_P
> integrator = md
> tinit = 0
> dt = 0.002
> nsteps = 400
> init_step = 0
> comm_mode = None
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstxtcout = 100
> nstcheckpoint = 1
> nstlog = 1
> nstenergy = 1000
> energygrps = POR SOL NA CL
> energygrp_excl = POR POR
> nstlist = 5
> ns_type = grid
> pbc = xyz
> periodic_molecules = yes
> rlist = 0.9
> domain-decomposition = yes
> coulombtype = PME
> rcoulomb-switch = 0
> rcoulomb = 0.9
> epsilon_r = 1
> epsilon_rf = 1
> vdwtype = Cut-Off
> rvdw-switch = 0.
> rvdw = 1.4
> DispCorr = EnerPres
> table-extension = 1
> energygrp_table =
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> ; EWALD/PME/PPPM parameters
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 3d
> epsilon_surface = 0
> optimize_fft = no
> implicit_solvent = No
> tcoupl = v-rescale
> tc-grps = Water_and_ions POR
> tau-t = 5.0 5.0
> ref-t = 300 300
> nsttcouple = 1
> pcoupl = no
> Pcoupltype = Isotropic
> tau-p = 1.0
> compressibility = 4.5e-5
> ref-p = 1.0
> gen_vel = yes
> gen_temp = 300
> gen_seed = 32293
> ld_seed = 32293
> E-x =
> E-xt =
> E-y =
> E-yt =
> E-z = 1 0.2 0
> E-zt =
> constraints = hbonds
>
>
> ---
> Stefan Kesselheim
> Institute for Computational Physics
> Allmandring 3
> +49 711 685 63630
> 70184 Stuttgart
> kes...@icp.uni-stuttgart.de
>
>
>
>
>
> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.or

Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

Thanks, now it's clearer.

> Now, how can I temp. from these, so that the replicas can exchange ...

You can't, I would say. The system you have requires so many replicas to
exchange properly from the two temperature extremes you set up. As you have
seen, if you pick up temperatures in that range randomly, they can't
exchange anymore. They are too far away.

I would choose a smaller temperature range. There is little else you can
do, I think.


2013/4/23 bharat gupta 

> Sorry for that, I explain it again. Actually, I used the this link to
> generate a temp. distribution. But I can do REMD for 56 replicas only, as I
> have 56 processors available. The t-remd calculator provides 220
> temperature values :
>
> 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14, 308.17,
> 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50, 317.56,
> 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10, 327.18,
> 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93, 337.04,
> 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00, 347.13,
> 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31, 357.47,
> 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86, 368.05,
> 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68, 378.90,
> 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75, 390.00,
> 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10, 401.38,
> 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74, 413.05,
> 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68, 425.03,
> 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89, 437.26,
> 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38, 449.79,
> 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18, 462.63,
> 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32, 475.80,
> 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76, 489.27,
> 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52, 503.07,
> 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65, 517.24,
> 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10, 531.73,
> 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90, 546.56,
> 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06, 561.76,
> 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60, 577.47,
> 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65, 593.44,
> 595.24, 597.04, 598.85, 600.66
>
>
> Now, how can I temp. from these, so that the replicas can exchange ...
>
>
> On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal  >wrote:
>
> > I don't understand your question. If you got the temperature
> distribution,
> > what else do you need?
> >
> >
> > 2013/4/23 bharat gupta 
> >
> > > I have got the temperature distribution from the same link, but how to
> > > select evenly spaced temperatures for 56 replicas, I need to know that
> > >
> > >
> > > On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal <
> deviceran...@gmail.com
> > > >wrote:
> > >
> > > > Look here: http://folding.bmc.uu.se/remd/
> > > >
> > > >
> > > >
> > > > 2013/4/23 bharat gupta 
> > > >
> > > > > Dear gmx users,
> > > > >
> > > > > I am planning to run REMD for a peptide (406 atoms )+ solvent
> system
> > > > > (27639). The temperature range I selected is from 300 to 500. I
> want
> > to
> > > > > select appropriate temp. for 56 replicas. I randomly chose some
> temp
> > > > > distribution and the exchange probabilities was 0.0. I know that we
> > can
> > > > use
> > > > > the formula  Ti=T0*ek*i, but what is the value for i and K here ??
> > > > >
> > > > > 
> > > > > BHARAT
> > > > > --
> > > > > gmx-users mailing listgmx-users@gromacs.org
> > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before
> posting!
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> > > > > www interface or send it to gmx-users-requ...@gromacs.org.
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> > > > >
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> > > >
> > >
> > >
> > >
> > > --
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

Sorry for that, I explain it again. Actually, I used the this link to
generate a temp. distribution. But I can do REMD for 56 replicas only, as I
have 56 processors available. The t-remd calculator provides 220
temperature values :

300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14, 308.17,
309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50, 317.56,
318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10, 327.18,
328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93, 337.04,
338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00, 347.13,
348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31, 357.47,
358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86, 368.05,
369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68, 378.90,
380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75, 390.00,
391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10, 401.38,
402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74, 413.05,
414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68, 425.03,
426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89, 437.26,
438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38, 449.79,
451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18, 462.63,
464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32, 475.80,
477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76, 489.27,
490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52, 503.07,
504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65, 517.24,
518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10, 531.73,
533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90, 546.56,
548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06, 561.76,
563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60, 577.47,
579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65, 593.44,
595.24, 597.04, 598.85, 600.66


Now, how can I temp. from these, so that the replicas can exchange ...


On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal wrote:

> I don't understand your question. If you got the temperature distribution,
> what else do you need?
>
>
> 2013/4/23 bharat gupta 
>
> > I have got the temperature distribution from the same link, but how to
> > select evenly spaced temperatures for 56 replicas, I need to know that
> >
> >
> > On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal  > >wrote:
> >
> > > Look here: http://folding.bmc.uu.se/remd/
> > >
> > >
> > >
> > > 2013/4/23 bharat gupta 
> > >
> > > > Dear gmx users,
> > > >
> > > > I am planning to run REMD for a peptide (406 atoms )+ solvent system
> > > > (27639). The temperature range I selected is from 300 to 500. I want
> to
> > > > select appropriate temp. for 56 replicas. I randomly chose some temp
> > > > distribution and the exchange probabilities was 0.0. I know that we
> can
> > > use
> > > > the formula  Ti=T0*ek*i, but what is the value for i and K here ??
> > > >
> > > > 
> > > > BHARAT
> > > > --
> > > > 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
> > > >
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > >
> >
> >
> >
> > --
> > --
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> --
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-- 
Bharat
Ph.D. Candidate
Biomolecular Engineering Laboratory
Pusan National University
South Korea
Mobile no. - 010-5818-3680
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ht

Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

I don't understand your question. If you got the temperature distribution,
what else do you need?


2013/4/23 bharat gupta 

> I have got the temperature distribution from the same link, but how to
> select evenly spaced temperatures for 56 replicas, I need to know that
>
>
> On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal  >wrote:
>
> > Look here: http://folding.bmc.uu.se/remd/
> >
> >
> >
> > 2013/4/23 bharat gupta 
> >
> > > Dear gmx users,
> > >
> > > I am planning to run REMD for a peptide (406 atoms )+ solvent system
> > > (27639). The temperature range I selected is from 300 to 500. I want to
> > > select appropriate temp. for 56 replicas. I randomly chose some temp
> > > distribution and the exchange probabilities was 0.0. I know that we can
> > use
> > > the formula  Ti=T0*ek*i, but what is the value for i and K here ??
> > >
> > > 
> > > BHARAT
> > > --
> > > 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
> > >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > 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] Fwd: Selecting the temperature distribution

[bharat gupta]

I have got the temperature distribution from the same link, but how to
select evenly spaced temperatures for 56 replicas, I need to know that


On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal wrote:

> Look here: http://folding.bmc.uu.se/remd/
>
>
>
> 2013/4/23 bharat gupta 
>
> > Dear gmx users,
> >
> > I am planning to run REMD for a peptide (406 atoms )+ solvent system
> > (27639). The temperature range I selected is from 300 to 500. I want to
> > select appropriate temp. for 56 replicas. I randomly chose some temp
> > distribution and the exchange probabilities was 0.0. I know that we can
> use
> > the formula  Ti=T0*ek*i, but what is the value for i and K here ??
> >
> > 
> > BHARAT
> > --
> > 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
> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Autocorrelation of C-N

[Steven Neumann]

Thanks. Which tool would provide me vectors over a time?

Steven


On Thu, Apr 18, 2013 at 8:17 PM, Mark Abraham wrote:

> Chapter 8 is your friend. Find a tool to feed data to g_analyze.
>
> Mark
>
>
> On Wed, Apr 17, 2013 at 4:23 PM, Steven Neumann  >wrote:
>
> > Dear Users,
> >
> > Could you advise me please how to calculate vector C-N autocorrelation
> > function  in my protein along the simulation time?
> >
> > Steven
> > --
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[gmx-users] Interaction across PBC

[Steven Neumann]

Dear Gmx users,


My protien has got some strong acidic and strong basic parts. I fold and
unfold my protein with different temperaturss. I bserved high affinity of
those regions towards each other, they are very close to each other over
the simulation.

How can I possibly check whether my two regions do not interact across the
boundary conditions with such high affinity?

Steven
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[gmx-users] Tabulated non-bonded potentials - regd

[ramesh cheerla]

Dear Gromacs users,

  In forcefield of  my system, I have non-bonded function of the form U
= A*exp(-Brij) - C/(rij^6) - D/(rij^4),  for this I wanted to use tabulated
potentials. I have defined functions f(r), g(r) and  h(r)  as the following,
f = 1/r;
fprime = 1/(pow(r,2));
g = (C*(-1/(pow(r,6;
gprime = (-6*C/(pow(r,7)));
h = A*exp(-B*r);
hprime = ((A*B)*(exp(-B*r)));
  Then I have tabulated all these  with a bin size (dr) of 0.002 nm and
given "nbfunc" as 1 in forcefield.itp and provided "C" and "A" as 1 in
ffnonbonded.itp (As I have used A,B & C values in generation of table
itself) . I have generated one such table for each  interaction.  While
running simulations with these tables  I am getting the following warning:

"WARNING: For the 3999 non-zero entries for table 2 in table.xvg the forces
deviate on average 78% from minus the numerical derivative of the potential"
After this job is crashing with error  "Segmentation fault"
1) Can anybody please tell me the reason for the above Warning  and how one
can rectify it ?
2) Can I define the functions for the above mentioned  non-bonded function
like this ?
I have checked potential energy of model system (single point energy
calculations i.e., zero step MD and the one that  obtained from the code
that I have written, both are matching.
I am using GROMACS version 4.5.5 and also tested the same thing in V 4.6.

Can anybody help me in this regard,

Thank you in advance.

Regards,
Ramesh.
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

Look here: http://folding.bmc.uu.se/remd/



2013/4/23 bharat gupta 

> Dear gmx users,
>
> I am planning to run REMD for a peptide (406 atoms )+ solvent system
> (27639). The temperature range I selected is from 300 to 500. I want to
> select appropriate temp. for 56 replicas. I randomly chose some temp
> distribution and the exchange probabilities was 0.0. I know that we can use
> the formula  Ti=T0*ek*i, but what is the value for i and K here ??
>
> 
> BHARAT
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Re: [gmx-users] Re: plots in gromacs

[pragna lakshmi]

It is there in every GROMACS manual or else you can even use xmgrace -h in
ur command prompt.


On Tue, Apr 23, 2013 at 1:41 AM, vansh  wrote:

> hi..thanks for the reply..can you please write a command for it..
>
>
>
>
>
> -
> thanks in advance :)
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/plots-in-gromacs-tp5007561p5007565.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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>



-- 
Pragna Lakshmi.T,
Ph.D. Scholar,
IPLS Project,
Pondicherry University,
Pondicherry,
India - 605014.
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[gmx-users] Compiling Gromacs

[Maciej Masłyk]

Dear all,

I'm facing a problem when compiling Gromacs. This is the message I got:
numa_malloc.c:117:73: error: expected ‘)’ before ‘Processor’
numa_malloc.c:118:78: error: expected ‘)’ before ‘ProcNumber’
numa_malloc.c:121:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or 
‘__attribute__’ be fore 
‘smalloc_GetNumaProcessorNodeEx’
numa_malloc.c:122:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or 
‘__attribute__’ be fore 
‘smalloc_GetCurrentProcessorNumberEx’

numa_malloc.c: In function ‘InitNumaHeapSupport’:
numa_malloc.c:151:5: error: ‘smalloc_GetCurrentProcessorNumberEx’ 
undeclared (fi rst use in this function)
numa_malloc.c:151:5: note: each undeclared identifier is reported only 
once for  each function it appears in
numa_malloc.c:151:44: error: ‘func_GetCurrentProcessorNumberEx_t’ 
undeclared (fi rst use in this function)

numa_malloc.c:151:79: error: expected ‘;’ before ‘GetProcAddress’
numa_malloc.c:152:5: error: ‘smalloc_GetNumaProcessorNodeEx’ undeclared 
(first u se in this function)
numa_malloc.c:152:39: error: ‘func_GetNumaProcessorNodeEx_t’ undeclared 
(first u se in this function)

numa_malloc.c:152:69: error: expected ‘;’ before ‘GetProcAddress’
numa_malloc.c: In function ‘ReturnHeapHandle’:
numa_malloc.c:246:5: error: ‘PROCESSOR_NUMBER’ undeclared (first use in 
this fun ction)

numa_malloc.c:246:22: error: expected ‘;’ before ‘CurrentProcessorNumber’
numa_malloc.c:285:5: warning: implicit declaration of function 
‘smalloc_GetCurre ntProcessorNumberEx’
numa_malloc.c:285:42: error: ‘CurrentProcessorNumber’ undeclared (first 
use in t his function)
numa_malloc.c:287:5: warning: implicit declaration of function 
‘smalloc_GetNumaP rocessorNodeEx’
numa_malloc.c:324:9: warning: implicit declaration of function 
‘HeapSetInformati on’

Makefile:332: recipe for target `numa_malloc.lo' failed
make[4]: *** [numa_malloc.lo] Error 1
make[4]: Opuszczenie katalogu 
`/cygdrive/c/Packages/gromacs-4.5.5/src/gmxlib/thr ead_mpi'

Makefile:599: recipe for target `all-recursive' failed
make[3]: *** [all-recursive] Error 1
make[3]: Opuszczenie katalogu 
`/cygdrive/c/Packages/gromacs-4.5.5/src/gmxlib'

Makefile:302: recipe for target `all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Opuszczenie katalogu `/cygdrive/c/Packages/gromacs-4.5.5/src'
Makefile:238: recipe for target `all' failed
make[1]: *** [all] Error 2
make[1]: Opuszczenie katalogu `/cygdrive/c/Packages/gromacs-4.5.5/src'
Makefile:347: recipe for target `all-recursive' failed
make: *** [all-recursive] Error 1

The configuration went ok. I used :

./configure --prefix=/cygdrive/c/Packages/Gromacs --enable-shared
 LDFLAGS='-L/cygdrive/c/Packages/fftw/lib/'
 CPPFLAGS='-I/cygdrive/c/Packages/fftw/include/'

The above error I get after "make" command.
Can you please help me with this as I'm not familiar with linux environment.

Thanks in advance

Maciek
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[gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

Dear gmx users,

I am planning to run REMD for a peptide (406 atoms )+ solvent system
(27639). The temperature range I selected is from 300 to 500. I want to
select appropriate temp. for 56 replicas. I randomly chose some temp
distribution and the exchange probabilities was 0.0. I know that we can use
the formula  Ti=T0*ek*i, but what is the value for i and K here ??


BHARAT
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[gmx-users] Re: plots in gromacs

[vansh]

hi..thanks for the reply..can you please write a command for it..





-
thanks in advance :)
--
View this message in context: 
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[gmx-users] Differences between 4.5.5 and 4.6.2-dev?

[Stefan Kesselheim]

Dear Gromacs users,
a short disclaimer first: I'm new to using GROMACS and new to doing atomistic 
resolution modelling. If I'm doing anything very wrong, I'd be very happy to 
hear. 

I'm trying to simulate ion current in a nanopore. My nanopore consists of LJ 
particles positioned on the surface of a cylinder, that is closed with itself 
over PBC, thus my system is quasi-infinite. The pore is filled with SPC/E water 
and (in this particular simulation) 128 NA+ and CL- ions where I'm using the 
gromos53a6 ion parameters. An electric field is applied in the periodic 
direction. The current is then the sum of the distances traveled by all ions in 
a production run divided by the length of the box times +- 1 (depending on the 
ion species), divided by the simulation time. 

I noticed now the following: 
With GROMACS 4.5.5 and 4.6.2 I obtained different values for the currents; the 
NA ions travel faster in 4.6.2 while the Cl ions travel faster in 4.5.5. The 
difference is about 20% in both cases and it is statistically significant (5 or 
more sigma). 

I'm using PME for electrostatics as later a DNA molecule will be added, and the 
long range nature of electrostatics will most likely be quite important. I am 
using a twin range cutoff scheme with 
rlist= 0.9
rcoulomb = 0.9
rvdw = 1.4
and
ewald_rtol   = 1e-05
and the default fourier_spacing (which should be 1.2 nm).
According to g_pme_error this choice is not particularly smart (I will do 
better, I promise) but however should not explain any differences between the 
two versions.

Comparing the gmxdump output of both tprs i noticed the following differences:
4.6.2   |   4.5.5
  verlet-buffer-drift  = 0.005|  
verlet-buffer-drift  = 0
  fourierspacing   = 0.12 |  fourierspacing 
  = 0
   dihre-fc = 0|dihre-fc
 = 1000  

These parameters are my top candidates to explain differences, but I have 
attached the rest of the production run mdp below.

My 4.5.5 version was the official one compiled on our local supercomputer (by 
the admins) and my 4.6.2 version is from the git repository, branch 
release-4.6, last commit 873b98540a47a5727e69342117ab71f8c8b75072. No GPU usage 
involved. 4.5.5 with "usual" mpi, 4.6.2 with thread-mpi. 

Can anybody think of an explanation? My hope would be that some default 
behaviour has changed between the versions. 
My short-term strategy is rerunning with a single cutoff of 1.4, an optimal 
choice of ewald_rtol (tuned with g_pme_error) and hope that the differences 
disappear. This however will take a while.
Cheers and thanks in advance
Stefan Kesselheim


Here is the rest of my mdp file.

define   = -DPOSRES_P
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 400
init_step= 0
comm_mode= None
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstxtcout= 100
nstcheckpoint= 1
nstlog   = 1
nstenergy= 1000
energygrps   = POR SOL NA CL
energygrp_excl   = POR POR
nstlist  = 5
ns_type  = grid
pbc  = xyz
periodic_molecules   = yes
rlist= 0.9
domain-decomposition = yes
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 0.9
epsilon_r= 1
epsilon_rf   = 1
vdwtype  = Cut-Off
rvdw-switch  = 0.
rvdw = 1.4
DispCorr = EnerPres
table-extension  = 1
energygrp_table  = 
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no
implicit_solvent = No
tcoupl   = v-rescale 
tc-grps  = Water_and_ions POR 
tau-t= 5.0 5.0  
ref-t= 300 300 
nsttcouple   = 1
pcoupl   = no 
Pcoupltype   = Isotropic
tau-p= 1.0
compressibility  = 4.5e-5
ref-p= 1.0
gen_vel  = yes
gen_temp = 300
gen_seed = 32293
ld_seed = 32293
E-x  = 
E-xt = 
E-y  = 
E-yt = 
E-z  = 1 0.2 0 
E-zt = 
constraints  = hbonds


---
Stefan Kesselheim
Institute for Computational Physics

Re: [gmx-users] plots in gromacs

[pragna lakshmi]

Use Xmgrace or grace to convert .xvg to .jpeg format.


On Tue, Apr 23, 2013 at 12:32 AM, vansh  wrote:

> as i am very new to it.. can anyone suggest me how to change the graph
> format
> obtained in gromacs (.xvg) into office 7 based system???
>
>
> tyhanks  in advance
>
>
>
> -
> thanks in advance :)
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/plots-in-gromacs-tp5007561.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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> www interface or send it to gmx-users-requ...@gromacs.org.
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>



-- 
Pragna Lakshmi.T,
Ph.D. Scholar,
IPLS Project,
Pondicherry University,
Pondicherry,
India - 605014.
-- 
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[gmx-users] Re: Selecting the temperature distribution

[bharat gupta]

Dear gmx users,

I am planning to run REMD for a peptide (406 atoms )+ solvent system
(27639). The temperature range I selected is from 300 to 500. I want to
select appropriate temp. for 56 replicas. I randomly chose some temp
distribution and the exchange probabilities was 0.0. I know that we can use
the formula  Ti=T0*ek*i, but what is the value for i and K here ??

-
Bharat
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[gmx-users] plots in gromacs

[vansh]

as i am very new to it.. can anyone suggest me how to change the graph format
obtained in gromacs (.xvg) into office 7 based system???


tyhanks  in advance



-
thanks in advance :)
--
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