[gmx-users] nanoparticles

[leila separdar]

I want to simulate nanoparticles and I want to know if it is possible to
simulate nanoparticles by Gromacs or not? and if yes how can I simulate a
nanoparticle.
thanks
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Re: [gmx-users] Questions concerning Gromacs

[Mark Abraham]

On 5/01/2011 6:14 PM, Thomas Koller wrote:

Hello,

I have some questions concerning the implementation in Gromacs:

1) I want to model a rigid anion of an IL (fixed bonds and angles). The cation 
is flexible. How can I do that without using constraint types? With LINCS or 
SHAKE, I can only fix, for instance, bonds with H atoms or all atoms.


Angles can be constrained. See manual 7.3


  Can I use high values for the force constants?


You can use anything you can validate...


2) When implementing improper dihedrals, I write the sequences of the four 
atoms in the [dihedraltypes] and then fix them in the [dihedral] directive. But 
I always get the error that the impropers are not defined in the default. What 
is my problem?


There are no parameters found. Unfortunately we can't tell why that is so.


I use function type 2. The sequence of impropers is: center atom - neighbor 
atom - neighbor atom- neighbor atom,
as I saw in the manual.

3) For function type 1 of the dihedrals, I implement the equilibrium angle, the 
force constant and the multiplicity (one value for all kinds). What should I do 
if I have, for instance, three equilibrium angles, different for the 
multiplicities (n=1,2,3). How can I implement that in the top file?


If you have functions that are meant to add together on the same 
dihedral, then simply list them and they will be added.


You've got a much better chance of useful feedback if you can provide 
short, simple examples of what you are doing, and what feedback you 
don't like.


Mark
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Re: [gmx-users] nanoparticles

[Mark Abraham]

On 5/01/2011 7:26 PM, leila separdar wrote:
I want to simulate nanoparticles and I want to know if it is possible 
to simulate nanoparticles by Gromacs or not? and if yes how can I 
simulate a nanoparticle.


It's simple to say that it can be done, but it is not a kind of 
simulation that GROMACS targets. You'll be far better served to see what 
has already been attempted in the literature and thus what some fruitful 
approaches might be, than to presuppose that GROMACS is the right tool.


Mark
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[gmx-users] Library file in.m2p not found

[ahmet yıldırım]

Dear users,

I receive the following error when I entered the command "xpm2ps -f ss.xpm
-o ss.eps -di in.m2p"
Fatal error:
Library file in.m2p not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)

I am using the Gromacs 4.05 on the Ubuntu 9.1 Operation System. I installed
the Gromacs from Synaptic Package Manager.
I used echo $GMXDATA but it did not show anything. The pdb2gmx,
g_gyrate,...etc files are in the directory /usr/bin/.
The GMXRC file is in the directory /usr/share/gromacs/shell-specific.
I could not find the problem.


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Re: [gmx-users] Library file in.m2p not found

[Mark Abraham]

On 5/01/2011 7:37 PM, ahmet yıldırım wrote:

Dear users,

I receive the following error when I entered the command "xpm2ps -f 
ss.xpm -o ss.eps -di in.m2p"

Fatal error:
Library file in.m2p not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)

I am using the Gromacs 4.05 on the Ubuntu 9.1 Operation System. I 
installed the Gromacs from Synaptic Package Manager.
I used echo $GMXDATA but it did not show anything. The pdb2gmx, 
g_gyrate,...etc files are in the directory /usr/bin/.

The GMXRC file is in the directory /usr/share/gromacs/shell-specific.


Are you following these instructions? 
http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation


Mark
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[gmx-users] Query about use of coulombtype for LIE in gromacs

[devawati dutta]

Dear Sir,
  Thanks for your prompt answer. In LIE method, if I will not
use the PME for coulombtype, then what is suitable for it? In gromacs
manual, there are several options under coulomb type.Which one I will select
for coulombtype and Vdwtype in .mdp file?

Your's sincerely
Devawati Dutta
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Re: [gmx-users] Library file in.m2p not found

[ahmet yıldırım]

Dear Mark,

I am using the Gromacs on the Ubuntu for month but have not encountered any
problems.I did a search in the file system of Ubuntu. I do not have a GMXLIB
folder in a file system.

What should I do?

05 Ocak 2011 10:42 tarihinde Mark Abraham  yazdı:

> On 5/01/2011 7:37 PM, ahmet yıldırım wrote:
>
>> Dear users,
>>
>> I receive the following error when I entered the command "xpm2ps -f ss.xpm
>> -o ss.eps -di in.m2p"
>> Fatal error:
>> Library file in.m2p not found in current dir nor in default directories.
>> (You can set the directories to search with the GMXLIB path variable)
>>
>> I am using the Gromacs 4.05 on the Ubuntu 9.1 Operation System. I
>> installed the Gromacs from Synaptic Package Manager.
>> I used echo $GMXDATA but it did not show anything. The pdb2gmx,
>> g_gyrate,...etc files are in the directory /usr/bin/.
>> The GMXRC file is in the directory /usr/share/gromacs/shell-specific.
>>
>
> Are you following these instructions?
> http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Questions concerning Gromacs

[Thomas Koller]

Mark, thanks for your reply.

The only problem are the improper dihedrals. I show you a example:

[ dihedraltypes ]
;improper ftypephik(phi)  mult
...
A  B  C  D 4  180 5.293   2

Sorry, I use ftype 4, not 2 :)

The impropers are listed in the dihedraltypes. The sequence is A B C D where A 
is the center atom and B, C, D are the surrounding atoms. I think this is right?

Later the impropers are specified in the [dihedrals]:

[dihedrals]
; i   j   k   lftype
...
  1   2   3   4  4 

I get the error:
ERROR 1 [file binary_ua.top, line 196]:
  No default Improper Dih. types

Fatal error:
unknown function type 20 in ../../../../src/kernel/convparm.c line 326

line 326 is: case F_VSITE2:

Do you see the error? I don't know what is going wrong.

Thanks!
Thomas



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Re: [gmx-users] Library file in.m2p not found

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear Mark,

I am using the Gromacs on the Ubuntu for month but have not encountered 
any problems.I did a search in the file system of Ubuntu. I do not have 
a GMXLIB folder in a file system.


What should I do?



If you're telling xpm2ps to use in.m2p, that file has to exist somewhere.  The 
error message is telling you that it does not exist in the working directory 
(i.e., the directory where you're issuing the command), or the standard Gromacs 
library directory 
(http://www.gromacs.org/Documentation/Terminology/Environment_Variables#GMXLIB).


If you tell any Gromacs tool to use certain input, it has to exist; Gromacs 
isn't going to magically create all the proper files for you.


-Justin

05 Ocak 2011 10:42 tarihinde Mark Abraham > yazdı:


On 5/01/2011 7:37 PM, ahmet yıldırım wrote:

Dear users,

I receive the following error when I entered the command "xpm2ps
-f ss.xpm -o ss.eps -di in.m2p"
Fatal error:
Library file in.m2p not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path
variable)

I am using the Gromacs 4.05 on the Ubuntu 9.1 Operation System.
I installed the Gromacs from Synaptic Package Manager.
I used echo $GMXDATA but it did not show anything. The pdb2gmx,
g_gyrate,...etc files are in the directory /usr/bin/.
The GMXRC file is in the directory
/usr/share/gromacs/shell-specific.


Are you following these instructions?

http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation

Mark
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--
Ahmet YILDIRIM



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Warning about (short) potential interruption - moving DNS servers for gromacs.org

[Erik Lindahl]

Hi,

We're in the process of transferring the domain name to a more convenient 
registrar, and this will also require us to change DNS servers. Thus, you might 
experience short interruptions in name resolutions for *.gromacs.org next week!

Cheers,

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Re: [gmx-users] Library file in.m2p not found

[ahmet yıldırım]

Dear Justin and Mark,

Problem solved.Thanks for your helps

I copied to the directory /usr/share/gromacs/top it (in.m2p).
r...@ubuntu:/home/ab/Desktop# cp in.m2p /usr/share/gromacs/top

05 Ocak 2011 13:45 tarihinde Justin A. Lemkul  yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear Mark,
>>
>> I am using the Gromacs on the Ubuntu for month but have not encountered
>> any problems.I did a search in the file system of Ubuntu. I do not have a
>> GMXLIB folder in a file system.
>>
>> What should I do?
>>
>>
> If you're telling xpm2ps to use in.m2p, that file has to exist somewhere.
>  The error message is telling you that it does not exist in the working
> directory (i.e., the directory where you're issuing the command), or the
> standard Gromacs library directory (
> http://www.gromacs.org/Documentation/Terminology/Environment_Variables#GMXLIB
> ).
>
> If you tell any Gromacs tool to use certain input, it has to exist; Gromacs
> isn't going to magically create all the proper files for you.
>
> -Justin
>
>  05 Ocak 2011 10:42 tarihinde Mark Abraham > mark.abra...@anu.edu.au>> yazdı:
>>
>>
>>On 5/01/2011 7:37 PM, ahmet yıldırım wrote:
>>
>>Dear users,
>>
>>I receive the following error when I entered the command "xpm2ps
>>-f ss.xpm -o ss.eps -di in.m2p"
>>Fatal error:
>>Library file in.m2p not found in current dir nor in default
>>directories.
>>(You can set the directories to search with the GMXLIB path
>>variable)
>>
>>I am using the Gromacs 4.05 on the Ubuntu 9.1 Operation System.
>>I installed the Gromacs from Synaptic Package Manager.
>>I used echo $GMXDATA but it did not show anything. The pdb2gmx,
>>g_gyrate,...etc files are in the directory /usr/bin/.
>>The GMXRC file is in the directory
>>/usr/share/gromacs/shell-specific.
>>
>>
>>Are you following these instructions?
>>
>> http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation
>>
>>Mark
>>-- 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
>>
>>
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
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[gmx-users] HFIP solvent box...

[sharada]

Hello everybody,


Wish you a happy new year 2011.


 I need to simulate a peptide in HFIP ( hexafluoro-propanol) solvent. As I was 
browsing I came across a reprint in J.Phys.Chem.B 2001 titled 

'Model of 1,1,1,3,3,3-Hexafluoro-propan-2-ol for Molecular Dynamics 
Simulations'  published from Groningen Biomolecular Sciences group.Expecting 
that

it will be available on the gromacs wiki I searched there,  however to my 
dissappointment I  could't find it there. Can the authors of the paper be kind 
enough to

provide me the  solvent box if possible. The help will be appreciated. Thanks a 
ton!


Sharada



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Re: [gmx-users] HFIP solvent box...

[Justin A. Lemkul]

sharada wrote:


Hello everybody,

Wish you a happy new year 2011.

 I need to simulate a peptide in HFIP ( hexafluoro-propanol) solvent. As 
I was browsing I came across a reprint in J.Phys.Chem.B 2001 titled 
*/'Model of 1,1,1,3,3,3-Hexafluoro-propan-2-ol for Molecular Dynamics 
Simulations'/*  published from Groningen Biomolecular Sciences 
group.Expecting that
it will be available on the gromacs wiki I searched there,  however to 
my dissappointment I  could't find it there. Can the authors of the 
paper be kind enough to
provide me the  solvent box if possible. The help will be appreciated. 
Thanks a ton!




Rather than hope that these authors are members of the users' list, you'd 
probably have more immediate success if you contact the corresponding author of 
the paper directly.  That why such information is listed.


-Justin


Sharada


"The person addressed in the email is the sole authorized recipient. 
Should you receive it in error, immediately notify the sender of the 
error and delete the e-mail. Any unauthorized dissemination or copying 
of this e-mail (or any attachment to this e-mail) or the wrongful 
disclosure of the information herein contained is prohibited. Also note 
that this form of communication is not secure, it can be intercepted, 
and may not necessarily be free of errors and viruses in spite of 
reasonable efforts to secure this medium."




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] gromacs on Lynnfield processors

[Guilherme Menegon Arantes]

Hi folks,

Does anyone have timings/benchmarks for GMX running on Intel processors
codename Lynnfield, like Xeon X34??, Core i7 8?? or yet Core i5 7?? .
I am looking for both 1-node multi(4)-thread runs as well as multi-node 
MPI runs. In particular, I am wondering how the cheaper but slower DMI
chipset/bus compares with QuickPath based machines.

Cheers,

Guilherme

--

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Instituto de Química
Universidade de São Paulo, Brasil

http://gaznevada.iq.usp.br/
___

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[gmx-users] How to include FE2+ in ions.itp ?

[Tanos Franca]

Dear GROMACS users,
We're trying to perform a MD simulation of a system with a hematin 
group but realized that GROMACS does not have parameters for the ion 
FE2+. We tried to include the parametrs in the file ions.itp but did not 
suceed yet. Does anybody knows the right procedure to introduce this 
ions into the file ions.itp ? Do we have to change anything more in 
order to GROMACS recognize the new ion ?

With my best regards,
Tanos C. C. Franca.
Coordinator of the Graduate Program in Chemistry
Military Institute of Engineering.
Rio de Janeiro/RJ
Brazil.



Em 05/01/2011 10:47, gmx-users-requ...@gromacs.org escreveu:

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Today's Topics:

1. Re: Library file in.m2p not found (Justin A. Lemkul)
2. Warning about (short) potential interruption - movingDNS
   servers for gromacs.org (Erik Lindahl)
3. Re: Library file in.m2p not found (ahmet y?ld?r?m)
4. HFIP solvent box... (sharada)
5. Re: HFIP solvent box... (Justin A. Lemkul)


--

Message: 1
Date: Wed, 05 Jan 2011 06:45:52 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Library file in.m2p not found
To: Discussion list for GROMACS users
Message-ID:<4d2459f0.2020...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-9; format=flowed



ahmet yýldýrým wrote:

Dear Mark,

I am using the Gromacs on the Ubuntu for month but have not encountered
any problems.I did a search in the file system of Ubuntu. I do not have
a GMXLIB folder in a file system.

What should I do?


If you're telling xpm2ps to use in.m2p, that file has to exist somewhere.  The
error message is telling you that it does not exist in the working directory
(i.e., the directory where you're issuing the command), or the standard Gromacs
library directory
(http://www.gromacs.org/Documentation/Terminology/Environment_Variables#GMXLIB).

If you tell any Gromacs tool to use certain input, it has to exist; Gromacs
isn't going to magically create all the proper files for you.

-Justin


05 Ocak 2011 10:42 tarihinde Mark Abrahammailto:mark.abra...@anu.edu.au>>  yazdý:

 On 5/01/2011 7:37 PM, ahmet yýldýrým wrote:

 Dear users,

 I receive the following error when I entered the command "xpm2ps
 -f ss.xpm -o ss.eps -di in.m2p"
 Fatal error:
 Library file in.m2p not found in current dir nor in default
 directories.
 (You can set the directories to search with the GMXLIB path
 variable)

 I am using the Gromacs 4.05 on the Ubuntu 9.1 Operation System.
 I installed the Gromacs from Synaptic Package Manager.
 I used echo $GMXDATA but it did not show anything. The pdb2gmx,
 g_gyrate,...etc files are in the directory /usr/bin/.
 The GMXRC file is in the directory
 /usr/share/gromacs/shell-specific.


 Are you following these instructions?
 
http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation

 Mark
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Re: [gmx-users] How to include FE2+ in ions.itp ?

[Justin A. Lemkul]

Tanos Franca wrote:

Dear GROMACS users,
We're trying to perform a MD simulation of a system with a hematin 
group but realized that GROMACS does not have parameters for the ion 
FE2+. We tried to include the parametrs in the file ions.itp but did not 
suceed yet. Does anybody knows the right procedure to introduce this 


It would be helpful to know exactly where you're stuck, otherwise we're left 
guessing as to what you've tried.


ions into the file ions.itp ? Do we have to change anything more in 
order to GROMACS recognize the new ion ?


You may have to introduce a new atom type into the .atp file, and set nonbonded 
parameters for it in ffnonbonded.itp, but also be aware that a crude 
representation of a transition metal as a normal point charge may not be 
terribly accurate:


http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

Also, please do not send messages that copy the entire digest (or any unrelated 
content, for that matter).  It confuses the archive.


-Justin


With my best regards,
Tanos C. C. Franca.
Coordinator of the Graduate Program in Chemistry
Military Institute of Engineering.
Rio de Janeiro/RJ
Brazil.


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_msd Utility - (Unexpected) Different Results Depending on Output Flag

[Solomon Berman]

Greetings friends!

I have a question this morning about the g_msd utility related to the output 
generated by different flags.

I'm working with an LJ Liquid and am trying to determine the diffusion constant 
for the system.  I'm employing both the Einstein formulation and the Green Kubo 
formula.  Obviously, for the Einstein equation, I need the mean square 
displacement versus time.  The box I am using is cubic, with a length of a side 
of 3.602 nm. 

Now, when I pass the flag -o for an output (to get the data of the MSD of the 
system versus time) with g_msd, and plot the results in xmgrace, I find that 
the slope of the resulting graph continuously increases linearly once in the 
diffusion regime until the end of the simulation time.  However, if I pass the 
flag -mol (to get the average MSD per atom) alongside -o, the curve saturates 
at two-thirds of the maximum mean square displacement and the slope goes to 
zero.

I would like to inquire as to why I receive two different results between 
"g_msd -o" and "g_msd -o -mol"?  In particular, is it possible that the 
boundary conditions are treated differently for each output, where -o ignores 
the periodic boundary conditions and -mol uses the periodic boundary 
conditions?  I have tried combing the internet, and the man pages, and haven't 
been able to find anything on the reason for the difference in results.

Thank you, again, for the help everyone is so willing to provide a neophyte 
like myself!

Best,

Solomon Berman
Chemistry Department
Boston University--
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[gmx-users] Sampling windows

[Gavin Melaugh]

Dear all

I have generated a PMF curve for introducing a guest molecule into a
host molecule using the umbrella sampling method. The curve seems fine,
but there are no overlaps between histograms in the barrier region. To
circumvent this I have added more windows in this region and to ensure
sampling have increased the force constant only in this region. The
windows in this problematic region are now not equally spaced. Does this
matter for g_WHAM? Could someone please reply to me on this matter as it
has been a sticking point for me for quite sometime?

Many thanks
Gavin
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Re: [gmx-users] Sampling windows

[XAvier Periole]

On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote:


Dear all

I have generated a PMF curve for introducing a guest molecule into a
host molecule using the umbrella sampling method. The curve seems  
fine,

but there are no overlaps between histograms in the barrier region. To
circumvent this I have added more windows in this region and to ensure
sampling have increased the force constant only in this region. The
windows in this problematic region are now not equally spaced. Does  
this

matter for g_WHAM?

Nope it does not matter.

Could someone please reply to me on this matter as it
has been a sticking point for me for quite sometime?

Many thanks
Gavin
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[gmx-users] md simulation for ternary complex

[kala]

Dear All,

I am planning to perform a simulation of a protein ternary complex with 2
ligands and Zn molecule. The protein has 2 chains with 430aa.Is it possible
to do simulation for the protein complex. I have got sufficient hardware
configuration for the dynamics study. As am new to perform such complex
simulations kindly help me to start with.

kala bharath
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Re: [gmx-users] md simulation for ternary complex

[Justin A. Lemkul]

kala wrote:

Dear All,

I am planning to perform a simulation of a protein ternary complex with 
2 ligands and Zn molecule. The protein has 2 chains with 430aa.Is it 
possible to do simulation for the protein complex. I have got sufficient 
hardware configuration for the dynamics study. As am new to perform such 
complex simulations kindly help me to start with.




You can certainly simulate such a complex, but it may not be very easy.  You 
should start with basic tutorial material, including the tutorial about a 
drug-enzyme complex to get yourself familiarized with proper topology organization.


http://www.gromacs.org/Documentation/Tutorials#General

Then, you should prepare yourself for the potentially arduous task of proper 
ligand parameterization.  This is an advanced topic, so be prepared to invest a 
significant amount of time in getting ligand parameters right.  This may be a 
matter of weeks or months, if done properly.  PRODRG is not sufficient for 
generating reliable parameters, though this is not stated in the drug-enzyme 
tutorial.


http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

The other complication is the Zn ion.  Proper treatment of transition metals is 
not trivial, and if this residue plays some important role in the function of 
the protein, a standard MM treatment may not be appropriate.  See the above 
Parameterization page, particularly the Exotic Species section.


-Justin



kala bharath



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Sampling windows

[Gavin Melaugh]

Hi Xavier

Many thanks for the reply. When I compare the two curves
Curve 1) lack of overlap in barrier region; force constant = 1000
Curve 2) with increased number of sampling windows with increased force
constant (note I have only increased the force constant of the windows
in the barrier region).
Force constant =1000, Force constant in barrier region  = 5000

The barrier increases due to better sampling in this region (expected),
but the rest of the curve in 2) is shifted upward compared to curve 1).
Why is this so when the only difference is the increased number of
windows and force constant in one region?

Gavin



XAvier Periole wrote:
>
> On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote:
>
>> Dear all
>>
>> I have generated a PMF curve for introducing a guest molecule into a
>> host molecule using the umbrella sampling method. The curve seems fine,
>> but there are no overlaps between histograms in the barrier region. To
>> circumvent this I have added more windows in this region and to ensure
>> sampling have increased the force constant only in this region. The
>> windows in this problematic region are now not equally spaced. Does this
>> matter for g_WHAM?
> Nope it does not matter.
>> Could someone please reply to me on this matter as it
>> has been a sticking point for me for quite sometime?
>>
>> Many thanks
>> Gavin
>> -- 
>> 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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Re: [gmx-users] Sampling windows

[XAvier Periole]

On Jan 5, 2011, at 5:01 PM, Gavin Melaugh wrote:


Hi Xavier

Many thanks for the reply. When I compare the two curves
Curve 1) lack of overlap in barrier region; force constant = 1000
Curve 2) with increased number of sampling windows with increased  
force

constant (note I have only increased the force constant of the windows
in the barrier region).
Force constant =1000, Force constant in barrier region  = 5000

The barrier increases due to better sampling in this region  
(expected),
but the rest of the curve in 2) is shifted upward compared to curve  
1).

Why is this so when the only difference is the increased number of
windows and force constant in one region?
the relative position of the regions on the left and right of your  
"barrier"

region is completely depending on the barrier region!

you may have overestimated the difference between bound/unbound states
because the energy barrier region was not sampled.

Note also that cure one is simply wrong so comparing to it is dangerous.

You have to be careful that you might still not have a converged  
sampling:

you might have overlap of your histograms on the reaction coordinate but
other degrees of freedom are not fully sampled ... that might result  
in a

funny and wrong profile. You might want to look at your simulations for
funny things ...



Gavin



XAvier Periole wrote:


On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote:


Dear all

I have generated a PMF curve for introducing a guest molecule into a
host molecule using the umbrella sampling method. The curve seems  
fine,
but there are no overlaps between histograms in the barrier  
region. To
circumvent this I have added more windows in this region and to  
ensure

sampling have increased the force constant only in this region. The
windows in this problematic region are now not equally spaced.  
Does this

matter for g_WHAM?

Nope it does not matter.

Could someone please reply to me on this matter as it
has been a sticking point for me for quite sometime?

Many thanks
Gavin
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Re: [gmx-users] Sampling windows

[Gavin Melaugh]

Hi Xavier

Many thanks. Two more quick questions (both refering to barrier region):
Does the value of the force constant affect the height of the barrier
providing that there is reasonable overlap? Obviously there is a
compromise between the size of the constant and the number of windows.
If I increase the force constant and number of windows to obtain a high
density of sampling, does this give a more accurate curve?

Gavin

XAvier Periole wrote:
>
> On Jan 5, 2011, at 5:01 PM, Gavin Melaugh wrote:
>
>> Hi Xavier
>>
>> Many thanks for the reply. When I compare the two curves
>> Curve 1) lack of overlap in barrier region; force constant = 1000
>> Curve 2) with increased number of sampling windows with increased force
>> constant (note I have only increased the force constant of the windows
>> in the barrier region).
>> Force constant =1000, Force constant in barrier region  = 5000
>>
>> The barrier increases due to better sampling in this region (expected),
>> but the rest of the curve in 2) is shifted upward compared to curve 1).
>> Why is this so when the only difference is the increased number of
>> windows and force constant in one region?
> the relative position of the regions on the left and right of your
> "barrier"
> region is completely depending on the barrier region!
>
> you may have overestimated the difference between bound/unbound states
> because the energy barrier region was not sampled.
>
> Note also that cure one is simply wrong so comparing to it is dangerous.
>
> You have to be careful that you might still not have a converged
> sampling:
> you might have overlap of your histograms on the reaction coordinate but
> other degrees of freedom are not fully sampled ... that might result in a
> funny and wrong profile. You might want to look at your simulations for
> funny things ...
>
>>
>> Gavin
>>
>>
>>
>> XAvier Periole wrote:
>>>
>>> On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote:
>>>
 Dear all

 I have generated a PMF curve for introducing a guest molecule into a
 host molecule using the umbrella sampling method. The curve seems
 fine,
 but there are no overlaps between histograms in the barrier region. To
 circumvent this I have added more windows in this region and to ensure
 sampling have increased the force constant only in this region. The
 windows in this problematic region are now not equally spaced. Does
 this
 matter for g_WHAM?
>>> Nope it does not matter.
 Could someone please reply to me on this matter as it
 has been a sticking point for me for quite sometime?

 Many thanks
 Gavin
 -- 
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>>>
>>
>> -- 
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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Sampling windows

[XAvier Periole]

On Jan 5, 2011, at 6:03 PM, Gavin Melaugh wrote:


Hi Xavier

Many thanks. Two more quick questions (both refering to barrier  
region):

Does the value of the force constant affect the height of the barrier
providing that there is reasonable overlap?
No! The force constant used does not affect the PMF or the barrier.  
Neither

does the number of windows used. The only thing that can affect your
PMF is a change in the sampling you put in ...

Obviously there is a
compromise between the size of the constant and the number of windows.
True! And the objective being to get equilibrated distribution with  
reasonable

overlaps.
If I increase the force constant and number of windows to obtain a  
high

density of sampling, does this give a more accurate curve?

No! The only thing you need is to sample everything. Actually putting a
strong force constant might have the side effect to trap your system and
then you do not sample the "free" degrees of freedom! With weak force
constant you may have to wait very long to obtain an equilibrated  
distribution.


XAvier.


Gavin

XAvier Periole wrote:


On Jan 5, 2011, at 5:01 PM, Gavin Melaugh wrote:


Hi Xavier

Many thanks for the reply. When I compare the two curves
Curve 1) lack of overlap in barrier region; force constant = 1000
Curve 2) with increased number of sampling windows with increased  
force
constant (note I have only increased the force constant of the  
windows

in the barrier region).
Force constant =1000, Force constant in barrier region  = 5000

The barrier increases due to better sampling in this region  
(expected),
but the rest of the curve in 2) is shifted upward compared to  
curve 1).

Why is this so when the only difference is the increased number of
windows and force constant in one region?

the relative position of the regions on the left and right of your
"barrier"
region is completely depending on the barrier region!

you may have overestimated the difference between bound/unbound  
states

because the energy barrier region was not sampled.

Note also that cure one is simply wrong so comparing to it is  
dangerous.


You have to be careful that you might still not have a converged
sampling:
you might have overlap of your histograms on the reaction  
coordinate but
other degrees of freedom are not fully sampled ... that might  
result in a
funny and wrong profile. You might want to look at your simulations  
for

funny things ...



Gavin



XAvier Periole wrote:


On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote:


Dear all

I have generated a PMF curve for introducing a guest molecule  
into a

host molecule using the umbrella sampling method. The curve seems
fine,
but there are no overlaps between histograms in the barrier  
region. To
circumvent this I have added more windows in this region and to  
ensure
sampling have increased the force constant only in this region.  
The
windows in this problematic region are now not equally spaced.  
Does

this
matter for g_WHAM?

Nope it does not matter.

Could someone please reply to me on this matter as it
has been a sticking point for me for quite sometime?

Many thanks
Gavin
--
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Re: [gmx-users] Constraints and efficency

[Elton Carvalho]

On Tue, Jan 4, 2011 at 7:38 PM, Mark Abraham  wrote:
> On 5/01/2011 5:53 AM, Elton Carvalho wrote:
>> [...] Does the larger timestep allowed by eliminating
>> high-frequency O-H vibrations outweigh the time needed by SETTLE?
>
> Most definitely. Typical GROMACS simulations report up to a few percent of
> the total simulation time is spent in dealing with constraints. If the use
> of constraints permitted a 2fs timestep rather than 0.5fs, then it's nearly
> a four-fold speed-up.
>

Thanks :)

So, the larger ts allowed would be indeed the main reason to apply
constraints...

>> Any other reason I failed to notice?
>
> I seem to recall that bond constraints are held to model the essential QM
> nature of interatomic bonds better than a Morse or harmonic potential
> (particularly for bonds to hydrogen). I don't recall a reference for that
> offhand, unfortunately. Perhaps the original SHAKE paper.
>

Ok, I'll take a look at those papers, thank you

>> The only reason I see to constrain movement other than that fraquency
>> shaving (and, of course, isolating some behaviour of interest, but
>> this is case-specific) would be to reduce the number of dimensions of
>> the phase space and save computatuon time, but, as implemented, this
>> doesn't seem possible with the code as is.
>
> Various coarse-graining approaches exist to take advantage of that kind of
> saving, but they also gain from the higher maximum time step.

Oh, yes, coarse-graining methods definitely reduce the complexity of
the system, but I was focusing on all-atom simulations in my message.

Again, thank you for your response,

Best regards,
-- 
Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
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Re: [gmx-users] Constraints and efficency

[David van der Spoel]

On 2011-01-05 21.44, Elton Carvalho wrote:

On Tue, Jan 4, 2011 at 7:38 PM, Mark Abraham  wrote:

On 5/01/2011 5:53 AM, Elton Carvalho wrote:

[...] Does the larger timestep allowed by eliminating
high-frequency O-H vibrations outweigh the time needed by SETTLE?


Most definitely. Typical GROMACS simulations report up to a few percent of
the total simulation time is spent in dealing with constraints. If the use
of constraints permitted a 2fs timestep rather than 0.5fs, then it's nearly
a four-fold speed-up.



Thanks :)

So, the larger ts allowed would be indeed the main reason to apply
constraints...


No! Harmonic bonds are not good either. This is described in chapter 1 
of the manual.





Any other reason I failed to notice?


I seem to recall that bond constraints are held to model the essential QM
nature of interatomic bonds better than a Morse or harmonic potential
(particularly for bonds to hydrogen). I don't recall a reference for that
offhand, unfortunately. Perhaps the original SHAKE paper.



Ok, I'll take a look at those papers, thank you


The only reason I see to constrain movement other than that fraquency
shaving (and, of course, isolating some behaviour of interest, but
this is case-specific) would be to reduce the number of dimensions of
the phase space and save computatuon time, but, as implemented, this
doesn't seem possible with the code as is.


Various coarse-graining approaches exist to take advantage of that kind of
saving, but they also gain from the higher maximum time step.


Oh, yes, coarse-graining methods definitely reduce the complexity of
the system, but I was focusing on all-atom simulations in my message.

Again, thank you for your response,

Best regards,



--
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[gmx-users] problem running the demo

[Mao Mao]

Hi All,
I am a new user of Gromacs and Linux. I am using Ubuntu 10.10 and installed
Gromacs 4.5.3 following the instructions.
When I ran the demo, I found that when I pressed , the xterm window
which is supposed to appear separately just flashed and disappeared
immediately.
For instance, "the output of the genbox program should appear in a separate
xterm window", but when I pressed  the window flashed and disappeared
immediately. Is there anything wrong that I need to fix or is that the way
it should be?
Best,
Mao
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Re: [gmx-users] Library file in.m2p not found

[Mark Abraham]

On 5/01/2011 8:38 PM, ahmet yıldırım wrote:

Dear Mark,

I am using the Gromacs on the Ubuntu for month buthave not encountered 
any problems.


That's not the question I asked. If you're not using GMXRC properly, or 
doing its work yourself by hand, you will run into problems eventually.


I did a search in the file system of Ubuntu.I do not have a GMXLIB 
folder in a file system.


Nor should you. It's a variable name that contains a directory name, per 
the help text in the error message.


Mark



What should I do?

05 Ocak 2011 10:42 tarihinde Mark Abraham > yazdı:


On 5/01/2011 7:37 PM, ahmet yıldırım wrote:

Dear users,

I receive the following error when I entered the command
"xpm2ps -f ss.xpm -o ss.eps -di in.m2p"
Fatal error:
Library file in.m2p not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path
variable)

I am using the Gromacs 4.05 on the Ubuntu 9.1 Operation
System. I installed the Gromacs from Synaptic Package Manager.
I used echo $GMXDATA but it did not show anything. The
pdb2gmx, g_gyrate,...etc files are in the directory /usr/bin/.
The GMXRC file is in the directory
/usr/share/gromacs/shell-specific.


Are you following these instructions?

http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation

Mark
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Re: [gmx-users] problem running the demo

[Justin A. Lemkul]

Mao Mao wrote:

Hi All,
I am a new user of Gromacs and Linux. I am using Ubuntu 10.10 and 
installed Gromacs 4.5.3 following the instructions. 
When I ran the demo, I found that when I pressed , the xterm 
window which is supposed to appear separately just flashed and 
disappeared immediately. 
For instance, "the output of the genbox program should appear in a 
separate xterm window", but when I pressed  the window flashed 
and disappeared immediately. Is there anything wrong that I need to fix 
or is that the way it should be?


It is possible that something is wrong with the demo, but more likely something 
is wrong with your X window settings.  If you're looking for tutorial material, 
there are far better resources than this simple walkthrough:


http://www.gromacs.org/Documentation/Tutorials

-Justin


Best,
Mao



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Questions concerning Gromacs

[Mark Abraham]

On 5/01/2011 9:09 PM, Thomas Koller wrote:

Mark, thanks for your reply.

The only problem are the improper dihedrals. I show you a example:

[ dihedraltypes ]
;improper ftypephik(phi)  mult
...
A  B  C  D 4  180 5.293   2

Sorry, I use ftype 4, not 2 :)

The impropers are listed in the dihedraltypes. The sequence is A B C D where A 
is the center atom and B, C, D are the surrounding atoms. I think this is right?


When evaluating this function, GROMACS calculates the angle between 
planes ABC and BCD. Whether that angle is what you want to base the 
improper around is something only you know.



Later the impropers are specified in the [dihedrals]:

[dihedrals]
; i   j   k   lftype
...
   1   2   3   4  4

I get the error:
ERROR 1 [file binary_ua.top, line 196]:
   No default Improper Dih. types

Fatal error:
unknown function type 20 in ../../../../src/kernel/convparm.c line 326

line 326 is: case F_VSITE2:

Do you see the error? I don't know what is going wrong.


What are the atom types of atoms 1, 2, 3 and 4? Do they match a 
[dihedraltypes] entry in an .itp file you've #included? Order is 
important, but reverses are OK, IIRC.


Mark
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Re: Re: [gmx-users] Questions concerning Gromacs

[wibke . sudholt]

Dear Email Sender,

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office at the moment and cannot respond to your email. I will be able to handle 
your request starting again Monday, January 10, 2011.

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Re: [gmx-users] Query about use of coulombtype for LIE in gromacs

[Mark Abraham]

On 5/01/2011 7:55 PM, devawati dutta wrote:

Dear Sir,
  Thanks for your prompt answer. In LIE method, if I will 
not use the PME for coulombtype, then what is suitable for it? In 
gromacs manual, there are several options under coulomb type.Which one 
I will select for coulombtype and Vdwtype in .mdp file?


You should read about the LIE method and choose the GROMACS 
electrostatics method that best suits your context and force field.


Mark
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[gmx-users] Re: Average box size

[Navjeet Ahalawat]

Hi Tsjerk,

Thanks for your more clarification, but when I am running the command
editconf -f pr.gro -o new_box.gro -density 1.04364e+03 (where pr.gro
is end.gro) the results I am getting are...

Read 12348 atoms
Volume: 97.5411 nm^3, corresponds to roughly 43800 electrons
Velocities found
system size :  7.244  4.992  5.194 (nm)
center  :  0.534  2.027  2.438 (nm)
box vectors :  4.444  4.857  5.138 (nm)
box angles  :  88.30 107.40 112.20 (degrees)
box volume  :  97.54   (nm^3)
Volume  of input 97.5411 (nm^3)
Massof input 95417.2 (a.m.u.)
Density of input 1624.38 (g/l)
Scaling all box vectors by 1.1589
new system size :  8.395  5.785  6.019
new center  :  0.618  2.349  2.825 (nm)
new box vectors :  5.150  5.628  5.955 (nm)
new box angles  :  88.30 107.40 112.20 (degrees)
new box volume  : 151.82   (nm^3)

This new box volume is not matching with my average box volume
(97.6118). I think problem is with mass because my system (box)
contains 1 protein, 2595 water molecules(Tip4p-EW),and 8 CL ions. So
the total mass should be 61307.332 a.m.u. (14313.332+18*2595+8*35.50)
and when I am calculating the density using this mass and average
volume (97.6118), its coming 1042.94 g/l which is approximately same
to average density (1.04364e+03).

I would greatly appreciate if you could please let me know why
editconf is giving mass different from actual mass (my calculated
mass).

Thanks & Regards,
Navjeet Ahalawat



>Navjeet,

>The average lengths you already mentioned in your first mail:

>>>         Box-X          Box-Y          Box-Z         Volume   Density (SI)
>>>   4.44479e+00    4.49781e+00    4.88259e+00    9.76118e+01    1.04364e+03

>You also mentioned you used isotropic PC:

>>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
>>> 107.40, 112.20) and Isotropic pressure coupling.

Then the box only gets scaled during the simulation, with no changes
of one vector relative to the other. Then to set the box of your end
structure to match the average volume also means scaling. That means
taking the ratio of the average X-length and the actual X-length, and
feed that as a scaling factor...
Then again, you don't actually need to calculate anything, just think
a little bit harder. You're average box comes with an average density.
editconf has an option to scale the box to get a specific density, so
you can fetch the average density, given above and do:

editconf -f end.gro -o average.gro -density 1.04364e+03

Then go on with your NVT run using average.gro as input (don't forget
the energy minimization!).

Hope it helps,

Tsjerk

On Tue, Jan 4, 2011 at 3:03 PM, Navjeet Ahalawat  wrote:
> Hi Tsjerk,
>
> Thanks for your clarifications. I still couldn't follow how I can calculate
> the scaling factor. As I wrote earlier, I ran NPT simulation for 
> equilibration.
>
> Now to start the NVT production run, I need to know the AVERAGE LENGTHS
> (a, b, c) of the triclinic box vectors so that I can generate the
> triclinic box with the
> help of the corresponding angles (88.30, 107.40, 112.20) using the
> command "editconf".
>
> Now I understand that the box-x, box-y, and box-z represents the diagonal
> elements of triangular matrix and the average volume of my triclinic box
> is the product of these diagonal elements. However, as I understand the
> command "editconf" requires the length of the box vectors and the three angles
> to create a triclinic box.
>
> I would greatly appreciate if you could please let me know the command(s) that
> I would require to use to achieve my goal.
>
>
>
>
> Message: 4
> Date: Tue, 4 Jan 2011 12:35:36 +0100
> From: Tsjerk Wassenaar 
> Subject: Re: [gmx-users] Re: Average box size
> To: Discussion list for GROMACS users 
> Message-ID:
>        
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Navjeet,
>
> These you had in the log file as you showed in your mail. Note that
> you use isotropic pressure coupling, so you just need to calculate a
> scaling factor, which you can give to editconf to change your system
> to match the average box size.
>
>  Cheers,
>
> Tsjerk
>
> On Tue, Jan 4, 2011 at 12:03 PM, Navjeet Ahalawat  
> wrote:
>> Hi Tsjerk,
>>
>> Thanks for reply, Please can you tell me how can I get the average box
>> length (a b c) of my triclinic box for my next step.
>>
>>> Message: 2
>>> Date: Mon, 3 Jan 2011 18:17:15 +0100
>>> From: Tsjerk Wassenaar 
>>> Subject: Re: [gmx-users] Average box size
>>> To: Discussion list for GROMACS users 
>>> Message-ID:
>>>        
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> Hi Navjeet,
>>>
>>> The box is defined as a triangular matrix, so the volume equals the product
>>> of the diagonal elements.
>>>
>>> Hope it helps,
>>>
>>> Tsjerk
>>>
>>> On Jan 3, 2011 5:57 PM, "Navjeet Ahalawat"  wrote:
>>>
>>> Hi all
>>>
>>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
>>> 107.40, 112.20) and Isotropic pressure coupling. Now i want to use
>>> ave

Re: [gmx-users] Re: Average box size

[Mark Abraham]

On 01/06/11, Navjeet Ahalawat   wrote:
> Hi Tsjerk,
> 
> Thanks for your more clarification, but when I am running the command
> editconf -f pr.gro -o new_box.gro -density 1.04364e+03 (where pr.gro
> is end.gro) the results I am getting are...
> 


Please double check the contents of pr.gro are what you think they are. The 
simplest explanation is a file mismatch...


> 
> Read 12348 atoms
> 

Does that make sense?


> 
> Volume: 97.5411 nm^3, corresponds to roughly 43800 electrons
> Velocities found
>     system size :  7.244  4.992  5.194 (nm)
>     center  :  0.534  2.027  2.438 (nm)
>     box vectors :  4.444  4.857  5.138 (nm)
>     box angles  :  88.30 107.40 112.20 (degrees)
>     box volume  :  97.54   (nm^3)
> Volume  of input 97.5411 (nm^3)
> Mass    of input 95417.2 (a.m.u.)
> Density of input 1624.38 (g/l)
> Scaling all box vectors by 1.1589
> new system size :  8.395  5.785  6.019
> new center  :  0.618  2.349  2.825 (nm)
> new box vectors :  5.150  5.628  5.955 (nm)
> new box angles  :  88.30 107.40 112.20 (degrees)
> new box volume  : 151.82   (nm^3)
> 
> This new box volume is not matching with my average box volume
> (97.6118). I think problem is with mass because my system (box)
> contains 1 protein, 2595 water molecules(Tip4p-EW),and 8 CL ions. So
> 

I wondered if editconf was assigning mass to TIP4P vacant sites, but they'd 
have to have mass 13.1 per solvent molecule to make that work...

Mark


> 
> the total mass should be 61307.332 a.m.u. (14313.332+18*2595+8*35.50)
> and when I am calculating the density using this mass and average
> volume (97.6118), its coming 1042.94 g/l which is approximately same
> to average density (1.04364e+03).
> 
> I would greatly appreciate if you could please let me know why
> editconf is giving mass different from actual mass (my calculated
> mass).
> 
> Thanks & Regards,
> Navjeet Ahalawat
> 
> 
> 
> >Navjeet,
> 
> >The average lengths you already mentioned in your first mail:
> 
> >>>         Box-X          Box-Y          Box-Z         Volume   Density (SI)
> >>>   4.44479e+00    4.49781e+00    4.88259e+00    9.76118e+01    1.04364e+03
> 
> >You also mentioned you used isotropic PC:
> 
> >>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
> >>> 107.40, 112.20) and Isotropic pressure coupling.
> 
> Then the box only gets scaled during the simulation, with no changes
> of one vector relative to the other. Then to set the box of your end
> structure to match the average volume also means scaling. That means
> taking the ratio of the average X-length and the actual X-length, and
> feed that as a scaling factor...
> Then again, you don't actually need to calculate anything, just think
> a little bit harder. You're average box comes with an average density.
> editconf has an option to scale the box to get a specific density, so
> you can fetch the average density, given above and do:
> 
> editconf -f end.gro -o average.gro -density 1.04364e+03
> 
> Then go on with your NVT run using average.gro as input (don't forget
> the energy minimization!).
> 
> Hope it helps,
> 
> Tsjerk
> 
> On Tue, Jan 4, 2011 at 3:03 PM, Navjeet Ahalawat  
> wrote:
> > Hi Tsjerk,
> >
> > Thanks for your clarifications. I still couldn't follow how I can calculate
> > the scaling factor. As I wrote earlier, I ran NPT simulation for 
> > equilibration.
> >
> > Now to start the NVT production run, I need to know the AVERAGE LENGTHS
> > (a, b, c) of the triclinic box vectors so that I can generate the
> > triclinic box with the
> > help of the corresponding angles (88.30, 107.40, 112.20) using the
> > command "editconf".
> >
> > Now I understand that the box-x, box-y, and box-z represents the diagonal
> > elements of triangular matrix and the average volume of my triclinic box
> > is the product of these diagonal elements. However, as I understand the
> > command "editconf" requires the length of the box vectors and the three 
> > angles
> > to create a triclinic box.
> >
> > I would greatly appreciate if you could please let me know the command(s) 
> > that
> > I would require to use to achieve my goal.
> >
> >
> >
> >
> > Message: 4
> > Date: Tue, 4 Jan 2011 12:35:36 +0100
> > From: Tsjerk Wassenaar 
> > Subject: Re: [gmx-users] Re: Average box size
> > To: Discussion list for GROMACS users 
> > Message-ID:
> >        
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Hi Navjeet,
> >
> > These you had in the log file as you showed in your mail. Note that
> > you use isotropic pressure coupling, so you just need to calculate a
> > scaling factor, which you can give to editconf to change your system
> > to match the average box size.
> >
> >  Cheers,
> >
> > Tsjerk
> >
> > On Tue, Jan 4, 2011 at 12:03 PM, Navjeet Ahalawat  
> > wrote:
> >> Hi Tsjerk,
> >>
> >> Thanks for reply, Please can you tell me how can I get the average box
> >> length (a b c) of my triclinic box for my next step.
> >>
> >>> Message: 2
> >>> Date: Mon,