Re: [gmx-users] Tables with forcefield

[ms]

Hi,

Clarification: I may not be able to help you directly but I can suggest 
you which information you should perhaps give us to enable people more 
knowledgeable than me to help.


On 24/09/10 17:33, Sai Pooja wrote:

I use combination rule 1; but I also define all tabulated interactions for
all possible *pairs* under the [ nonbond_params ] section, so the
combination rule actually doesn't matter much.



Are you suggesting that I can change the combination rule in the
forcefield.itp file but I must also supply a table for pairs using -tablep
option for this to work?


I am not "suggesting": I am only saying what I am doing :)


Does this mean that one cannot use tables with forcefield parameters?






Clarification: I want to use forcefield parameters with user defined tables
i.e. I want to use sigma and epsilon values generated by pdb2gmx along
with a user-defined modified potential energy function using tables.


This is absolutely doable -I do it everyday, in fact. So, don't despair. :)

Now, it seems that you talked about a problem with convergence of the 
SETTLE algorithm. I know little about it, but, couldn't it simply be 
that your tables are "wrong" (that is, they don't play well with 
algorithms?) What is their shape, actually, and on which 
atomtypes/groups are you applying your table? What is the forcefield you 
are using along with the table?


M.
--
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] Re: MPI

[Justin A. Lemkul]

simon sham wrote:

Hi,
Our system system administrator configured the software with --MPI 
option according to the installation instructions. He told me there were 
lots of warning messages when he did it. My related question is that 
since there is LAM/MPI out there as well, can GROMACS 4.5 be configured 
with OPENMPI?
 


Yes, in fact OpenMPI has made LAM obsolete.

-Justin


Thanks in advance,
 
Simon Sham 



Hi,
This is the same email that I'd sent yesterday but has not got posted?
Hi,
I have some questions about installation of GROMACS with MPI.
Our system administrator
has installed the 4.5.1 version in our system. When I tested the
software with "openmpi/openmpi-1.3.3-gcc/bin/mpirun" with mdrun_mpi, I
got all sorts of error message such as
"opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol
`ompi_mpi_byte' has different size in shared object, consider
re-linking", and many others.

My questions:
1. When I prepare my system for simulations, do I have to
consistently use *_mpi functions in gromacs_4.5.1_mpi directory?
2. Are there any details that I need to pay attention when I
configure the software with openmpi?

Thanks for your help in advance.

Best,

Simon Sham




 
-- next part --

An HTML attachment was scrubbed...
URL:

http://lists.gromacs.org/pipermail/gmx-users/attachments/20100924/2a671694/attachment-0001.html

--

Message: 3
Date: Fri, 24 Sep 2010 15:18:27 -0400
From: "Justin A. Lemkul" http://us.mc367.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>
Subject: Re: [gmx-users] MPI
To: Discussion list for GROMACS users http://us.mc367.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>>
Message-ID: <4c9cf983.7010...@vt.edu
<http://us.mc367.mail.yahoo.com/mc/compose?to=4c9cf983.7010...@vt.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


Guess my reply never hit the list, either, but it's in the archive:

http://lists.gromacs.org/pipermail/gmx-users/2010-September/054259.html

-Justin

simon sham wrote:
 > Hi,
 > This is the same email that I'd sent yesterday but has not got
posted?
 > Hi,
 > I have some questions about installation of GROMACS with MPI.
 > Our system administrator has installed the 4.5.1 version in our
system.
 > When I tested the software with
"openmpi/openmpi-1.3.3-gcc/bin/mpirun"
 > with mdrun_mpi, I got all sorts of error message such as
 > "opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol
 > `ompi_mpi_byte' has different size in shared object, consider
 > re-linking", and many others.
 >
 > My questions:
 > 1. When I prepare my system for simulations, do I have to
consistently
 > use *_mpi functions in gromacs_4.5.1_mpi directory?
 > 2. Are there any details that I need to pay attention when I
configure
 > the software with openmpi?
 >
 > Thanks for your help in advance.
 >
 > Best,
 >
 > Simon Sham
 >
 >

-- 



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







--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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] Re: MPI

[simon sham]

Hi,
Our system system administrator configured the software with --MPI option 
according to the installation instructions. He told me there were lots of 
warning messages when he did it. My related question is that since there is 
LAM/MPI out there as well, can GROMACS 4.5 be configured with OPENMPI?
 
Thanks in advance,
 
Simon Sham 




Hi,
This is the same email that I'd sent yesterday but has not got posted?
Hi,
I have some questions about installation of GROMACS with MPI.
Our system administrator
has installed the 4.5.1 version in our system. When I tested the
software with "openmpi/openmpi-1.3.3-gcc/bin/mpirun" with mdrun_mpi, I
got all sorts of error message such as
"opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol
`ompi_mpi_byte' has different size in shared object, consider
re-linking", and many others.

My questions:
1. When I prepare my system for simulations, do I have to consistently use 
*_mpi functions in gromacs_4.5.1_mpi directory?
2. Are there any details that I need to pay attention when I configure the 
software with openmpi?

Thanks for your help in advance.

Best,

Simon Sham




      
-- next part --
An HTML attachment was scrubbed...
URL: 
http://lists.gromacs.org/pipermail/gmx-users/attachments/20100924/2a671694/attachment-0001.html

--

Message: 3
Date: Fri, 24 Sep 2010 15:18:27 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] MPI
To: Discussion list for GROMACS users 
Message-ID: <4c9cf983.7010...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


Guess my reply never hit the list, either, but it's in the archive:

http://lists.gromacs.org/pipermail/gmx-users/2010-September/054259.html

-Justin

simon sham wrote:
> Hi,
> This is the same email that I'd sent yesterday but has not got posted?
> Hi,
> I have some questions about installation of GROMACS with MPI.
> Our system administrator has installed the 4.5.1 version in our system. 
> When I tested the software with "openmpi/openmpi-1.3.3-gcc/bin/mpirun" 
> with mdrun_mpi, I got all sorts of error message such as 
> "opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol 
> `ompi_mpi_byte' has different size in shared object, consider 
> re-linking", and many others.
> 
> My questions:
> 1. When I prepare my system for simulations, do I have to consistently 
> use *_mpi functions in gromacs_4.5.1_mpi directory?
> 2. Are there any details that I need to pay attention when I configure 
> the software with openmpi?
> 
> Thanks for your help in advance.
> 
> Best,
> 
> Simon Sham
> 
> 

-- 


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







  -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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] data.xvg for g_kinetics ?

[Justin A. Lemkul]

feng chen wrote:

Hi gromacs user,
 
   We recently ran in this problem when try to analyise our REMD 
trajectories. g_kinetics module will be used for such kinda analysis, 
however it looks like we need provide 2 xvgs file as input. The temp.xvg 
we can get from demux.pl  and the other one (data.xvg) 
we are not sure how to get . To get a better understanding of this  
g_kinetics module, we have read through that reference paper, but 
throught the that whole paper (Phys. Rev. Lett. 96, 
) there's no hint about 
how to prepare this data.xvg file.
 
   So, we were wondering , can anybody kindly let us know how did u guys 
get this data.xvg file?
 


The content of the second input file is dependent upon how you assess folding. 
The paper you reference, IIRC, used RMSD as this indicator.  In principle, you 
should be able to use other metrics like R(g), native contacts, etc.


-Justin


   thanks a lot
 
   Kevin
 



--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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] local pressure

[Vitaly Chaban]

Hi all,

Is it possible to compute local pressure in gromacs (e.g. according to
Hoover et al., 1991)?

Thanks in advance.

-- 
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America
-- 
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] data.xvg for g_kinetics ?

[feng chen]

Hi gromacs user,

   We recently ran in this problem when try to analyise our REMD
trajectories. g_kinetics module will be used for such kinda analysis,
however it looks like we need provide 2 xvgs file as input. The temp.xvg we
can get from demux.pl and the other one (data.xvg) we are not sure how to
get . To get a better understanding of this  g_kinetics module, we have read
through that reference paper, but throught the that whole paper (Phys. Rev.
Lett. 96, ) there's no hint
about how to prepare this data.xvg file.

   So, we were wondering , can anybody kindly let us know how did u guys get
this data.xvg file?

   thanks a lot

   Kevin
-- 
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] vanadium non-bonded parameters

[Alexandre Suman de Araujo]

Hi Gonçalo

If you do not find the parameters for vanadium, you could try to develop 
them using experimental physical chemistry properties of the ion and MD 
simulations.
In the following reference you can find a suitable method to develop 
them that worked for me in the development of Pb and Cd ion parameters:


Alexandre S. de Araujo,*,† Milton T. Sonoda,† Oscar E. Piro,‡ and 
Eduardo E. Castellano, "Development of New Cd2+ and Pb2+ Lennard-Jones 
Parameters for Liquid Simulations", J. Phys. Chem. B 2007, 111, 2219-2224


Cheers

**
Alexandre Suman de Araujo*
Faculdade de Ciências Farmacêuticas de Ribeirão Preto*
Universidade de São Paulo*
Dep. de Física e Química *
Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br*
Av. do Café, s/n° * e-mail: ale.su...@gmail.com  *
CEP: 14040-903* Phone: +55 (16) 3602-4172*
Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222*
**


Em 24-09-2010 16:21, Gonçalo C. Justino escreveu:

Dear gmx'ers,

Does anyone know of any (published or not) non-bonded parameters for
vanadium species for any of the forcefields implemented in GROMACS ?

If not, my question is: what is the meaning of the null values for
sigma and epsilon in, e.g., amber03, for Fe:

FE  26  55.000.  A   0.0e+00  0.0e+00
[from the ffnonbonded.itp file]

Thks for any help,
Gonçalo
   

--
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] CHARMM -> gromacs epsilon and sigma conversiion

[Jianhui Tian]

eps(charmm)*4.184=epsilon(Gromacs)
0.15*4.184=0.6276

Rmin/2(Charmm)*2/(2^1/6)=sigma(Gromacs)
2.27*2/(2^(1/6))=0.404468(nm)

Cheers,
Jianhui

Date: Fri, 24 Sep 2010 15:55:44 +0200
From: "ABEL Stephane 175950" 
Subject: [gmx-users] CHARMM -> gromacs epsilon and sigma conversiion
   factors
To: 
Message-ID:
   
Content-Type: text/plain;   charset="iso-8859-1"

Hi all,

I would like to add new  atom types in the charmm27.ff for futures
simulations of glyolipids in water with gmx 4.5.1. I have finished to
convert the bonded in GROMACS format. However, I am little puzzled with the
vdW paramaters. I would like to know how to convert them (i.e. what are the
conversion factors used to convert the CHARMM sigma and epsilon parameters
to gromacs sigma and epsilon values ?).

For example for the chloride atom CLA

CHARMM 27

; atom  ignoredepsilon  Rmin/2   ignored   eps,1-4   Rmin/2,1-4
CLA  0.0   -0.150 2.27  ! chloride

GROMACS ffcharmmnb.itp

;name at.num mass charge ptype sigma epsilon
CLA 17 35.45 -1.00 A 0.404468018036 0.6276

Thanks in advance for your help

Stefane
-- 
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] vanadium non-bonded parameters

[Gonçalo C . Justino]

Dear gmx'ers,

Does anyone know of any (published or not) non-bonded parameters for
vanadium species for any of the forcefields implemented in GROMACS ?

If not, my question is: what is the meaning of the null values for
sigma and epsilon in, e.g., amber03, for Fe:

FE  26  55.000.  A   0.0e+00  0.0e+00
[from the ffnonbonded.itp file]

Thks for any help,
Gonçalo
--
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] MPI

[Justin A. Lemkul]

Guess my reply never hit the list, either, but it's in the archive:

http://lists.gromacs.org/pipermail/gmx-users/2010-September/054259.html

-Justin

simon sham wrote:

Hi,
This is the same email that I'd sent yesterday but has not got posted?
Hi,
I have some questions about installation of GROMACS with MPI.
Our system administrator has installed the 4.5.1 version in our system. 
When I tested the software with "openmpi/openmpi-1.3.3-gcc/bin/mpirun" 
with mdrun_mpi, I got all sorts of error message such as 
"opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol 
`ompi_mpi_byte' has different size in shared object, consider 
re-linking", and many others.


My questions:
1. When I prepare my system for simulations, do I have to consistently 
use *_mpi functions in gromacs_4.5.1_mpi directory?
2. Are there any details that I need to pay attention when I configure 
the software with openmpi?


Thanks for your help in advance.

Best,

Simon Sham




--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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] MPI

[simon sham]

Hi,
This is the same email that I'd sent yesterday but has not got posted?
Hi,
I have some questions about installation of GROMACS with MPI.
Our system administrator
has installed the 4.5.1 version in our system. When I tested the
software with "openmpi/openmpi-1.3.3-gcc/bin/mpirun" with mdrun_mpi, I
got all sorts of error message such as
"opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol
`ompi_mpi_byte' has different size in shared object, consider
re-linking", and many others.

My questions:
1. When I prepare my system for simulations, do I have to consistently use 
*_mpi functions in gromacs_4.5.1_mpi directory?
2. Are there any details that I need to pay attention when I configure the 
software with openmpi?

Thanks for your help in advance.

Best,

Simon Sham




  -- 
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] D-proline

[Tsjerk Wassenaar]

Hi Stefano,

Using C N CA CD instead of C CA N C inverts the improper dihedral. And
unlike all atom force fields, you can start from an L-proline  :)

Cheers,

Tsjerk

On Sep 24, 2010 10:46 AM, "Stefano Pieraccini" 
wrote:



Dear Gromacs users,



I would like to use gromacs to simulate a peptide containing a D-proline
using the opls force field. I guess that, considering that L- and D- PRO
differs only for chirality, the two a.a. topologies should little differ,
and that an improper torsion and/or torsional terms should be modified in
D-PRO topology with respect to L-PRO, but I am not sure on how to modify the
improper torsion ( it is _C CA N CD in L-pro) and if it is correct to do so
or only torsional terms should be modified.



Thank you in advance



Stefano Pieraccini

--
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/Support/Mailing_Lists

Re: [gmx-users] Tables with forcefield

[Sai Pooja]

Hi,

Clarifications inline...
On Wed, Sep 22, 2010 at 2:01 PM, ms  wrote:

> On 21/09/10 20:45, Sai Pooja wrote:
>
>> I wanted to change the interactions between the Protein and Solvent so I
>> tried using tables with the potential function scaled by a constant value.
>> I
>> wanted to use this in combination with forcefield parameters (charmm). I
>> changed the combination rule in the forcefield.itp file from '2' to '1'
>> since tables use C6 and C12 values. To test the system I started with
>> default tables.
>>
>> When I run grompp, it generates the .tpr file successfully but in the md
>> simulation using mdrun, settle does not converge. It does not converge for
>> 1
>> water molecule.
>>
>> If I go back to the combination rule '2' in the forcefield.itp file, I get
>> a
>> warning that using combination rule 2 with tables may generate error.
>>
>> With combination rule '2' and cutoff for both vanderwaals and coulombtype,
>> i
>> face no problem.
>>
>
> I use combination rule 1; but I also define all tabulated interactions for
> all possible *pairs* under the [ nonbond_params ] section, so the
> combination rule actually doesn't matter much.


Are you suggesting that I can change the combination rule in the
forcefield.itp file but I must also supply a table for pairs using -tablep
option for this to work?

>
>
> Does this mean that one cannot use tables with forcefield parameters?
>>
>

Clarification: I want to use forcefield parameters with user defined tables
i.e. I want to use sigma and epsilon values generated by pdb2gmx along
with a user-defined modified potential energy function using tables.



>
> I am not sure of understanding with question -can you clarify?
>
> Massimo
>




Pooja

>
> --
> 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
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
-- 
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] D-proline

[Anthony Costa]

On Fri, Sep 24, 2010 at 03:28, Stefano Pieraccini
 wrote:
> I would like to use gromacs to simulate a peptide containing a D-proline
> using the opls force field. I guess that, considering that L- and D- PRO
> differs only for chirality, the two a.a. topologies should little differ,
> and that an improper torsion and/or torsional terms should be modified in
> D-PRO topology with respect to L-PRO, but I am not sure on how to modify the
> improper torsion ( it is _C CA N CD in L-pro) and if it is correct to do so
> or only torsional terms should be modified.

As long as you're using an all-atom forcefield (OPLS, so I assume you
are) there is no reason to need to change any part of your topology.
Simply starting with the correct configuration is perfectly
sufficient. Otherwise though, for UA forcefields, there is no hydrogen
and therefore no configurational constraint. I remember a few
discussions on the mailing list about this issue, I think some from me
a few years ago.

Best,
Anthony
-- 
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] CHARMM -> gromacs epsilon and sigma conversiion factors

[ABEL Stephane 175950]

Hi all,
 
I would like to add new  atom types in the charmm27.ff for futures simulations 
of glyolipids in water with gmx 4.5.1. I have finished to convert the bonded in 
GROMACS format. However, I am little puzzled with the vdW paramaters. I would 
like to know how to convert them (i.e. what are the conversion factors used to 
convert the CHARMM sigma and epsilon parameters to gromacs sigma and epsilon 
values ?).
 
For example for the chloride atom CLA
 
CHARMM 27 
 
; atom  ignoredepsilon  Rmin/2   ignored   eps,1-4   Rmin/2,1-4
CLA  0.0   -0.150 2.27  ! chloride
 
GROMACS ffcharmmnb.itp
 
;name at.num mass charge ptype sigma epsilon
CLA 17 35.45 -1.00 A 0.404468018036 0.6276 
 
Thanks in advance for your help
 
Stefane 
 
--
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] reg QM/MM mdrun error

[Timo M.D. Graen]

There is a page on how to compile mopac and gromacs to enable qm/mm 
simulations:

http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions/compiling_QMMM
as you seem to have all the dependencies now(?), you will have to modify 
and compile both mopac, as well as gromacs as described in the link 
above (Mopac section). If you are not familiar with compiling programs 
from source code I suggest you ask your local system administrator to do 
this.

Good luck

On 09/23/2010 02:39 PM, vidhya sankar wrote:

Dear Timo Thank you for your reply.
i successfullly run pure mopac7-1.11 and Pure MD in gromacs as u said
but still got same error when i run QM/MM mopac/gromacs interface as
follollows

when i trying with AM1/STO-3Gi got error as follows
 > Program mdrun_d, VERSION 4.0.7
 > Source code file: qmmm.c, line: 684
 > Fatal error:
 > Semi-empirical QM only supported with Mopac
 > is there is any installation problem in Mopac/gromacs?. i have
 > succesfully installed No compilation error during installation? THEN
 > WHAT WILL BE THE SOURCE OF ERROR
 > I expecting your worthfull reply

--
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] Problem with pressure coupling

[Ondrej Marsalek]

Dear all,

running a box of neat water with the below mdp file in GROMACS 4.5.1
results in a fast linear increase of the volume of the box, the water
getting torn into clusters. The same simulation in 4.0.7 (with
nstcalcenergy removed, of course) runs just fine, with the box volume
stable and fluctuating. In 4.5.1 the problem can be fixed by setting
nstlist = 1. I assume this would also be the case for other positive
numbers. The same behavior can be seen for the Parrinello-Rahman
barostat. I can of course provide full testcases ready to run, if
needed.

This looks like a bug to me. Can anyone help me resolve this?

Thanks,
Ondrej


; RUN CONTROL PARAMETERS
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 5000
comm-mode= Linear
nstcomm  = 10

; OUTPUT CONTROL OPTIONS
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 100
nstcalcenergy= 10
nstenergy= 100
nstxtcout= 100
xtc-precision= 1000

; NEIGHBORSEARCHING PARAMETERS
nstlist  = -1
ns_type  = grid
pbc  = xyz
periodic_molecules   = no
rlist= 1.3

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = PME-Switch
rcoulomb-switch  = 0.6
rcoulomb = 0.8
vdw-type = Shift
rvdw-switch  = 0.6
rvdw = 0.8
DispCorr = EnerPres
fourierspacing   = 0.12
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
optimize_fft = yes

; OPTIONS FOR WEAK COUPLING ALGORITHMS
Tcoupl   = v-rescale
tc-grps  = system
tau_t= 0.5
ref_t= 300
Pcoupl   = berendsen
Pcoupltype   = isotropic
tau_p= 1
compressibility  = 4.5e-5
ref_p= 1.0

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = no

; OPTIONS FOR BONDS
constraints  = none
-- 
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] reg QM/MM mdrun error

[vidhya sankar]

Dear Timo Thank you for your reply.
 i successfullly run pure mopac7-1.11 and Pure MD in gromacs as u said 
 but still got same  error when i run QM/MM mopac/gromacs interface as 
follollows
  
when i trying with AM1/STO-3Gi got error as follows
> Program 
mdrun_d, VERSION 4.0.7
> Source code file: qmmm.c, line: 684
>
 Fatal error:
> Semi-empirical QM only supported with Mopac
>
 is there is any installation problem in Mopac/gromacs?. i have
> 
succesfully installed No compilation error during installation? THEN
>
 WHAT WILL BE THE SOURCE OF ERROR
> I expecting your worthfull 
reply


--- On Wed, 22/9/10, Timo M.D. Graen  wrote:

From: Timo M.D. Graen 
Subject: Re: [gmx-users] reg QM/MM mdrun error
To: "Discussion list for GROMACS users" 
Date: Wednesday, 22 September, 2010, 8:09 PM

Did you try to run a pure QM job using MOPAC as well as running a pure MD job 
using GROMACS? This might be a good start before trying to mix the two

On 09/22/2010 04:25 PM, vidhya sankar wrote:
> THAHNKS for your reply
> when i trying with AM1/STO-3Gi got error as follows
> Program mdrun_d, VERSION 4.0.7
> Source code file: qmmm.c, line: 684
> Fatal error:
> Semi-empirical QM only supported with Mopac
> is there is any installation problem in Mopac/gromacs?. i have
> succesfully installed No compilation error during installation? THEN
> WHAT WILL BE THE SOURCE OF ERROR
> I expecting your worthfull reply

-- gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] ffyw3f library not found..

[Mark Abraham]

- Original Message -
From: Kamalesh Roy 
Date: Friday, September 24, 2010 21:36
Subject: Re: [gmx-users] ffyw3f library not found..
To: jalem...@vt.edu, Discussion list for GROMACS users 

> Thanks for your answer.
> I have given the command ./configure then make then make install for fftw and 
> then ./configure for gromacs then 
> it returns a command that fftwf library not found. 

Read the GROMACS installation instructions. This is not sufficient for FFTW.

Mark

> 
> I kept the fftw and gromacs file in the same directory /usr/local and was 
> trying to install this.
>  Thank you again.
> 
> On Thu, Sep 23, 2010 at 4:03 PM, Justin A. Lemkul  wrote:
 > 
 > 
>  Kamalesh Roy wrote:
 >  Dear users
 > 
>  I am trying to install Gromacs-4.5 with fftw-3.2.2  in Fedora version 9, 
> when I am trying to install the Groamcs
>  after installing fftw it is giving me an error that ftwf library not found.
 > 
>  Please hep me.
 > 
  > 
>  At the very least you need to provide us with the command you gave.  
> Detailed installation instructions are available on the Gromacs site:
 > 
 > http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions
 > 
>  -Justin
 > 
 >  -- 
>  Regards
>  Kamalesh Roy
 > 
  > 
>  -- 
>  
 > 
>  Justin A. Lemkul
>  Ph.D. Candidate
>  ICTAS Doctoral Scholar
>  MILES-IGERT Trainee
>  Department of Biochemistry
>  Virginia Tech
>  Blacksburg, VA
>  jalemkul[at]vt.edu | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 > 
>  
>  -- 
>  gmx-users mailing listgmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/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
 > 
> > 
> -- 
> Regards
> Kamalesh Roy
> Lecturer 
> Institute of Genetic Engineering, India
 > -- 
> 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/Support/Mailing_Lists

[gmx-users] Getting started - Peptide

[Artur Panczakiewicz]

Dear Gromacs Users,

I'm a freshman and would like to lear how to use GROMACS in my
research starting from tutorial. I've just installed the newest
version and try to repeat all of the steps from the chapter that
describes the preparation of Ribonuclease A to MD simulation. In my
case it is not possible, unfortunatelly. The grompp program crashes
such a way:

---
Program grompp, VERSION 4.5.1
Source code file: toppush.c, line: 1987

Fatal error:
No such moleculetype SOL
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I tried to install GROMACS on other machine with different Linux
distribution but the error in grompp was the same.
What is important, I installed version 4.0.7 and it works well! I
don't have any idea what is going on.
Does anyone have a similar problem?

Regards,
Artur
-- 
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] atomtype problem (was Re: gmx-users Digest, Vol 77, Issue 150)

[Justin A. Lemkul]

lloyd riggs wrote:


Dear Users and Justin,

Included below is the origional message and reply.  The only error message
was " Atom type CH2r not found fatal error ".

After looking at all the files though, I realized if I change everything to
either CH2r or CH2R , it runs.  I don't know if it was somones joke on my


Are you saying there's actually a mixture of both CH2r and CH2R in the pdb2gmx 
topology?  As far as I can tell, all Gromos96 parameter sets (45a3, 53a5, 53a6) 
now use CH2r.  In past versions of Gromacs, 45a3 used CH2r, but 53a5 and 53a6 
used CH2R.



end, or if it is just a typo in the last release.  Basically the nonbonded
atom files and all the other files had seperate lables at least for me



Sounds like someone was playing with your force field files.  Start from a fresh 
Gromacs installation and see if that solves your problem.  Version 4.5.1 is 
internally self-consistent and should have no problems.


-Justin


Well, proline isn't aromatic at all...


yeah I know, the terminal C on the ring can be CHR or CH1 , at least the
definitions are the same...

Origional post:

To: Discussion list for GROMACS users  Message-ID:
<4c9a67de.6060...@vt.edu> Content-Type: text/plain; charset=UTF-8;
format=flowed


I've gone ahead and changed the subject line to potentially attract the 
attention of others who might help.


lloyd riggs wrote:

Dear All,

I'm not sure if this is a bug or not.  I downloaded and installed the new 
version of Gromacs, and compiled it fine, and recompiled just mdrun_mpi



The problem I now encounter.  U was using 53a6 FF, which worked in the
past, although I am partial to all atoms.  In Pro residues, the topolog
output from grompp lables three of the CH2 in the ring as CH2r.  When I
then do an EM or MD, gromacs complains that it can not find atom type CH2r.
I looked through all the .itp, .rtp and amino acid definitions, and CH2r is
there.  If I re-lable the topology and .gro file by hand to CHR1 the system
works, but the overall geometry is slightly off (if you look at the atom
definitions and take into account that prolines are not completly
aeromatic, only partially...



Well, proline isn't aromatic at all, but CHR1 will try to force the atoms to
be planar.  None of this should be necessary (nor is it right to do).

In any case, is this a bug or is there some other problem I missed?  I did 
look at the input .pdb file, and the same nomenclature I used before with

the same ff now does not work?



All signs point to the fact that processing of proline should work out of the
 box, so to speak.  The CH2r atom type is properly defined in all the
relevant files.  Can you post a bit more detail, like the exact error
message, snippet from the topology, etc?  I haven't had any problem with
proline-containing proteins with 53a6 in the newest version.

-Justin


Sincerely

Stephan Watkins


Aminoacids.rtp --PRO entry

[ PRO ] [ atoms ] N N 0.0 0 CA   CH1 0.0 1 CB
CH2r 0.0 1 CG  CH2r 0.0 2 CD  CH2r 0.0 2 
C C   0.450 3 O O  -0.450 3 [ bonds ] NCA

gb_21 NCDgb_21 CACBgb_27 CA Cgb_27 CBCGgb_27
 CGCDgb_27 C Ogb_5 C+Ngb_10 [ angles ] ;  aiaj
ak   gromos type -C NCA ga_31 -C NCD ga_31 CA N
CD ga_21 NCACB ga_13 NCA C ga_13 CBCA C
ga_13 CACBCG ga_13 CBCGCD ga_13 NCDCG
ga_13 CA C O ga_30 CA C+N ga_19 O C+N
ga_33 [ impropers ] ;  aiajakal   gromos type N-CCACD
gi_1 CA N CCB gi_2 CCA+N O gi_1 [ dihedrals ]
 ;  aiajakal   gromos type -CA-C NCA gd_14 -C
NCA C gd_39 CA NCDCG gd_39 NCACBCG
gd_34 NCA C+N gd_40 CACBCGCD gd_34 CBCG
CD N gd_34


Atom Definitions---Bonded

O  15.99940 ; carbonyl oxygen (C=O) OM  15.99940 ; carboxyl oxygen
(CO-) OA  15.99940 ; hydroxyl, sugar or ester oxygen OE  15.99940 ;
ether or ester oxygen OW  15.99940 ; water oxygen N  14.00670 ;
peptide nitrogen (N or NH) NT  14.00670 ; terminal nitrogen (NH2) NL
14.00670 ; terminal nitrogen (NH3) NR  14.00670 ; aromatic nitrogen 
NZ  14.00670 ; Arg NH (NH2) NE  14.00670 ; Arg NE (NH) C  12.01100 ;

bare carbon CH0  12.0110  ; bare sp3 carbon, 4 bound heavy atoms CH1
13.01900 ; aliphatic or sugar CH-group CH2  14.02700 ; aliphatic or
sugar CH2-group CH3  15.03500 ; aliphatic CH3-group CH4  16.04300 ;
methane CH2r  14.02700 ; CH2-group in a ring  *** CR1
13.01900 ; aromatic CH-group HC   1.00800 ; hydrogen bound to carbon 
H   1.00800 ; hydrogen not bound to carbon DUM   0.0 ; dummy

atom, no idea what the mass should be. PT3-99 S  32.06000 ; sulfur CU1+
63.54600 ; copper (charg

Re: [gmx-users] Getting started - Peptide

[Justin A. Lemkul]

Artur Panczakiewicz wrote:

Dear Gromacs Users,

I'm a freshman and would like to lear how to use GROMACS in my
research starting from tutorial. I've just installed the newest
version and try to repeat all of the steps from the chapter that
describes the preparation of Ribonuclease A to MD simulation. In my
case it is not possible, unfortunatelly. The grompp program crashes
such a way:

---
Program grompp, VERSION 4.5.1
Source code file: toppush.c, line: 1987

Fatal error:
No such moleculetype SOL
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I tried to install GROMACS on other machine with different Linux
distribution but the error in grompp was the same.
What is important, I installed version 4.0.7 and it works well! I
don't have any idea what is going on.
Does anyone have a similar problem?



Did you follow the link provided by grompp?  There is some helpful information 
there...


http://www.gromacs.org/Documentation/Errors#Fatal_error.3a_No_such_moleculetype_XXX

Was there water in the input structure?  There have been some changes to pdb2gmx 
since the 4.0.x series, perhaps related to the way water is named/renamed. 
Check what is in your coordinate file (before pdb2gmx and after), what is in 
your topology, and whether any of this is wrong or unexpected.


-Justin


Regards,
Artur


--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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] ffyw3f library not found..

[Kamalesh Roy]

Thanks for your answer.
I have given the command ./configure then make then make install for fftw
and then ./configure for gromacs then
it returns a command that fftwf library not found.

I kept the fftw and gromacs file in the same directory /usr/local and was
trying to install this.
Thank you again.

On Thu, Sep 23, 2010 at 4:03 PM, Justin A. Lemkul  wrote:

>
>
> Kamalesh Roy wrote:
>
>> Dear users
>>
>> I am trying to install Gromacs-4.5 with fftw-3.2.2  in Fedora version 9,
>> when I am trying to install the Groamcs
>> after installing fftw it is giving me an error that ftwf library not
>> found.
>>
>> Please hep me.
>>
>>
> At the very least you need to provide us with the command you gave.
>  Detailed installation instructions are available on the Gromacs site:
>
>
> http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions
>
> -Justin
>
>  --
>> Regards
>> Kamalesh Roy
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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
>



-- 
Regards
Kamalesh Roy
Lecturer
Institute of Genetic Engineering, India
-- 
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] make_ndx: execlude one group from another

[Thomas Schlesier]

Hi all,
I'm trying to execlude all atoms of group 2 (140 atoms) from group 1 
(300 atoms), so that i have a new group 3 (with 160 atoms).

| is for merging with OR
& for merging with AND
so ! should be for merging with NOT
But i tried
1 ! 2
2 ! 1
but in both cases make_ndx complains about syntax errors
Syntax error: "! 1" ; or same with "! 2"
To use NOT instead of ! doesn't work. But using AND insted of & also 
doesn't work.


So what's the right command for merging with the NOT option?

Greetings Thomas
--
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] Getting started - Peptide

[#ZHAO LINA#]

Are you sure you installed the  version 4.0.7?

Hint : your program run on VERSION 4.5.1, 
Answer : You know.


lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Artur Panczakiewicz [apanczakiew...@gmail.com]
Sent: Thursday, September 23, 2010 10:02 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Getting started - Peptide

Dear Gromacs Users,

I'm a freshman and would like to lear how to use GROMACS in my
research starting from tutorial. I've just installed the newest
version and try to repeat all of the steps from the chapter that
describes the preparation of Ribonuclease A to MD simulation. In my
case it is not possible, unfortunatelly. The grompp program crashes
such a way:

---
Program grompp, VERSION 4.5.1
Source code file: toppush.c, line: 1987

Fatal error:
No such moleculetype SOL
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I tried to install GROMACS on other machine with different Linux
distribution but the error in grompp was the same.
What is important, I installed version 4.0.7 and it works well! I
don't have any idea what is going on.
Does anyone have a similar problem?

Regards,
Artur
--
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/Support/Mailing_Lists

[gmx-users] Re: gmx-users Digest, Vol 77, Issue 150

[lloyd riggs]

Dear Users and Justin,

Included below is the origional message and reply.  The only error message was 
" Atom type CH2r not found fatal error ".

After looking at all the files though, I realized if I change everything to 
either CH2r or CH2R , it runs.  I don't know if it was somones joke on my end, 
or if it is just a typo in the last release.  Basically the nonbonded atom 
files and all the other files had seperate lables at least for me

>Well, proline isn't aromatic at all...

yeah I know, the terminal C on the ring can be CHR or CH1 , at least the 
definitions are the same...

Origional post:

To: Discussion list for GROMACS users 
Message-ID: <4c9a67de.6060...@vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed


I've gone ahead and changed the subject line to potentially attract the 
attention of others who might help.

lloyd riggs wrote:
> 
> Dear All,
> 
> I'm not sure if this is a bug or not.  I downloaded and installed the new
> version of Gromacs, and compiled it fine, and recompiled just mdrun_mpi
> 
> The problem I now encounter.  U was using 53a6 FF, which worked in the past,
> although I am partial to all atoms.  In Pro residues, the topolog output from
> grompp lables three of the CH2 in the ring as CH2r.  When I then do an EM or
> MD, gromacs complains that it can not find atom type CH2r.  I looked through
> all the .itp, .rtp and amino acid definitions, and CH2r is there.  If I
> re-lable the topology and .gro file by hand to CHR1 the system works, but the
> overall geometry is slightly off (if you look at the atom definitions and
> take into account that prolines are not completly aeromatic, only
> partially...
> 

Well, proline isn't aromatic at all, but CHR1 will try to force the atoms to be 
planar.  None of this should be necessary (nor is it right to do).

> In any case, is this a bug or is there some other problem I missed?  I did
> look at the input .pdb file, and the same nomenclature I used before with the
> same ff now does not work?
> 

All signs point to the fact that processing of proline should work out of the 
box, so to speak.  The CH2r atom type is properly defined in all the relevant 
files.  Can you post a bit more detail, like the exact error message, snippet 
from the topology, etc?  I haven't had any problem with proline-containing 
proteins with 53a6 in the newest version.

-Justin

> Sincerely
> 
> Stephan Watkins

Aminoacids.rtp --PRO entry

[ PRO ]
 [ atoms ]
N N 0.0 0
   CA   CH1 0.0 1
   CB  CH2r 0.0 1
   CG  CH2r 0.0 2
   CD  CH2r 0.0 2
C C   0.450 3
O O  -0.450 3
 [ bonds ]
NCAgb_21   
NCDgb_21   
   CACBgb_27   
   CA Cgb_27   
   CBCGgb_27   
   CGCDgb_27   
C Ogb_5
C+Ngb_10   
 [ angles ]
;  aiajak   gromos type
   -C NCA ga_31   
   -C NCD ga_31   
   CA NCD ga_21   
NCACB ga_13   
NCA C ga_13   
   CBCA C ga_13   
   CACBCG ga_13   
   CBCGCD ga_13   
NCDCG ga_13   
   CA C O ga_30   
   CA C+N ga_19   
O C+N ga_33   
 [ impropers ]
;  aiajakal   gromos type
N-CCACD gi_1
   CA N CCB gi_2
CCA+N O gi_1
 [ dihedrals ]
;  aiajakal   gromos type
  -CA-C NCA gd_14   
   -C NCA C gd_39   
   CA NCDCG gd_39   
NCACBCG gd_34   
NCA C+N gd_40   
   CACBCGCD gd_34   
   CBCGCD N gd_34   


Atom Definitions---Bonded

O  15.99940 ; carbonyl oxygen (C=O)
   OM  15.99940 ; carboxyl oxygen (CO-)
   OA  15.99940 ; hydroxyl, sugar or ester oxygen
   OE  15.99940 ; ether or ester oxygen
   OW  15.99940 ; water oxygen
N  14.00670 ; peptide nitrogen (N or NH)
   NT  14.00670 ; terminal nitrogen (NH2)
   NL  14.00670 ; terminal nitrogen (NH3)
   NR  14.00670 ; aromatic nitrogen
   NZ  14.00670 ; Arg NH (NH2)
   NE  14.00670 ; Arg NE (NH)
C  12.01100 ; bare carbon
  CH0  12.0110  ; bare sp3 carbon, 4 bound heavy atoms
  CH1  13.01900 ; aliphatic or sugar CH-group
  CH2  14.02700 ; aliphatic or sugar CH2-group
  CH3  15.03500 ; aliphatic CH3-group
  CH4  16.04300 ; methane
 CH2r  14.02700 ; CH2-group in a ring  ***
  CR1  13.01900 ; aromatic CH-group 
   HC   1.00800 ; hydrogen bound to carbon
H   1.00800 ; hydrogen not bound to carbon
  DUM   0.0 ; dummy atom, no idea what the mass should be. PT3-99
S  32.06000 ; sulfur
 CU1+  63.54600 ; copper (charge 1+)
 CU2+  63.54600 ; copper (charge 2+)
   FE  55.84700 ; iron (heme)
 ZN2+  65.37000 ; zinc (charge 2+)
 

Re: [gmx-users] make_ndx: execlude one group from another

[Mark Abraham]

- Original Message -
From: Thomas Schlesier 
Date: Friday, September 24, 2010 18:43
Subject: [gmx-users] make_ndx: execlude one group from another
To: "gmx-users@gromacs.org" 

> Hi all,
> I'm trying to execlude all atoms of group 2 (140 atoms) from 
> group 1 (300 atoms), so that i have a new group 3 (with 160 atoms).
> | is for merging with OR
> & for merging with AND
> so ! should be for merging with NOT

No. "NOT" is a unary operator, which (in this case) negates the sense of a set. 
You can be in A or NOT in A. In English we might say "in B not A" which makes 
sense (sloppily), but there's an implicit AND binary operator to combine the 
two operands, viz "in B AND NOT in A". make_ndx requires the precise version.

Mark

> But i tried
> 1 ! 2
> 2 ! 1
> but in both cases make_ndx complains about syntax errors
> Syntax error: "! 1" ; or same with "! 2"
> To use NOT instead of ! doesn't work. But using AND insted of & 
> also doesn't work.
> 
> So what's the right command for merging with the NOT option?
> 
> Greetings Thomas
> -- 
> 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/Support/Mailing_Lists

[gmx-users] PMF on dihedral

[chris . neale]

Landry,

you can't do  it using the  pull code, but it is possible. We did  US  
over Phi and Psi in the following paper, and you can  get the methods  
from  there. I also posted many more specifics and examples to the  
mailing list during  that time.


C. Neale, T. Rodinger, and R. Pomès, "Equilibrium exchange enhances  
the convergence rate of umbrella sampling", Chemical Physics Letters  
460, 375-381 (2008)


 -- original  message --

Message: 7
Date: Thu, 23 Sep 2010 10:26:32 +0200
From: charl...@cermav.cnrs.fr
Subject: [gmx-users] PMF on dihedral
To: gmx-users@gromacs.org
Message-ID:

Content-Type: text/plain;charset=iso-8859-1

Hi

I would like to perform calculations of potential of mean force on a
dihedral angle.
But it seems that all the options are parametrized for a PMF
calculation on a distance.

This question has been already posted 4 years ago
(http://www.mail-archive.com/gmx-users@gromacs.org/msg00384.html) without
any answer. I hope that somebody will be able to help me.

Thanks,

Landry

--
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] Re: Problem with pressure coupling

[Ondrej Marsalek]

And I have just noticed that this was an mdp after some testing with
changed values. It behaves the same also with the more sensible values
below. Moreover, it looks like something that will not be sensitive to
the details of the the FF evaluation.

rlist= 1.2
rcoulomb-switch  = 0.8
rcoulomb = 1
rvdw-switch  = 0.8
rvdw = 1


On Thu, Sep 23, 2010 at 15:16, Ondrej Marsalek
 wrote:
> Dear all,
>
> running a box of neat water with the below mdp file in GROMACS 4.5.1
> results in a fast linear increase of the volume of the box, the water
> getting torn into clusters. The same simulation in 4.0.7 (with
> nstcalcenergy removed, of course) runs just fine, with the box volume
> stable and fluctuating. In 4.5.1 the problem can be fixed by setting
> nstlist = 1. I assume this would also be the case for other positive
> numbers. The same behavior can be seen for the Parrinello-Rahman
> barostat. I can of course provide full testcases ready to run, if
> needed.
>
> This looks like a bug to me. Can anyone help me resolve this?
>
> Thanks,
> Ondrej
>
>
> ; RUN CONTROL PARAMETERS
> integrator               = md
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 5000
> comm-mode                = Linear
> nstcomm                  = 10
>
> ; OUTPUT CONTROL OPTIONS
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> nstlog                   = 100
> nstcalcenergy            = 10
> nstenergy                = 100
> nstxtcout                = 100
> xtc-precision            = 1000
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist                  = -1
> ns_type                  = grid
> pbc                      = xyz
> periodic_molecules       = no
> rlist                    = 1.3
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype              = PME-Switch
> rcoulomb-switch          = 0.6
> rcoulomb                 = 0.8
> vdw-type                 = Shift
> rvdw-switch              = 0.6
> rvdw                     = 0.8
> DispCorr                 = EnerPres
> fourierspacing           = 0.12
> pme_order                = 4
> ewald_rtol               = 1e-05
> ewald_geometry           = 3d
> optimize_fft             = yes
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> Tcoupl                   = v-rescale
> tc-grps                  = system
> tau_t                    = 0.5
> ref_t                    = 300
> Pcoupl                   = berendsen
> Pcoupltype               = isotropic
> tau_p                    = 1
> compressibility          = 4.5e-5
> ref_p                    = 1.0
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel                  = no
>
> ; OPTIONS FOR BONDS
> constraints              = none
>
-- 
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] Reg: Putting molecules on one side of the box

[Mark Abraham]

Use genconf to replicate some suitable smaller box of decane to the full size, 
delete the second half of the decane molecules, then use genbox to fill the 
rest with water. Cunning use of genconf should allow you to select where the 
division lies.

Mark

- Original Message -
From: vinothkumar mohanakrishnan 
Date: Friday, September 24, 2010 17:22
Subject: [gmx-users] Reg: Putting molecules on one side of the box
To: Discussion list for GROMACS users 

> Hi all
> 
> I have a triclinic box of length of 8*3*3 nm. i want to put water on one side 
> of the box and say decane on the other side of the box. How to generate .gro 
> for the water-decane mixture such that they form two distinct parts of the 
> box.
 > 
> Regards
> Vinoth
 > -- 
> 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/Support/Mailing_Lists

Re: [gmx-users] ffyw3f library not found..

[Justin A. Lemkul]

Kamalesh Roy wrote:

Thanks for your answer.
I have given the command ./configure then make then make install for 
fftw and then ./configure for gromacs then

it returns a command that fftwf library not found.

I kept the fftw and gromacs file in the same directory /usr/local and 
was trying to install this.


By default, /usr/local/fftw is not a location that your system will search to 
find libraries, so doing a plain ./configure will not work.  Please read the 
installation guide, particularly the section about CPPFLAGS and LDFLAGS.


-Justin


Thank you again.

On Thu, Sep 23, 2010 at 4:03 PM, Justin A. Lemkul > wrote:




Kamalesh Roy wrote:

Dear users

I am trying to install Gromacs-4.5 with fftw-3.2.2  in Fedora
version 9, when I am trying to install the Groamcs
after installing fftw it is giving me an error that ftwf library
not found.

Please hep me.


At the very least you need to provide us with the command you gave.
 Detailed installation instructions are available on the Gromacs site:


http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions

-Justin

-- 
Regards

Kamalesh Roy


-- 



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


-- 
gmx-users mailing listgmx-users@gromacs.org


http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/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




--
Regards
Kamalesh Roy
Lecturer
Institute of Genetic Engineering, India


--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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] make_ndx: execlude one group from another

[Erik Marklund]

 Thomas Schlesier skrev 2010-09-23 13.03:

Hi all,
I'm trying to execlude all atoms of group 2 (140 atoms) from group 1 
(300 atoms), so that i have a new group 3 (with 160 atoms).

| is for merging with OR
& for merging with AND
so ! should be for merging with NOT
But i tried
1 ! 2
2 ! 1
but in both cases make_ndx complains about syntax errors
Syntax error: "! 1" ; or same with "! 2"
To use NOT instead of ! doesn't work. But using AND insted of & also 
doesn't work.


So what's the right command for merging with the NOT option?

Greetings Thomas
I guess that's because ! is not a binary operator. If you want the union 
of 1 and all that is not in 2, then try '1 | ! 2'.


--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

--
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] D-proline

[Stefano Pieraccini]

 

Dear Gromacs users,

 

I would like to use gromacs to simulate a peptide containing a D-proline
using the opls force field. I guess that, considering that L- and D- PRO
differs only for chirality, the two a.a. topologies should little differ,
and that an improper torsion and/or torsional terms should be modified in
D-PRO topology with respect to L-PRO, but I am not sure on how to modify the
improper torsion ( it is _C CA N CD in L-pro) and if it is correct to do so
or only torsional terms should be modified.

 

Thank you in advance

 

Stefano Pieraccini

-- 
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] trouble in energy minimization.

[Taeho Kim]

Hi, I used gromacs package (ver 4.0.3) for energy minimization of protein homology model.After em, some residues were mangled if I see structure using jV protein structure view (http://www.pdbj.org/jv/index.html) and rasmol.Especially, some glycine were disappeared on jV viewer and rasmol. It maybe because that distance between two atoms are far apart, I think.I used em.mdp and commands for em like below and I attached pdb file of mangled region:EM.mdp==cpp = /usr/bin/cppdefine = -DFLEX_SPCconstraints = noneintegrator = steepdt = 0.002nsteps = 5000emtol = 1000emstep = 0.01nstcomm = 1ns_type = gridnstlist = 1rlist = 1.2coulombtype = PMErcoulomb = 1.2rvdw = 1.2pbc = xyz$ pdb2gmx -nointer -ff G43a1 -ignh -missing -f min_struct.pdb -p min_struct -o min_struct -i min_struct$ grompp -f min_struct_scaffold_1 -c min_struct -n min_struct -p min_struct -o min_struct$ mdrun -nice 0 -s min_struct -o min_struct -c min_struct_out.pdb -e min_struct -g min_struct.log 

mangled_region.pdb
Description: Binary data
-- Taeho Kim (Ph.D) PostDoctoral ResearcherSystems Immunology LaboratoryWPI Immunology Frontier Research CenterOsaka University, Osaka, 565-0871, Japanemail : t...@ifrec.osaka-u.ac.jphome: http://www.ifrec.osaka-u.ac.jp-- 
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] make_ndx: execlude one group from another

[Thomas Schlesier]

Hi all,
I'm trying to execlude all atoms of group 2 (140 atoms) from group 1 
(300 atoms), so that i have a new group 3 (with 160 atoms).

| is for merging with OR
& for merging with AND
so ! should be for merging with NOT
But i tried
1 ! 2
2 ! 1
but in both cases make_ndx complains about syntax errors
Syntax error: "! 1" ; or same with "! 2"
To use NOT instead of ! doesn't work. But using AND insted of & also 
doesn't work.


So what's the right command for merging with the NOT option?

Greetings Thomas
--
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] Re: rotational correlation function

[David van der Spoel]

On 2010-09-23 21.10, Paymon Pirzadeh wrote:

OK, To summurize:

1. I calculate the Ctot(t) with g_rotacf using N-H index files.

2. Use trjconv to get a trajectory of internal motions.
 =>  How I get the Cint(t)???

3. Crot = Ctot/Cint

But, is there any way to calculate the Crot(t) directly? Is trjconv the
solution again?

No and no.
Maybe when you use the -debug option to trjconv it spits out the 
rotation matrix but I'm not sure.


Anyway you need to start trying things out from here.

regards,

Paymon








On Thu, 2010-09-23 at 20:40 +0200, David van der Spoel wrote:

On 2010-09-23 20.38, Paymon Pirzadeh wrote:

Great tips and advices. I appreciate your attention.
But, what would the g_rms -fit rot+trans  do?


compute the rmsd. something different. I said trjconv.


Paymon



On Thu, 2010-09-23 at 20:07 +0200, David van der Spoel wrote:

On 2010-09-23 18.14, Paymon Pirzadeh wrote:

Dear Dr. van der Spoel,
Thanks a lot for your clarification. But some questions yet:

1. If I do not provide the "-aver" option, will the program calculate
the C(t) for individual N-H bond?


Yes.


2. In a paper that I just read, JCP vol. 131 155103 (2009),  they claim
they have calculated the Ctot(t) which could be factorized into
rotational and internal components, Ctot(t)=Crot(t)*Cint(t). I assume
g_rotacf gives the rotational part. How one can calculate the Ctot(t)
(they claim they calculatetd the Ctot and Crot with GROMACS utilities)?
How can we generate the rotation matrix (omega(t)) and use it? What's
the use of "-fitfn"? Is it sth that could be done in other data
processing softwares?

If your sim is long enough (10-20 times the rotation time, which for a
small protein is on the order of a couple of ns) you can fit all the
individual NH -acfs to two exponentials, 1 for the NH relaxation and one
for the overall.



3. How can we generate a trajectory with no internal motions? Does it
have anything to do with g_rms?

You can do the reverse by fitting trjconv -fit rot+trans this will give
you a protein with no overall rotation+translation from which you can
derive the order parameters and relaxation times of individual NH vectors.


Check this ref too:
@Article{Villa2006a,
  author  = {A. Villa and G. Stock},
 title   = {What NMR relaxation can tell us about the internal motion
of an RNA
hairpin: A molecular dynamics simulation study},
 journal = {J. Chem. Theory Comput.},
 volume  = {2},
 year= {2006},
 pages   = {1228-1236},
}



Sorry for mass of questions.
Regards,

Paymon


On Thu, 2010-09-23 at 08:20 +0200, David van der Spoel wrote:

On 2010-09-23 01.27, Paymon Pirzadeh wrote:

Dear Dr. Chaban,
I meant the N-H bond vectors of protein backbone for calculation of
rotational time correlation function to calculate the rotational
diffusion constant of my protein. I need a protocol which walks me step
by step through the procedure.
Thanks for your Attention.

define all NH bonds in an index file as
[ NH ]
5 6
10 11
23 24

etc.

Then run g_rotacf -P 2 [ more flags ] -aver
Analyze the ACF to extract the order parameters.
You will need to read Lipari&Szabo papers:
@Article{ Lipari82a,
  author =   "G. Lipari and A. Szabo and R. M. Levy",
  title ="Protein Dynamics and {NMR} relaxation: comparison of
  simulations with experiment",
  journal =  BTnature,
  year = 1982,
  volume =   300,
  pages ="197-198"
}

@Article{ Lipari82b,
  author =   "G. Lipari and A. Szabo",
  title ="Model-Free Approach to the Interpretation of Nuclear
  Magnetic Resonance Relaxation in
  Macromolecules. 1. Theory and Range of Validity",
  journal =  BTjacs,
  year = 1982,
  volume =   104,
  pages ="4546-4559"
}




Paymon


On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote:

Message: 2
Date: Wed, 22 Sep 2010 12:07:27 -0600
From: Paymon Pirzadeh
Subject: [gmx-users] rotational correlation function
To: gmx-users@gromacs.org
Message-ID:<1285178847.11669.66.ca...@paymon-desktop>
Content-Type: text/plain

Hello,
Imagine if the total correlation function of a protein could be
factorized into rotational and internal portions:
Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t)
and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)?
What does the g_rms -fit do? I am confused on how I can use gromacs
commands on my output files. Sorry for mass of e-mails.

Paymon



Hey, Paymon -

Do you mean the correlation function of the velocity (VACF)? Why not
to use g_velacc and g_rotacf for translational and rotational VACFs? I
suppose, your molecule is rigid (enough) for rotational velocoty to
make sense.

--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America





--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell&  

Re: [gmx-users] ffyw3f library not found..

[Fabio Affinito]

Hi Mark,
thanks for the explanation. Anyway, I had this kind of problem only when
configuring for the frontend, whilst everything was ok with fftw3 when I
configured and compiled for the computation nodes.

Fabio

On 09/23/2010 03:20 PM, Mark Abraham wrote:
> 
> 
> - Original Message -
> From: Fabio Affinito 
> Date: Thursday, September 23, 2010 20:54
> Subject: Re: [gmx-users] ffyw3f library not found..
> To: Discussion list for GROMACS users 
> 
>> On 09/23/2010 12:27 PM, Kamalesh Roy wrote:
>> > Dear users
>> >
>> > I am trying to install Gromacs-4.5 with fftw-3.2.2  in
>> Fedora version 9,
>> > when I am trying to install the Groamcs
>> > after installing fftw it is giving me an error that ftwf
>> library not found.
>> >
>> > Please hep me.
>> >
>> > --
>> > Regards
>> > Kamalesh Roy
>> >
>>
>> Same problem here.
>> Using:
>> ./configure --prefix=/bgp/userinternal/cin0644a/gromacs \
>>  --enable-ppc-sqrt \
>>  --disable-ppc-altivec \
>>  --with-fft=fftw3 \
>>  --without-x \
>>  CFLAGS="-O3 -qarch=auto -qtune=auto" \
>>  CC="xlc_r -q64" \
>>  CXX="xlC_r -q64" \
>>  CXXFLAGS="-O3 -qarch=auto -qtune=auto" \
>>  CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \
>>  F77="xlf_r -q64" \
>>  FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \
>>  LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib"
>> is fine with 4.0.7 but it generates
>> checking for main in -lfftw3f... no
>> configure: error: Cannot find fftw3f library
>> in 4.5.1
>>
>> I successfully installed 4.5.1 only using the --with-fft=fftpack
> 
> Don't use that, it will be diabolically slow for PME simulations!
> 
> Unfortunately, the BlueGene-specific GROMACS installation instructions
> didn't have the clue that the precision of GROMACS and FFTW has to
> match. It does now.
> 
> Presumably both you and the original poster need to install a
> single-precision copy of FFTW, or configure a double-precision version
> of GROMACS (if you know you need double precision, or don't mind your
> simulation being much slower).
> 
> Mark
> 


-- 
*
Fabio Affinito, PhD
CINECA
InterUniversity Computer Center
Via Magnanelli, 6/3
Casalecchio di Reno (Bologna) ITALY
+39/051/6171794 (Phone)
e-mail: f.affin...@cineca.it
-- 
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] Re: rotational correlation function

[Paymon Pirzadeh]

OK, To summurize:

1. I calculate the Ctot(t) with g_rotacf using N-H index files.

2. Use trjconv to get a trajectory of internal motions. 
=> How I get the Cint(t)??? 

3. Crot = Ctot/Cint

But, is there any way to calculate the Crot(t) directly? Is trjconv the
solution again?
regards,

Paymon








On Thu, 2010-09-23 at 20:40 +0200, David van der Spoel wrote:
> On 2010-09-23 20.38, Paymon Pirzadeh wrote:
> > Great tips and advices. I appreciate your attention.
> > But, what would the g_rms -fit rot+trans  do?
> 
> compute the rmsd. something different. I said trjconv.
> >
> > Paymon
> >
> >
> >
> > On Thu, 2010-09-23 at 20:07 +0200, David van der Spoel wrote:
> >> On 2010-09-23 18.14, Paymon Pirzadeh wrote:
> >>> Dear Dr. van der Spoel,
> >>> Thanks a lot for your clarification. But some questions yet:
> >>>
> >>> 1. If I do not provide the "-aver" option, will the program calculate
> >>> the C(t) for individual N-H bond?
> >>>
> >> Yes.
> >>
> >>> 2. In a paper that I just read, JCP vol. 131 155103 (2009),  they claim
> >>> they have calculated the Ctot(t) which could be factorized into
> >>> rotational and internal components, Ctot(t)=Crot(t)*Cint(t). I assume
> >>> g_rotacf gives the rotational part. How one can calculate the Ctot(t)
> >>> (they claim they calculatetd the Ctot and Crot with GROMACS utilities)?
> >>> How can we generate the rotation matrix (omega(t)) and use it? What's
> >>> the use of "-fitfn"? Is it sth that could be done in other data
> >>> processing softwares?
> >> If your sim is long enough (10-20 times the rotation time, which for a
> >> small protein is on the order of a couple of ns) you can fit all the
> >> individual NH -acfs to two exponentials, 1 for the NH relaxation and one
> >> for the overall.
> >>
> >>>
> >>> 3. How can we generate a trajectory with no internal motions? Does it
> >>> have anything to do with g_rms?
> >> You can do the reverse by fitting trjconv -fit rot+trans this will give
> >> you a protein with no overall rotation+translation from which you can
> >> derive the order parameters and relaxation times of individual NH vectors.
> >>
> >>
> >> Check this ref too:
> >> @Article{Villa2006a,
> >>  author  = {A. Villa and G. Stock},
> >> title   = {What NMR relaxation can tell us about the internal motion
> >> of an RNA
> >>hairpin: A molecular dynamics simulation study},
> >> journal = {J. Chem. Theory Comput.},
> >> volume  = {2},
> >> year= {2006},
> >> pages   = {1228-1236},
> >> }
> >>
> >>>
> >>> Sorry for mass of questions.
> >>> Regards,
> >>>
> >>> Paymon
> >>>
> >>>
> >>> On Thu, 2010-09-23 at 08:20 +0200, David van der Spoel wrote:
>  On 2010-09-23 01.27, Paymon Pirzadeh wrote:
> > Dear Dr. Chaban,
> > I meant the N-H bond vectors of protein backbone for calculation of
> > rotational time correlation function to calculate the rotational
> > diffusion constant of my protein. I need a protocol which walks me step
> > by step through the procedure.
> > Thanks for your Attention.
>  define all NH bonds in an index file as
>  [ NH ]
>  5 6
>  10 11
>  23 24
> 
>  etc.
> 
>  Then run g_rotacf -P 2 [ more flags ] -aver
>  Analyze the ACF to extract the order parameters.
>  You will need to read Lipari&   Szabo papers:
>  @Article{ Lipari82a,
>   author =   "G. Lipari and A. Szabo and R. M. Levy",
>   title ="Protein Dynamics and {NMR} relaxation: comparison of
>   simulations with experiment",
>   journal =  BTnature,
>   year = 1982,
>   volume =   300,
>   pages ="197-198"
>  }
> 
>  @Article{ Lipari82b,
>   author =   "G. Lipari and A. Szabo",
>   title ="Model-Free Approach to the Interpretation of Nuclear
>   Magnetic Resonance Relaxation in
>   Macromolecules. 1. Theory and Range of Validity",
>   journal =  BTjacs,
>   year = 1982,
>   volume =   104,
>   pages ="4546-4559"
>  }
> 
> 
> >
> > Paymon
> >
> >
> > On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote:
> >>> Message: 2
> >>> Date: Wed, 22 Sep 2010 12:07:27 -0600
> >>> From: Paymon Pirzadeh
> >>> Subject: [gmx-users] rotational correlation function
> >>> To: gmx-users@gromacs.org
> >>> Message-ID:<1285178847.11669.66.ca...@paymon-desktop>
> >>> Content-Type: text/plain
> >>>
> >>> Hello,
> >>> Imagine if the total correlation function of a protein could be
> >>> factorized into rotational and internal portions:
> >>> Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the 
> >>> Ctot(t)
> >>> and with which I can get the Crot(t)? Does g_rotacf produce the 
> >>> Crot(t)?
> >>> What does the g_rms -fit do? I am confused on

[gmx-users] PMF on dihedral

[chris . neale]

Landry,

I replied earlier, but it didn't seem to make it to the list. If 2  
show up then they are identical.


The mailing list archive post that you cite is actually talking about  
a (3-point) angle and not a (4-point) dihedral angle.


If you want dihedral angles,   then  take a look at how we did US  on  
dihedrals:


C. Neale, T. Rodinger, and R. Pomès, "Equilibrium exchange enhances  
the convergence rate of umbrella sampling", Chemical Physics Letters  
460, 375-381 (2008).


I also posted to the list about how to  do it around that time. If you  
search you should be able to find it.


Chris.

-- original message --

charlier at cermav.cnrs.fr charlier at cermav.cnrs.fr
Thu Sep 23 10:26:32 CEST 2010

* Previous message: [gmx-users] Re: rotational correlation function
* Next message: [gmx-users] ffyw3f library not found..
* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

Hi

I would like to perform calculations of potential of mean force on a
dihedral angle.
But it seems that all the options are parametrized for a PMF
calculation on a distance.

This question has been already posted 4 years ago
(http://www.mail-archive.com/gmx-users@gromacs.org/msg00384.html) without
any answer. I hope that somebody will be able to help me.

Thanks,

Landry




--
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] fftw and configure in 4.0.7 vs 4.5.1

[Mark Abraham]

- Original Message -
From: Fabio Affinito 
Date: Friday, September 24, 2010 17:23
Subject: [gmx-users] fftw and configure in 4.0.7 vs 4.5.1
To: gmx-users@gromacs.org

> Hi everybody,
> I'm experiencing several problems by running configure in 4.5.1. More
> specifically, it seems it doesn't find fftw libraries.
> It seems strange 'cause the same options used in 4.0.7 work fine.
> These are my configure flags:
> 
> ./configure --prefix=/bgp/userinternal/cin0644a/gromacs \
>  --enable-ppc-sqrt \
>  --disable-ppc-altivec \
>  --with-fft=fftw3 \
>  --without-x \
>  --enable-shared \
>  CFLAGS="-O3 -qarch=auto -qtune=auto" \
>  CC="xlc_r -q64" \
>  CXX="xlC_r -q64" \
>  CXXFLAGS="-O3 -qarch=auto -qtune=auto" \
>  CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \
>  F77="xlf_r -q64" \
>  FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \
>  LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib"
> 
> This is my error in 4.5.1
> checking for sqrt in -lm... yes
> checking for fftw3.h... yes
> checking for main in -lfftw3f... no
> configure: error: Cannot find fftw3f library
> 
> Whilst in 4.0.7 everything works.
> 
> Any hints?

Here you're compiling for the BlueGene front end, so you have to be sure you're 
pointing at FFTW compiled for the front end at the right precision. These will 
differ from those for the back end. However, for the front end, FFTW is more of 
a nice optional extra that might never be used, and fftpack is OK.

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

Re: [gmx-users] Getting started - Peptide

[Artur Panczakiewicz]

Hi All,

Thank you very much for suggestions!
It turned out that there was a missing entry in the top file.
After adding the following:
#include "spc.itp"
grommp finished without any errors :-)

Cheers,
Artur

2010/9/23 TJ Mustard :
> On September 23, 2010 at 3:02 PM Artur Panczakiewicz
>  wrote:
>
>> Dear Gromacs Users,
>>
>> I'm a freshman and would like to lear how to use GROMACS in my
>> research starting from tutorial. I've just installed the newest
>> version and try to repeat all of the steps from the chapter that
>> describes the preparation of Ribonuclease A to MD simulation. In my
>> case it is not possible, unfortunatelly. The grompp program crashes
>> such a way:
>>
>> ---
>> Program grompp, VERSION 4.5.1
>> Source code file: toppush.c, line: 1987
>>
>> Fatal error:
>> No such moleculetype SOL
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>
>
>
> This usually means you have "SOL" coupled to a temperature, and if you don't
> have SOL in your system/.top/.gro you will get this error. This coupling is
> in the .mdp file. If you are running the system in a vacuum you must remove
> the SOL from the mdp file. If you want some kind of SOL (SPC, TIP3P, etc),
> you must add this in by making a box with solvent in it. The tutorial will
> most likely have this in it.
>
>
>
>
>
>> > I tried to install GROMACS on other machine with different Linux
>> distribution but the error in grompp was the same.
>> What is important, I installed version 4.0.7 and it works well! I
>> don't have any idea what is going on.
>> Does anyone have a similar problem?
>>
>> Regards,
>> Artur
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/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
>>
>
>
>
> TJ Mustard
> Email: musta...@onid.orst.edu
>
> --
> gmx-users mailing list    gmx-us...@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/Support/Mailing_Lists

[gmx-users] fftw and configure in 4.0.7 vs 4.5.1

[Fabio Affinito]

Hi everybody,
I'm experiencing several problems by running configure in 4.5.1. More
specifically, it seems it doesn't find fftw libraries.
It seems strange 'cause the same options used in 4.0.7 work fine.
These are my configure flags:

./configure --prefix=/bgp/userinternal/cin0644a/gromacs \
 --enable-ppc-sqrt \
 --disable-ppc-altivec \
 --with-fft=fftw3 \
 --without-x \
 --enable-shared \
 CFLAGS="-O3 -qarch=auto -qtune=auto" \
 CC="xlc_r -q64" \
 CXX="xlC_r -q64" \
 CXXFLAGS="-O3 -qarch=auto -qtune=auto" \
 CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \
 F77="xlf_r -q64" \
 FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \
 LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib"

This is my error in 4.5.1
checking for sqrt in -lm... yes
checking for fftw3.h... yes
checking for main in -lfftw3f... no
configure: error: Cannot find fftw3f library

Whilst in 4.0.7 everything works.

Any hints?

Thanks in advance,

Fabio

-- 
*
Fabio Affinito, PhD
CINECA
InterUniversity Computer Center
Via Magnanelli, 6/3
Casalecchio di Reno (Bologna) ITALY
+39/051/6171794 (Phone)
e-mail: f.affin...@cineca.it
-- 
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] Reg: Putting molecules on one side of the box

[vinothkumar mohanakrishnan]

Hi all

I have a triclinic box of length of 8*3*3 nm. i want to put water on one
side of the box and say decane on the other side of the box. How to generate
.gro for the water-decane mixture such that they form two distinct parts of
the box.

Regards
Vinoth
-- 
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: Re: [gmx-users] Issue with Atom Types/Charges/Mass when

[aschug]

Dear Tom,

I know that there were some ATP-related issues in past versions of gromacs
using the gromos-ff: Gromos used some 5-letter atom types which was a
problem as the pdb file format only has 4 columns for them so you had to
do some renaming. I thought this not to be an issue anymore and am
surprised by your solution- but very, very happy that it works :)

So thank you very much for your help,
Alex



-- 
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] Getting started - Peptide

[Artur Panczakiewicz]

Hi All,

Thank you very much for suggestions!
It turned out that there was a missing entry in the top file.
After adding the following:
#include "spc.itp"
grommp finished without any errors :-)

Cheers,
Artur



2010/9/23 TJ Mustard :
> On September 23, 2010 at 3:02 PM Artur Panczakiewicz
>  wrote:
>
>> Dear Gromacs Users,
>>
>> I'm a freshman and would like to lear how to use GROMACS in my
>> research starting from tutorial. I've just installed the newest
>> version and try to repeat all of the steps from the chapter that
>> describes the preparation of Ribonuclease A to MD simulation. In my
>> case it is not possible, unfortunatelly. The grompp program crashes
>> such a way:
>>
>> ---
>> Program grompp, VERSION 4.5.1
>> Source code file: toppush.c, line: 1987
>>
>> Fatal error:
>> No such moleculetype SOL
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>
>
>
> This usually means you have "SOL" coupled to a temperature, and if you don't
> have SOL in your system/.top/.gro you will get this error. This coupling is
> in the .mdp file. If you are running the system in a vacuum you must remove
> the SOL from the mdp file. If you want some kind of SOL (SPC, TIP3P, etc),
> you must add this in by making a box with solvent in it. The tutorial will
> most likely have this in it.
>
>
>
>
>
>> > I tried to install GROMACS on other machine with different Linux
>> distribution but the error in grompp was the same.
>> What is important, I installed version 4.0.7 and it works well! I
>> don't have any idea what is going on.
>> Does anyone have a similar problem?
>>
>> Regards,
>> Artur
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/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
>>
>
>
>
> TJ Mustard
> Email: musta...@onid.orst.edu
>
> --
> gmx-users mailing list    gmx-us...@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/Support/Mailing_Lists