[gmx-users] trajectory analysis

[oguz gurbulak]

Dear All,
 
I want to
ask some questions about trajectory analysis. I have some md simulation output
files that includes coordinate, force and velocity information. And these files
are huge ( more than 5 GB ) . Could you please recommend a free text editor 
which
works on Linux or Windows to  open and editthese huge files? And I will run
these files with fortran codes and get again huge output files . In order to do
this operation faster and seamlessly what should I do ? Which facilities do I 
have on pc ? Could you please share
your experiences with me ?
 
Thanks for
any help.
 
Kind regards.-- 
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] How to install GROMACS in 64-bit?

[Mark Abraham]

On 30/05/2012 1:50 AM, a a wrote:

Dear Mark,

I have overlook it.  Sorry.

I have already added the following two sentences in .bashrc file in my 
home directory (when I login as user).


export CPPFLAGS="-I/home/softwares/fftw301/include"
export LDFLAGS="-L/home/softwares/fftw301/lib"

Should I type in another lines?


They won't help until you start a new shell. Or, instead, use them on 
the command line like the installation instructions suggest - since you 
don't need these settings on an ongoing basis.




Did I do any common mistakes in using the command export with .bash shell?

Should I add these two lines at the root directory as it seems I have 
a role as root during installation?


Definitely not. "make install" is the only command for which you should 
be root, and only then if the installation location requires it. Unless 
you like pain from risking needing to reinstall your trashed system.


Mark



Please kindly give me some more guidance.

Many thanks,

Catherine



Date: Tue, 29 May 2012 18:48:15 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] How to install GROMACS in 64-bit?

On 29/05/2012 6:37 PM, a a wrote:

Dear Sir/Madam,

Thanks for the insightful comments from the experts.Follows
the steps, I found the source of error:

This what I have done:


In the following directory /home/softwares/fftw-3.0.1:
./configure --enable-shared --prefix=/home/softwares/fftw301
make
make install

In the .bash file:
export CPPFLAGS="-I/home/softwares/fftw301/include"
export LDFLAGS="-L/home/softwares/fftw301/lib"

go to the following directory /home/softwares/gromacs-4.5.5:
./configure --enable-shared --prefix=/home/softwares/g455
make
= ==

In the middle of the make, I found this error message:

==

/usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation
R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/local/lib/libfftw3f.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [libmd.la] Error 1
make[3]: Leaving directory `/home/softwares/gromacs-4.5.5/src/mdlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/softwares/gromacs-4.5.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/softwares/gromacs-4.5.5/src'
make: *** [all-recursive] Error 1



It seems to be a problem of 64 and 32 bit, my workstation is a 64
bit machine and the OS is also 64 bit, what should I do to make
sure both the fftw-3.0.1 library and GROMACS are compiled with 64
bit settings?


I would start by observing that those error messages pertain to an 
installation of FFTW that configure found in /usr/local/lib, and not 
the one in /home/softwares. You have to sort that out first, since 
this error messages indicates the need to use FFTW configured with 
--enable-shared, per the link I gave last time.


Mark

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

[francesco oteri]

nice suggestioncoletta for ever


PS. Lo so che è un commento inutile, ma qualcosa la devo pur dire :D

2012/5/29 Andrea Coletta 

>  One option is to calculate the rdf (radial distribution function g_rdf
> [-surf]) of water oxygen atoms and find the position of the first few
> peaks...
>
> Il 29/05/2012 12:28, Bala subramanian ha scritto:
>
> Friends,
> I read in many articles explaining the behaviour of water in the first (or
> second etc) hydration layers around a protein. I am curious to know if
> there is any way to obtain/guess the thickness of this layer. How does one
> defines the thickness ?
>
> Thanks,
> Bala
>
> --
> C. Balasubramanian
>
>
>
>
>
> --
> ***
> Andrea Coletta - PhD
> Dip.to di Biologia - Stanza 326
> Facoltà di Scienze - Università degli Studi di Roma "Tor Vergata"
> Via della Ricerca Scientifica snc, 00133, Roma, Italia
> Tel. +390672594326
> Fax +39062022798
> E-Mail: andrea.coletta_at_uniroma2_dot_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
>



-- 
Cordiali saluti, Dr.Oteri Francesco
-- 
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: How to generate the initial coordinates file?

[Justin A. Lemkul]

On 5/29/12 4:19 PM, Bao Kai wrote:

Hi, Justin,

Thank you very much for your help.

It seems that genbox will need really huge memory even with thousands
of molecules.

If we want to to further to tens or hundreds of thousands molecules,
do we need some cluster to run genbox in parallel?



genbox is not parallelized.  If you need to create a very large system, create a 
smaller system and replicate it with genconf -nbox.  If memory is still an 
issue, consider whether or not you need such a large system ;)


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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: How to generate the initial coordinates file?

[Bao Kai]

Hi, Justin,

Thank you very much for your help.

It seems that genbox will need really huge memory even with thousands
of molecules.

If we want to to further to tens or hundreds of thousands molecules,
do we need some cluster to run genbox in parallel?

Best Regards,
Kai


>
> Message: 3
> Date: Tue, 29 May 2012 08:50:06 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] How to generate the initial coordinates file?
> To: Discussion list for GROMACS users 
> Message-ID: <4fc4c5fe.9060...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 5/29/12 8:46 AM, Bao Kai wrote:
>> Hi,  all,
>>
>> I am new to Gromacs and MD.  I just went through a few tutorials on
>> Gromacs quickly.  I have a question now.
>>
>> I know the structure of molecule A and B, such as the atoms
>> compositions and the relative position of the atoms and the charge.
>>
>> Now, I want to use 500 A and 100 B to do the simulation. I want to
>> know how I can get the initial coordinate file or how I should start.
>>
>> It seems all the tutorials use either one big protein molecule the add
>> some water or the coordinate files have been ready.
>>
>> Thank you very much.
>
> You will need to obtain coordinate files of both of your molecules using some
> external software.  Several suggestions are provided here, though there are
> others, as well:
>
> http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources
>
> You will need to obtain or create topologies for each of these.
>
> To construct the system, use genbox in conjunction with the -ci -nmol flags, 
> as
> suggested here:
>
> http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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] How to install GROMACS in 64-bit?

[a a]

Dear Mark,

I have overlook it.  Sorry.

I have already added the following two sentences in .bashrc file in my home 
directory (when I login as user).

export
  CPPFLAGS="-I/home/softwares/fftw301/include"
  export LDFLAGS="-L/home/softwares/fftw301/lib"

Should I type in another lines?

Did I do any common mistakes in using the command export with .bash shell?

Should I add these two lines at the root directory as it seems I have a role as 
root during installation?

Please kindly give me some more guidance.

Many thanks,

Catherine
  

Date: Tue, 29 May 2012 18:48:15 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] How to install GROMACS in 64-bit?


  

  
  
On 29/05/2012 6:37 PM, a a wrote:

  
  
Dear Sir/Madam,



Thanks for the insightful comments from the experts.  
   Follows the steps, I found the source of error:



This what I have done:




  
  In the following directory /home/softwares/fftw-3.0.1:
  ./configure --enable-shared
--prefix=/home/softwares/fftw301
  make
  make install
  


  In the .bash file:
  export
  CPPFLAGS="-I/home/softwares/fftw301/include"
  export LDFLAGS="-L/home/softwares/fftw301/lib"
  

  
  go to the following directory
/home/softwares/gromacs-4.5.5:
  ./configure --enable-shared --prefix=/home/softwares/g455
  make
  =

  ==
  

  
  In the middle of the make, I found this error message:
  

  
  ==
  

  
  /usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be
used when making a shared object; recompile with -fPIC
  /usr/local/lib/libfftw3f.a: could not read symbols: Bad
value
  collect2: ld returned 1 exit status
  make[3]: *** [libmd.la] Error 1
  make[3]: Leaving directory
`/home/softwares/gromacs-4.5.5/src/mdlib'
  make[2]: *** [all-recursive] Error 1
  make[2]: Leaving directory
`/home/softwares/gromacs-4.5.5/src'
  make[1]: *** [all] Error 2
  make[1]: Leaving directory
`/home/softwares/gromacs-4.5.5/src'
  make: *** [all-recursive] Error 1








It seems to be a problem of 64 and 32 bit, my workstation
  is a 64 bit machine and the OS is also 64 bit, what should I
  do to make sure both the fftw-3.0.1
library and GROMACS are compiled with 64 bit settings?
  



I would start by observing that those error messages pertain to an
installation of FFTW that configure found in /usr/local/lib, and not
the one in /home/softwares. You have to sort that out first, since
this error messages indicates the need to use FFTW configured with
--enable-shared, per the link I gave last time.



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   
  -- 
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] Possible bug: energy changes with the number of nodes for energy minimization

[Justin A. Lemkul]

On 5/29/12 6:22 AM, Stephen Cox wrote:

Hi,

I'm running a number of energy minimizations on a clathrate supercell and I get
quite significantly different values for the total energy depending on the
number of mpi processes / number of threads I use. More specifically, some
numbers I get are:

#cores  energy
1-2.41936409202696e+04
2-2.43726425776809e+04
3-2.45516442350804e+04
4-2.47003944216983e+04

#threadsenergy
1-2.41936409202696e+04
2-2.43726425776792e+04
3-2.45516442350804e+04
4-2.47306458924815e+04


I'd expect some numerical noise, but these differences seem to0 large for that.


The difference is only 2%, which by MD standards, is quite good, I'd say ;) 
Consider the discussion here:


http://www.gromacs.org/Documentation/Terminology/Reproducibility

To an extent, the information here may also be relevant:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation


Before submitting a bug report, I'd like to check:
a) if someone has seen something similar;


Sure.  Energies can be different due to a whole host of factors (discussed 
above), and MPI only complicates matters.



b) should I just trust the serial version?


Maybe, but I don't know that there's evidence to say that any of the above tests 
are more or less accurate than the others.  What happens if you run with mdrun 
-reprod on all your tests?



c) have I simply done something stupid (grompp.mdp appended below);



Nope, looks fine.

-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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] How to generate the initial coordinates file?

[Justin A. Lemkul]

On 5/29/12 8:46 AM, Bao Kai wrote:

Hi,  all,

I am new to Gromacs and MD.  I just went through a few tutorials on
Gromacs quickly.  I have a question now.

I know the structure of molecule A and B, such as the atoms
compositions and the relative position of the atoms and the charge.

Now, I want to use 500 A and 100 B to do the simulation. I want to
know how I can get the initial coordinate file or how I should start.

It seems all the tutorials use either one big protein molecule the add
some water or the coordinate files have been ready.

Thank you very much.


You will need to obtain coordinate files of both of your molecules using some 
external software.  Several suggestions are provided here, though there are 
others, as well:


http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources

You will need to obtain or create topologies for each of these.

To construct the system, use genbox in conjunction with the -ci -nmol flags, as 
suggested here:


http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents

-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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] How to generate the initial coordinates file?

[Bao Kai]

Hi,  all,

I am new to Gromacs and MD.  I just went through a few tutorials on
Gromacs quickly.  I have a question now.

I know the structure of molecule A and B, such as the atoms
compositions and the relative position of the atoms and the charge.

Now, I want to use 500 A and 100 B to do the simulation. I want to
know how I can get the initial coordinate file or how I should start.

It seems all the tutorials use either one big protein molecule the add
some water or the coordinate files have been ready.

Thank you very much.

Cheers,
Kai
-- 
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] Position Restraints of one of the moleculetpye

[Steven Neumann]

On Tue, May 29, 2012 at 12:21 PM, Justin A. Lemkul  wrote:

>
>
> On 5/29/12 6:52 AM, Steven Neumann wrote:
>
>> Ok. My topology:
>>
>> ; Include forcefield parameters
>> #include "./charmm27.ff/forcefield.itp"
>>
>> ; Include ligand topology
>> #include "ligand1.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_1
>> #include "posre_ligand1.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand2.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_2
>> #include "posre_ligand2.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand3.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_3
>> #include "posre_ligand3.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand4.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_4
>> #include "posre_ligand4.itp"
>> #endif
>>
>>
>> ; Include ligand topology
>> #include "ligand5.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_5
>> #include "posre_ligand5.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand6.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_6
>> #include "posre_ligand6.itp"
>> #endif
>>
>> ; Include water topology
>> #include "./charmm27mod.ff/tip3p.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct   fcxfcyfcz
>>11   1000   1000   1000
>> #endif
>>
>> ; Include topology for ions
>> #include "./charmm27.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Protein in water
>>
>> [ molecules ]
>> ; Compound#mols
>> ligand1   1
>> ligand2   1
>> ligand3   1
>> ligand4   1
>> ligand5   1
>> ligand6   1
>> SOL  4617
>>
>>
>> Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other
>> information
>> is the same
>>
>> posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.
>>
>> Then when I grompp:
>>
>> Syntax error - File ligand2.itp, line 7
>> Last line read:
>> '[ atomtypes ] '
>> Invalid order for directive atomtypes
>>
>> Any suggestions appreciated,
>>
>>
> Once you declare a [moleculetype], the other force field-level directives
> cannot be called.  If all the ligand topologies are the same, remove
> [atomtypes] from all but the first.
>
>
> -Justin
>

Thanks Justin. Removing [pairtypes] and [atomtypes] from all but not the
first helped.

Steven



> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
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] Position Restraints of one of the moleculetpye

[Justin A. Lemkul]

On 5/29/12 6:52 AM, Steven Neumann wrote:

Ok. My topology:

; Include forcefield parameters
#include "./charmm27.ff/forcefield.itp"

; Include ligand topology
#include "ligand1.itp"

; Include Position restraint file
#ifdef POSRES_1
#include "posre_ligand1.itp"
#endif

; Include ligand topology
#include "ligand2.itp"

; Include Position restraint file
#ifdef POSRES_2
#include "posre_ligand2.itp"
#endif

; Include ligand topology
#include "ligand3.itp"

; Include Position restraint file
#ifdef POSRES_3
#include "posre_ligand3.itp"
#endif

; Include ligand topology
#include "ligand4.itp"

; Include Position restraint file
#ifdef POSRES_4
#include "posre_ligand4.itp"
#endif


; Include ligand topology
#include "ligand5.itp"

; Include Position restraint file
#ifdef POSRES_5
#include "posre_ligand5.itp"
#endif

; Include ligand topology
#include "ligand6.itp"

; Include Position restraint file
#ifdef POSRES_6
#include "posre_ligand6.itp"
#endif

; Include water topology
#include "./charmm27mod.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
#endif

; Include topology for ions
#include "./charmm27.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
ligand1   1
ligand2   1
ligand3   1
ligand4   1
ligand5   1
ligand6   1
SOL  4617


Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other information
is the same

posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.

Then when I grompp:

Syntax error - File ligand2.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes

Any suggestions appreciated,



Once you declare a [moleculetype], the other force field-level directives cannot 
be called.  If all the ligand topologies are the same, remove [atomtypes] from 
all but the first.


-Justin

--


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


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

[Steven Neumann]

Ok. My topology:

; Include forcefield parameters
#include "./charmm27.ff/forcefield.itp"

; Include ligand topology
#include "ligand1.itp"

; Include Position restraint file
#ifdef POSRES_1
#include "posre_ligand1.itp"
#endif

; Include ligand topology
#include "ligand2.itp"

; Include Position restraint file
#ifdef POSRES_2
#include "posre_ligand2.itp"
#endif

; Include ligand topology
#include "ligand3.itp"

; Include Position restraint file
#ifdef POSRES_3
#include "posre_ligand3.itp"
#endif

; Include ligand topology
#include "ligand4.itp"

; Include Position restraint file
#ifdef POSRES_4
#include "posre_ligand4.itp"
#endif


; Include ligand topology
#include "ligand5.itp"

; Include Position restraint file
#ifdef POSRES_5
#include "posre_ligand5.itp"
#endif

; Include ligand topology
#include "ligand6.itp"

; Include Position restraint file
#ifdef POSRES_6
#include "posre_ligand6.itp"
#endif

; Include water topology
#include "./charmm27mod.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "./charmm27.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
ligand1   1
ligand2   1
ligand3   1
ligand4   1
ligand5   1
ligand6   1
SOL  4617


Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other
information is the same

posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.

Then when I grompp:

Syntax error - File ligand2.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes

Any suggestions appreciated,

Steven




On Mon, May 28, 2012 at 5:25 PM, Justin A. Lemkul  wrote:

>
>
> On 5/28/12 10:48 AM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> I am fighting with the position restraints. My system cosnsists of 6
>> ligands -
>> all of them have the same topology - ligand.itp. I want to:
>>
>> 1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L,
>> posre
>> ligand1.itp
>> 2. Restrain 5 of them and pull one of them away.
>>
>> Here I came across some difficulties.
>>
>> I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp
>>
>> and by index files I create an index of the ligands I wan to restrain.
>> Each my
>> ligands has 46 atoms. When I process to grompp:
>>
>> Atom index (256) in position_restraints out of bounds (1-46).
>> This probably means that you have inserted topology section
>> "position_restraints
>>
>> Shall I rename Ligands as different residue names? If my posre includes
>> 1-46
>> atom all ligands are restraints? How to restrain just 5 out of 6 of them?
>>
>>
> Position restraints are applied on a per-moleculetype basis.  If you have
> six copies of a ligand, the only way to do this is to define the sixth as a
> special [moleculetype] (even if it contains identical information) with a
> different name, such that it can be restrained in the absence of restraints
> on the others.  See the logic here:
>
> http://www.gromacs.org/**Documentation/Errors#Atom_**index_n_in_position_*
> *restraints_out_of_bounds
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
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] hydration layers around protein

[Andrea Coletta]

One option is to calculate the rdf (radial distribution function g_rdf 
[-surf]) of water oxygen atoms and find the position of the first few 
peaks...


Il 29/05/2012 12:28, Bala subramanian ha scritto:

Friends,
I read in many articles explaining the behaviour of water in the first 
(or second etc) hydration layers around a protein. I am curious to 
know if there is any way to obtain/guess the thickness of this layer. 
How does one defines the thickness ?


Thanks,
Bala

--
C. Balasubramanian






--
***
Andrea Coletta - PhD
Dip.to di Biologia - Stanza 326
Facoltà di Scienze - Università degli Studi di Roma "Tor Vergata"
Via della Ricerca Scientifica snc, 00133, Roma, Italia
Tel. +390672594326
Fax +39062022798
E-Mail: andrea.coletta_at_uniroma2_dot_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] hydration layers around protein

[Bala subramanian]

Friends,
I read in many articles explaining the behaviour of water in the first (or
second etc) hydration layers around a protein. I am curious to know if
there is any way to obtain/guess the thickness of this layer. How does one
defines the thickness ?

Thanks,
Bala

-- 
C. Balasubramanian
-- 
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] Possible bug: energy changes with the number of nodes for energy minimization

[Stephen Cox]

Hi,

I'm running a number of energy minimizations on a clathrate supercell and I
get quite significantly different values for the total energy depending on
the number of mpi processes / number of threads I use. More specifically,
some numbers I get are:

#cores  energy
1-2.41936409202696e+04
2-2.43726425776809e+04
3-2.45516442350804e+04
4-2.47003944216983e+04

#threadsenergy
1-2.41936409202696e+04
2-2.43726425776792e+04
3-2.45516442350804e+04
4-2.47306458924815e+04


I'd expect some numerical noise, but these differences seem to0 large for
that. Before submitting a bug report, I'd like to check:
a) if someone has seen something similar;
b) should I just trust the serial version?
c) have I simply done something stupid (grompp.mdp appended below);

Any help greatly appreciated.

Steve

NB I am using a flexible methane and settles for TIP4P/2005. I have
reproduced the above trend with ubuntu repository versions of
gromacs/openmpi and my own compiled versions of gromacs/mpich2.

; run control
integrator = steep
dt = 0.001
nsteps = -1
comm_mode  = linear
nstcomm= 1

; energy minimization
emtol  = 0.01
emstep = 0.01

; output control
nstxout   = 1000
nstvout   = 1000
nstfout   = 1000
nstlog= 1000
nstcalcenergy = 1
nstenergy = 1000

; neighbour searching
nstlist= 1
ns_type= grid
pbc= xyz
periodic_molecules = no
rlist  = 0.9

; electrostatics
coulombtype = pme
rcoulomb= 0.9

; vdw
vdwtype  = cut-off
rvdw = 0.9
dispcorr = ener

; ewald
fourierspacing = 0.1
pme_order  = 4
ewald_geometry = 3d
optimize_fft   = yes

; temperature coupling
tcoupl  = nose-hoover
nh-chain-length = 10
tau_t   = 0.5
ref_t   = 300.0
tc_grps = system

constraints
constraint_algorithm = lincs
shake_tol= 0.0001
lincs_order  = 8
lincs_iter   = 2
-- 
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] How to install GROMACS in 64-bit?

[Mark Abraham]

On 29/05/2012 6:37 PM, a a wrote:

Dear Sir/Madam,

Thanks for the insightful comments from the experts.Follows the 
steps, I found the source of error:


This what I have done:


In the following directory /home/softwares/fftw-3.0.1:
./configure --enable-shared --prefix=/home/softwares/fftw301
make
make install

In the .bash file:
export CPPFLAGS="-I/home/softwares/fftw301/include"
export LDFLAGS="-L/home/softwares/fftw301/lib"

go to the following directory /home/softwares/gromacs-4.5.5:
./configure --enable-shared --prefix=/home/softwares/g455
make
= ==

In the middle of the make, I found this error message:

==

/usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation 
R_X86_64_32 against `.rodata.str1.1' can not be used when making a 
shared object; recompile with -fPIC

/usr/local/lib/libfftw3f.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [libmd.la] Error 1
make[3]: Leaving directory `/home/softwares/gromacs-4.5.5/src/mdlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/softwares/gromacs-4.5.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/softwares/gromacs-4.5.5/src'
make: *** [all-recursive] Error 1



It seems to be a problem of 64 and 32 bit, my workstation is a 64 bit 
machine and the OS is also 64 bit, what should I do to make sure both 
the fftw-3.0.1 library and GROMACS are compiled with 64 bit settings?


I would start by observing that those error messages pertain to an 
installation of FFTW that configure found in /usr/local/lib, and not the 
one in /home/softwares. You have to sort that out first, since this 
error messages indicates the need to use FFTW configured with 
--enable-shared, per the link I gave last time.


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

[gmx-users] How to install GROMACS in 64-bit?

[a a]

Dear Sir/Madam,
Thanks for the insightful comments from the experts.Follows the steps, I 
found the source of error:
This what I have done:
In the following directory 
/home/softwares/fftw-3.0.1:./configure --enable-shared 
--prefix=/home/softwares/fftw301makemake install
In the .bash file:export CPPFLAGS="-I/home/softwares/fftw301/include"export 
LDFLAGS="-L/home/softwares/fftw301/lib"
go to the following directory /home/softwares/gromacs-4.5.5:./configure 
--enable-shared 
--prefix=/home/softwares/g455make===
In the middle of the make, I found this error message:
==
/usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation R_X86_64_32 
against `.rodata.str1.1' can not be used when making a shared object; recompile 
with -fPIC/usr/local/lib/libfftw3f.a: could not read symbols: Bad 
valuecollect2: ld returned 1 exit statusmake[3]: *** [libmd.la] Error 1make[3]: 
Leaving directory `/home/softwares/gromacs-4.5.5/src/mdlib'make[2]: *** 
[all-recursive] Error 1make[2]: Leaving directory 
`/home/softwares/gromacs-4.5.5/src'make[1]: *** [all] Error 2make[1]: Leaving 
directory `/home/softwares/gromacs-4.5.5/src'make: *** [all-recursive] Error 1

It seems to be a problem of 64 and 32 bit, my workstation is a 64 bit machine 
and the OS is also 64 bit, what should I do to make sure both the fftw-3.0.1 
library and GROMACS are compiled with 64 bit settings?
Best regards and many thanks,
Catherine -- 
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] Regarding error

[Emanuel Birru]

I guess you have duplicate the "moleculetype" entries for CU1 in your topology 
file. Check your topology file again. You can not  have more than one 
"moleculetype" definition per molecule type.

Cheers,
Emmanuel







=
Emmanuel Birru
PhD Candidate

Faculty of Pharmacy and Pharmaceutical Sciences
Monash University (Parkville Campus)
381 Royal Parade, Parkville
Victoria 3052, Australia

Tel: Int + 61 3 9903 9187
E-mail: emanuel.bi...@monash.edu
www.pharm.monash.edu.au

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Seera Suryanarayana
Sent: Tuesday, 29 May 2012 5:02 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Regarding error

Dear all gromacs users,

I tried the  "grompp -c 3I40_ion.gro -p 3I40.top -o 
3I40_b4em.tpr -f em.mdp" and i got the following error.



Option Filename  Type Description

  -f em.mdp  Inputgrompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c   3I40_ion.gro  InputStructure file: gro g96 pdb tpr etc.
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n  index.ndx  Input, Opt.  Index file
  -p   3I40.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -o  3I40_b4em.tpr  Output   Run input file: tpr tpb tpa
  -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e   ener.edr  Input, Opt.  Energy file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-[no]v   bool   no  Be loud and noisy
-timereal   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
sites
-maxwarn int0   Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zerobool   no  Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum   bool   yes Renumber atomtypes and minimize number of
atomtypes

Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.19#
Generated 279 of the 1225 non-bonded parameter combinations

---
Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1228



Fatal error:
moleculetype CU1 is redefined.

Is there any explanation why is thid happening?

I would appreciate any help. Iam new in using MD and gromac in particular.

Suryanarayana Seera,
PhD student,
Hyderabad,
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] Regarding error

[Seera Suryanarayana]

Dear all gromacs users,

I tried the  "grompp -c 3I40_ion.gro -p 3I40.top -o
3I40_b4em.tpr -f em.mdp" and i got the following error.



Option Filename  Type Description

  -f em.mdp  Inputgrompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c   3I40_ion.gro  InputStructure file: gro g96 pdb tpr etc.
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n  index.ndx  Input, Opt.  Index file
  -p   3I40.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -o  3I40_b4em.tpr  Output   Run input file: tpr tpb tpa
  -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e   ener.edr  Input, Opt.  Energy file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-[no]v   bool   no  Be loud and noisy
-timereal   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
sites
-maxwarn int0   Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zerobool   no  Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum   bool   yes Renumber atomtypes and minimize number of
atomtypes

Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.19#
Generated 279 of the 1225 non-bonded parameter combinations

---
Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1228



Fatal error:
moleculetype CU1 is redefined.

Is there any explanation why is thid happening?

I would appreciate any help. Iam new in using MD and gromac in particular.

Suryanarayana Seera,
PhD student,
Hyderabad,
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