[gmx-users] how to include ionic strength

[amri ta]

Dear gromacs users,
 
I am simulating a protein which works in salt solution within cell. I have to 
include 4M salt (say, NaCl) to the simulation box. How can i include such ionic 
strength? Please outline me the procedure.
 
Thanks in advance.
Amrita Paul
 
 


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Re: [gmx-users] Replacing the PRODRG charges

[Mark Abraham]

Lucio Ricardo Montero Valenzuela wrote:

I want to run a MD in an unparameterized molecule similar to adenine. I can get
the approximated parameters in PRODRG. But I have read that PRODRG not always
give the correct charge. Is it a good idea to replace that charges using the
charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM and
OPLS forcefields)?. Or will it be mixing forcefields?.


That depends on your target forcefield for your MD.

Mark
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[gmx-users] Replacing the PRODRG charges

[Lucio Ricardo Montero Valenzuela]

I want to run a MD in an unparameterized molecule similar to adenine. I can get
the approximated parameters in PRODRG. But I have read that PRODRG not always
give the correct charge. Is it a good idea to replace that charges using the
charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM and
OPLS forcefields)?. Or will it be mixing forcefields?.

Lucio Ricardo Montero Valenzuela
Instituto de Biotecnologia, UNAM
Departamento de Biologia Molecular de Plantas
Av. Universidad 2001, Col. Chamilpa
Cuernavaca 62210
Mexico


Este mensaje fue enviado desde el servidor Webmail del Instituto de 
Biotecnologia.
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[gmx-users] about PMF calculation

[mircial]

Dear All:

 I want to do some PMF (Potenial of Mean Force) calculation by  
AFM pulling method using the pull code to study the unbinding of a  
protein and a ligand.


 I want pull the ligand from its binding site and calculate the  
PMF of the procedure, does it possible?


 I have read the user manual about PMF calculation carefully, but  
still not clear how to do . Does anyone have any tutorial about how to  
do this kind of calculation or any published papers doing this things?  
anyhelp is greatly appreciate!



   Best Wishes
R-X Gu

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Re: [gmx-users] PME on BlueGene

[Mark Abraham]

Jakob Wohlert wrote:

Mark Abraham wrote:

Jakob Wohlert wrote:

Hi,

I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the
configuration options from the wiki I have succeeded insofar that I 
have a

working program as long as I don't use PME.

I have tried many different variants of fftw - 2.1.5, 3.2.1, single
precision, double precision, different compiler optimizations and so on,
but it all ends the same: mdrun getting stuck somewhere in the
initialization process.

However, by using the built in fft library FFTPACK instead of FFTW, PME
will work, but that is not really an alternative.

In at least a few cases I have been able to pinpoint the location 
where it

hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls
MPI_Sendrecv, but then nothing else happens as far as I can tell.

I'm confused and I have sort of ran out of ideas right now. Has anyone
else encountered a problem like this, or has anyone any suggestions 
how to

proceed from here?

Thanks for your answer!

That looks to me like the separate PME nodes are dying through some 
linking problem and the problem is only manifest on node 0 when its 
sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this when 
all the nodes die at the first point they refer to a symbol in the FFT 
library.


Otherwise, looking at warnings/errors from the linker will be required. 
Ok, can you be a little more specific? Do you mean when compiling fftw, 
gromacs or both? I'm not very experienced with these kind of things.


GROMACS links with the FFTW library, so there ought to be warnings of 
potential problems at link time, i.e. the final stage of a GROMACS "make 
mdrun" (having started with a clean configuration, either freshly 
unpacked or after "make clean"). The last 100 or so lines of the output 
of "make mdrun" should have any relevant data.


Are you compiling an FFT library version for the back end, or the 
front end?
I'm trying to get it to work on the back end, on the front end it works 
fine! (So, I have fftw libraries for both).


My BG/L FFTW-3.2 configure line is

../configure --prefix /hpc/home/mja163/progs CC=blrts_xlc --host=powerpc 
--build=ppc64 CFLAGS=-qbgl -qarch=440d -qtune=440 -qnoautoconfig -O5 
--disable-fortran --enable-float


but you may need to tweak that for BG/P for all I know. Let me know 
when/if something works and I'll update the wiki.


Mark
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Re: [gmx-users] spc.itp for the amber force field

[Mark Abraham]

Rebeca García Fandiño wrote:

Hi,
I am trying to simulate a system using the parameters for ions developed 
by Joung et al. and implemented in Amber (frcmod.ionsjc_spce).
I have the topology and the crd file. Now, I want to obtain the topology 
for Gromacs using amb2gmx.pl, so I must change the default parameters 
(for tip3p) included in amb2gmx.pl.
I have seen that in the .tar file ffamber_v4.0 there is no a 
corresponding itp file for spc model of water in amber, so what 
parameters should I include for the section of bondtypes, angletypes, 
atoms, bonds, angles, settles,...? Those corresponding to the SCP in 
Gromacs directly?


Maybe. The required form for the nonbonded parameters depends on 
combination rules in force. First you should find out if SPC should work 
with AMBER, because literature that says that will probably also specify 
the parameters.


Perhaps simpler is use amb2gmx.pl to convert the non-solvent part, and 
then solvate with genbox and add ions with genion later. You'd still 
need SPC parameters for AMBER however.


Mark


Thank you very much for your help.
Best wishes,
 
Rebeca Garcia

Academic Visitor
Oxford University


Charlas más divertidas con el nuevo Windows Live Messenger 






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[gmx-users] ??using pull code when orientation of system changes during MD??

[DayleMarieSmith]

Greetings gromacs users--
I'm using the pull code to calculate the binding affinity of a small drug  
molecule to DNA, and I have a concern. Does the pull code (see my pull.ppa  
below) account for the fact that the DNA rotates/translates during MD, and  
therefore the x- y- and z- directions of pulling are changing with time?


verbose = no
runtype = afm
group_1 = drug
reference_group = DNA_site
reftype = com
afm_k1 = 1000

Have a great day,
Dayle Smith

Department of Physics
Whitman College
Walla Walla, WA, USA
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Re: [gmx-users] g_dist: extract distances between any two atom pairs

[Erik Marklund]

Justin A. Lemkul skrev:



Joern Lenz wrote:

Dear Gromacs Users,


I need to extract all possible distances between any two atom pairs 
of a small hexa- to dodecamer from a trajectory. The same is 
necessary for all dihedral angles of this protein. Now I wonder if 
this is possible without defining all of them manually in the ndx 
file and call g_dist for each of them ? Is there a short answer on 
that ? Maybe I missed the answer to that question in the forum ?!




Actually, this is one reason why open source is such a fantastic thing! 
With a little C-skill that functionality ought to be relatively simple 
to incorporate in some existing analysis tool. Not saying that it takes 
less time than scripting multiple calls to g_dist, but it can be reused 
in the future.
That level of detail might just require some iterative calls to g_dist 
and g_angle, unfortunately.  Scripts are your friend, here.  Also, 
g_mdmat might be useful, but it plots minimum distances between 
*residue* pairs, not atom pairs.  Much more convenient than repeated 
calls to g_dist, however :)


-Justin


greetings,
joern
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--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
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://xray.bmc.uu.se/molbiophys

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Re: [gmx-users] Gromacs output analysis

[Justin A. Lemkul]

rituraj purohit wrote:

Hello to everybody
I need the gromacs analysis document. I mean i want to do analysis 
(like; RMSD, traj)of my result which I got after simulation of protein 
molecule.
If anybody having any PDF or web link emphasis the analysis part, please 
forword me...


Chapter 8 of the manual contains information on all of the analysis programs.

-Justin


Thank you


Rituraj

On Wed, Jun 3, 2009 at 9:05 PM, <mailto:gmx-users-requ...@gromacs.org>> wrote:


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Today's Topics:

  1. protein running out of box (sheerychen)
  2. Re: protein running out of box (Justin A. Lemkul)
  3. Re: protein running out of box (ravi sharma)
  4. spc.itp for the amber force field (Rebeca Garc?a Fandi?o)
  5. Some questions regarding generating topologies (Manik Mayur)
  6. Re: Some questions regarding generating topologies
 (Justin A. Lemkul)


--

Message: 1
Date: Wed, 3 Jun 2009 15:37:57 +0200
From: sheerychen mailto:sheeryc...@gmail.com>>
Subject: [gmx-users] protein running out of box
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID:
   mailto:e1b92dfb0906030637y6cc57951oaf959aafd2b46...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"

Hello, every body. I have running a MD for 10ns. However, after 5ns
part of
protein will running out of the box and be located at other part of the
water box. And the whole structure seems ver strange. It seems that
it was
caused by the mass translation but  I have used the
comm_mode=Linear. Any
suggestions?

--
Zhen Chen,
Department of Bioprocess and Biosystem Engineering,
Hamburg University of Technology, Denickestr. 15, D-21071,
Hamburg,Germany
Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de
<mailto:zhen.c...@tuhh.de>
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Message: 2
Date: Wed, 03 Jun 2009 09:46:08 -0400
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] protein running out of box
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <4a267ea0.8090...@vt.edu <mailto:4a267ea0.8090...@vt.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



sheerychen wrote:
 > Hello, every body. I have running a MD for 10ns. However, after
5ns part
 > of protein will running out of the box and be located at other
part of
 > the water box. And the whole structure seems ver strange. It
seems that
 > it was caused by the mass translation but  I have used the
 > comm_mode=Linear. Any suggestions?
 >

What you are seeing is a normal consequence of periodicity.  There
is no "side"
in an infinite system:

http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions

-Justin

 > --
 > Zhen Chen,
 > Department of Bioprocess and Biosystem Engineering,
 > Hamburg University of Technology, Denickestr. 15, D-21071,
Hamburg,Germany
 > Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail:
zhen.c...@tuhh.de <mailto:zhen.c...@tuhh.de>
 > <mailto:zhen.c...@tuhh.de <mailto:zhen.c...@tuhh.de>>
 >
 >
 >

 >
 > ___
 > gmx-users mailing listgmx-users@gromacs.org
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 > http://www.gromacs.org/mailman/listinfo/gmx-users
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-

Re: [gmx-users] Gromacs output analysis

[XAvier Periole]

You should have a look at the manual/wiki/online documentation.
You'll find everything you need.

On Jun 3, 2009, at 8:28 PM, rituraj purohit wrote:


Hello to everybody
I need the gromacs analysis document. I mean i want to do analysis  
(like; RMSD, traj)of my result which I got after simulation of  
protein molecule.
If anybody having any PDF or web link emphasis the analysis part,  
please forword me...

Thank you

Rituraj

On Wed, Jun 3, 2009 at 9:05 PM,  wrote:
Send gmx-users mailing list submissions to
   gmx-users@gromacs.org

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When replying, please edit your Subject line so it is more specific
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Today's Topics:

  1. protein running out of box (sheerychen)
  2. Re: protein running out of box (Justin A. Lemkul)
  3. Re: protein running out of box (ravi sharma)
  4. spc.itp for the amber force field (Rebeca Garc?a Fandi?o)
  5. Some questions regarding generating topologies (Manik Mayur)
  6. Re: Some questions regarding generating topologies
 (Justin A. Lemkul)


--

Message: 1
Date: Wed, 3 Jun 2009 15:37:57 +0200
From: sheerychen 
Subject: [gmx-users] protein running out of box
To: gmx-users@gromacs.org
Message-ID:
   
Content-Type: text/plain; charset="iso-8859-1"

Hello, every body. I have running a MD for 10ns. However, after 5ns  
part of
protein will running out of the box and be located at other part of  
the
water box. And the whole structure seems ver strange. It seems that  
it was
caused by the mass translation but  I have used the  
comm_mode=Linear. Any

suggestions?

--
Zhen Chen,
Department of Bioprocess and Biosystem Engineering,
Hamburg University of Technology, Denickestr. 15, D-21071,  
Hamburg,Germany

Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de
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Message: 2
Date: Wed, 03 Jun 2009 09:46:08 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] protein running out of box
To: Discussion list for GROMACS users 
Message-ID: <4a267ea0.8090...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



sheerychen wrote:
> Hello, every body. I have running a MD for 10ns. However, after  
5ns part
> of protein will running out of the box and be located at other  
part of
> the water box. And the whole structure seems ver strange. It seems  
that

> it was caused by the mass translation but  I have used the
> comm_mode=Linear. Any suggestions?
>

What you are seeing is a normal consequence of periodicity.  There  
is no "side"

in an infinite system:

http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions

-Justin

> --
> Zhen Chen,
> Department of Bioprocess and Biosystem Engineering,
> Hamburg University of Technology, Denickestr. 15, D-21071,  
Hamburg,Germany

> Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de
> <mailto:zhen.c...@tuhh.de>
>
>
>  


>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

--


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




--

Message: 3
Date: Wed, 3 Jun 2009 07:07:57 -0700 (PDT)
From: ravi sharma 
Subject: Re: [gmx-users] protein running out of box
To: Discussion list for GROMACS users 
Message-ID: <147031.55861...@web54606.mail.re2.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear Zhen Chen

Protein is located stranger(sometime at the one side of the  
protein,in other frame other  side). Its not a problem.  Your  
simulation is fine. it is due to you had given PBC. thats why. You  
can reset your trejectory using trjconv.



regards

Ravi Datta Sharma  Lecturer,  Bioinformatics,
Depar

[gmx-users] Gromacs output analysis

[rituraj purohit]

Hello to everybody
I need the gromacs analysis document. I mean i want to do analysis (like;
RMSD, traj)of my result which I got after simulation of protein molecule.
If anybody having any PDF or web link emphasis the analysis part, please
forword me...
Thank you

Rituraj

On Wed, Jun 3, 2009 at 9:05 PM,  wrote:

> Send gmx-users mailing list submissions to
>gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>gmx-users-requ...@gromacs.org
>
> You can reach the person managing the list at
>gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>   1. protein running out of box (sheerychen)
>   2. Re: protein running out of box (Justin A. Lemkul)
>   3. Re: protein running out of box (ravi sharma)
>   4. spc.itp for the amber force field (Rebeca Garc?a Fandi?o)
>   5. Some questions regarding generating topologies (Manik Mayur)
>   6. Re: Some questions regarding generating topologies
>  (Justin A. Lemkul)
>
>
> --
>
> Message: 1
> Date: Wed, 3 Jun 2009 15:37:57 +0200
> From: sheerychen 
> Subject: [gmx-users] protein running out of box
> To: gmx-users@gromacs.org
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello, every body. I have running a MD for 10ns. However, after 5ns part of
> protein will running out of the box and be located at other part of the
> water box. And the whole structure seems ver strange. It seems that it was
> caused by the mass translation but  I have used the comm_mode=Linear. Any
> suggestions?
>
> --
> Zhen Chen,
> Department of Bioprocess and Biosystem Engineering,
> Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany
> Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de
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> An HTML attachment was scrubbed...
> URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/20c8cd2e/attachment-0001.html
>
> --
>
> Message: 2
> Date: Wed, 03 Jun 2009 09:46:08 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] protein running out of box
> To: Discussion list for GROMACS users 
> Message-ID: <4a267ea0.8090...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> sheerychen wrote:
> > Hello, every body. I have running a MD for 10ns. However, after 5ns part
> > of protein will running out of the box and be located at other part of
> > the water box. And the whole structure seems ver strange. It seems that
> > it was caused by the mass translation but  I have used the
> > comm_mode=Linear. Any suggestions?
> >
>
> What you are seeing is a normal consequence of periodicity.  There is no
> "side"
> in an infinite system:
>
> http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions
>
> -Justin
>
> > --
> > Zhen Chen,
> > Department of Bioprocess and Biosystem Engineering,
> > Hamburg University of Technology, Denickestr. 15, D-21071,
> Hamburg,Germany
> > Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de
> > <mailto:zhen.c...@tuhh.de>
> >
> >
> > 
> >
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
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> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
> --
>
> Message: 3
> Date: Wed, 3 Jun 2009 07:07:57 -0700 (PDT)
> From: ravi sharma 
> Subject: Re: [gmx-users] protein running out of box
> To: Discussion list for GROMACS users 
> Message-ID: <147031.55861...@web54606.mail.

RE: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)

[Shay Amram]

Hi Nicolas, 

 

I'll try that too since I am somewhat familiar with VMD scripting to I may
equilibrate a 2X 2Y 1Z membrane like you specified, 

and have a script find a timeframe where lipid composition fits what I need.


 

Thanks,

-Shay

 

 

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Nicolas Sapay
Sent: Wednesday, June 03, 2009 15:23 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)

 

 

 

Shay Amram a écrit :

> 

> Dear GROMACS users,

> 

> I have been trying to expand a membrane by a non-integer multiplier 

> (for example X1.5). This can be done using

> 

> *genbox -cs Membrane.gro -o Expanded_membrane.gro –box 1.5X 1.5Y Z***

> 

> This has worked very good with _homogenous_ membranes, and only very 

> short equilibrium times were required to re-equilibrate the membrane 

> (~10-20ns).

> 

> Now I am trying to deal the same way with _heterogeneous_ membrane 

> (POPG/POPE mixture, Mikko Karttunen et. al).

> 

> When trying to invoke the above command to the POPG/POPE membrane I 

> get a membrane with different compositions of lipids in the upper and 

> lower leaflets.

> 

> This happens (so I suspect) because the arrangement of lipids in each 

> leaflet is somewhat different so that the molecules that "get' to be 

> multiplied do not conserve the

> 

> same ratio of different lipids as in the original structure (which has 

> ratio of 1:3 POPG/POPE).

> 

> Is there a way to multiply the membrane by a _non-integer_ number AND 

> somehow conserve the ratio of different lipid species too?

> 

> Or at the very least, to have both upper and lower leaflets identical 

> after multiplication? (This, too, would help immensely).

> 

This is quite a difficult task unfortunately. Personally, I create a 

membrane patch larger than the one I want (e.g. 2x 2y 1z), load the gro 

file into VMD, then cut a patch the size/composition I need. That means 

doing selections like:

 

set sel [atomselect top "same resid as (x<... and x>... and y<...

and y>...)"]

 

Checking the number of lipids in each layer:

 

[atomselect top "resname DOPG and name P1 and z>... and (same resid

as (x<... and x>... and y<... and y>...))"] num

[atomselect top "resname DOPG and name P1 and z<... and (same resid

as (x<... and x>... and y<... and y>...))"] num

 

Completing the selection by manually adding the residues I need:

 

set sel [atomselect top "same resid as (x<... and x>... and y<...

and y>...) or resid ..."]

 

Saving the coordinates:

 

animate write pdb sel $sel

 

This is a tidy task and some equilibration is still required after that. 

Basic knowledge of TCL/VMD scripting languages may be required to 

facilitate/automate the work.

 

Nicolas

> 

> Thanks,

> 

> -Shay

> 

> 

> 

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Re: [gmx-users] PME on BlueGene

[Jakob Wohlert]

Mark Abraham wrote:

Jakob Wohlert wrote:

Hi,

I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the
configuration options from the wiki I have succeeded insofar that I 
have a

working program as long as I don't use PME.

I have tried many different variants of fftw - 2.1.5, 3.2.1, single
precision, double precision, different compiler optimizations and so on,
but it all ends the same: mdrun getting stuck somewhere in the
initialization process.

However, by using the built in fft library FFTPACK instead of FFTW, PME
will work, but that is not really an alternative.

In at least a few cases I have been able to pinpoint the location 
where it

hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls
MPI_Sendrecv, but then nothing else happens as far as I can tell.

I'm confused and I have sort of ran out of ideas right now. Has anyone
else encountered a problem like this, or has anyone any suggestions 
how to

proceed from here?

Thanks for your answer!

That looks to me like the separate PME nodes are dying through some 
linking problem and the problem is only manifest on node 0 when its 
sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this when 
all the nodes die at the first point they refer to a symbol in the FFT 
library.


Otherwise, looking at warnings/errors from the linker will be required. 
Ok, can you be a little more specific? Do you mean when compiling fftw, 
gromacs or both? I'm not very experienced with these kind of things.
Are you compiling an FFT library version for the back end, or the 
front end?
I'm trying to get it to work on the back end, on the front end it works 
fine! (So, I have fftw libraries for both).


/Jakob

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Re: [gmx-users] Some questions regarding generating topologies

[Justin A. Lemkul]

Manik Mayur wrote:
On Wed, Jun 3, 2009 at 9:04 PM, Justin A. Lemkul > wrote:




Manik Mayur wrote:

Hi,

Even though after going through the manual, I still have some
basic confusions regarding generating topologies.

1) I have generated an itp file after adding some Cl- ions using
genion. It goes like this:


This is unnecessary.  Just #include "ions.itp" and the parameters
for Cl- for whatever force field you're using are included.


Thanks for the reply. I will try to follow your suggestion, but just for 
clarification, setting nrexcl=0 will allow nb interaction between all 
the atoms in a molecule?


Using nrexcl only applies to intramolecular nonbonded interactions.  There has 
to be some reason with nrexcl = 1 is specified for ions in ions.itp, but that 
may have to do with something in the code.  I suppose, in general, nrexcl = 0 
would include all interactions, but you probably don't want to do that for most 
molecules, since, i.e. neighboring (bonded) atoms interact principally through 
the bonded interaction; nonbonded calculations should not be applied to this 
atom pair.




[ moleculetype ]
; Namenrexcl
Cl_ion   0

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge  
mass  typeBchargeB  massB
1CL-  1Cl- Cl  1 -1
35.453   ; qtot -1
2CL-  2Cl- Cl  2 -1
35.453   ; qtot -2
3CL-  3Cl- Cl  3 -1
35.453   ; qtot -3




To allow nb interactions between all the atoms in the molecule
Cl_ion, is setting nrexcl = 0 okay?

2) In spce.itp provided with GROMACS,

[ moleculetype ]
; molname   nrexcl
SOL 2

while in the manual, on pg. 100 (Chapter-5 Topologies)
[ moleculetype ]
; molname   nrexcl
SOL 1

why is the inconsistency?


Probably just a typo.


So the correct version will be nrexcl=2, which means atoms no more than 
2 bonds away will be excluded from nb interactions. Is my undestanding 
correct?




Should be.

-Justin



3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is
recommended). Since SPC/E is one of the most used model, should
I consider using OPLS rather than GROMOS96, otherwise how
significant will be the errors?


An excellent comparison of different force fields and different
water models can be found in:

Hess and van der Vegt (2006) J. Phys. Chem. B 110: 17616-17626.


4) I am using GROMOS96 43a1, so am I allowed to change
combination rule to '2' ( '1'  is the default). How
significantly will it affect the simulations?


I would say it invalidates everything.  The defaults for combination
rules, bonded parameters, etc. are as much a part of each force
field as the atom types and charges.

-Justin

Any relevant idea/suggestion/reference is appreciated.

Thanks,

Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA




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-- 



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


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
De

Re: [gmx-users] Some questions regarding generating topologies

[Justin A. Lemkul]

Manik Mayur wrote:

Hi,

Even though after going through the manual, I still have some basic 
confusions regarding generating topologies.


1) I have generated an itp file after adding some Cl- ions using genion. 
It goes like this:




This is unnecessary.  Just #include "ions.itp" and the parameters for Cl- for 
whatever force field you're using are included.



[ moleculetype ]
; Namenrexcl
Cl_ion   0

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  
typeBchargeB  massB
 1CL-  1Cl- Cl  1 -1 35.453   ; 
qtot -1
 2CL-  2Cl- Cl  2 -1 35.453   ; 
qtot -2
 3CL-  3Cl- Cl  3 -1 35.453   ; 
qtot -3




To allow nb interactions between all the atoms in the molecule Cl_ion, 
is setting nrexcl = 0 okay?


2) In spce.itp provided with GROMACS,

[ moleculetype ]
; molname   nrexcl
SOL 2

while in the manual, on pg. 100 (Chapter-5 Topologies)
[ moleculetype ]
; molname   nrexcl
SOL 1

why is the inconsistency?



Probably just a typo.

3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is 
recommended). Since SPC/E is one of the most used model, should I 
consider using OPLS rather than GROMOS96, otherwise how significant will 
be the errors?




An excellent comparison of different force fields and different water models can 
be found in:


Hess and van der Vegt (2006) J. Phys. Chem. B 110: 17616-17626.

4) I am using GROMOS96 43a1, so am I allowed to change combination rule 
to '2' ( '1'  is the default). How significantly will it affect the 
simulations?




I would say it invalidates everything.  The defaults for combination rules, 
bonded parameters, etc. are as much a part of each force field as the atom types 
and charges.


-Justin


Any relevant idea/suggestion/reference is appreciated.

Thanks,

Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA




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--


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


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Re: [gmx-users] Some questions regarding generating topologies

[Manik Mayur]

On Wed, Jun 3, 2009 at 9:04 PM, Justin A. Lemkul  wrote:

>
>
> Manik Mayur wrote:
>
>> Hi,
>>
>> Even though after going through the manual, I still have some basic
>> confusions regarding generating topologies.
>>
>> 1) I have generated an itp file after adding some Cl- ions using genion.
>> It goes like this:
>>
>>
> This is unnecessary.  Just #include "ions.itp" and the parameters for Cl-
> for whatever force field you're using are included.
>

Thanks for the reply. I will try to follow your suggestion, but just for
clarification, setting nrexcl=0 will allow nb interaction between all the
atoms in a molecule?

 [ moleculetype ]
>> ; Namenrexcl
>> Cl_ion   0
>>
>> [ atoms ]
>> ;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
>>chargeB  massB
>> 1CL-  1Cl- Cl  1 -1 35.453   ;
>> qtot -1
>> 2CL-  2Cl- Cl  2 -1 35.453   ;
>> qtot -2
>> 3CL-  3Cl- Cl  3 -1 35.453   ;
>> qtot -3
>> 
>> 
>>
>> To allow nb interactions between all the atoms in the molecule Cl_ion, is
>> setting nrexcl = 0 okay?
>>
>> 2) In spce.itp provided with GROMACS,
>>
>> [ moleculetype ]
>> ; molname   nrexcl
>> SOL 2
>>
>> while in the manual, on pg. 100 (Chapter-5 Topologies)
>> [ moleculetype ]
>> ; molname   nrexcl
>> SOL 1
>>
>> why is the inconsistency?
>>
>>
> Probably just a typo.


So the correct version will be nrexcl=2, which means atoms no more than 2
bonds away will be excluded from nb interactions. Is my undestanding
correct?


>  3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is
>> recommended). Since SPC/E is one of the most used model, should I consider
>> using OPLS rather than GROMOS96, otherwise how significant will be the
>> errors?
>>
>>
> An excellent comparison of different force fields and different water
> models can be found in:
>
> Hess and van der Vegt (2006) J. Phys. Chem. B 110: 17616-17626.
>
>  4) I am using GROMOS96 43a1, so am I allowed to change combination rule to
>> '2' ( '1'  is the default). How significantly will it affect the
>> simulations?
>>
>>
> I would say it invalidates everything.  The defaults for combination rules,
> bonded parameters, etc. are as much a part of each force field as the atom
> types and charges.
>
> -Justin
>
>  Any relevant idea/suggestion/reference is appreciated.
>>
>> Thanks,
>>
>> Manik Mayur
>> Graduate student
>> Microfluidics Lab
>> Dept. of Mechanical Engg.
>> IIT Kharagpur
>> INDIA
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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[gmx-users] Some questions regarding generating topologies

[Manik Mayur]

Hi,

Even though after going through the manual, I still have some basic
confusions regarding generating topologies.

1) I have generated an itp file after adding some Cl- ions using genion. It
goes like this:

[ moleculetype ]
; Namenrexcl
Cl_ion   0

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
 1CL-  1Cl- Cl  1 -1 35.453   ; qtot
-1
 2CL-  2Cl- Cl  2 -1 35.453   ; qtot
-2
 3CL-  3Cl- Cl  3 -1 35.453   ; qtot
-3



To allow nb interactions between all the atoms in the molecule Cl_ion, is
setting nrexcl = 0 okay?

2) In spce.itp provided with GROMACS,

[ moleculetype ]
; molname   nrexcl
SOL 2

while in the manual, on pg. 100 (Chapter-5 Topologies)
[ moleculetype ]
; molname   nrexcl
SOL 1

why is the inconsistency?

3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is recommended).
Since SPC/E is one of the most used model, should I consider using OPLS
rather than GROMOS96, otherwise how significant will be the errors?

4) I am using GROMOS96 43a1, so am I allowed to change combination rule to
'2' ( '1'  is the default). How significantly will it affect the
simulations?

Any relevant idea/suggestion/reference is appreciated.

Thanks,

Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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[gmx-users] spc.itp for the amber force field

[Rebeca García Fandiño]

Hi,

I am trying to simulate a system using the parameters for ions developed by 
Joung et al. and implemented in Amber (frcmod.ionsjc_spce).

I have the topology and the crd file. Now, I want to obtain the topology for 
Gromacs using amb2gmx.pl, so I must change the default parameters (for tip3p) 
included in amb2gmx.pl.

I have seen that in the .tar file ffamber_v4.0 there is no a corresponding itp 
file for spc model of water in amber, so what parameters should I include for 
the section of bondtypes, angletypes, atoms, bonds, angles, settles,...? Those 
corresponding to the SCP in Gromacs directly? 

Thank you very much for your help.

Best wishes,

 

Rebeca Garcia 

Academic Visitor

Oxford University

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Re: [gmx-users] protein running out of box

[ravi sharma]

Dear Zhen Chen

Protein is located stranger(sometime at the one side of the protein,in other 
frame other  side). Its not a problem.  Your simulation is fine. it is due to 
you had given PBC. thats why. You can reset your trejectory using trjconv.


regards

Ravi Datta Sharma  Lecturer,  Bioinformatics,
Department of Microbiology,
CCS Unversity,
Meerut
  


--- On Wed, 3/6/09, sheerychen  wrote:

From: sheerychen 
Subject: [gmx-users] protein running out of box
To: gmx-users@gromacs.org
Date: Wednesday, 3 June, 2009, 7:07 PM

Hello, every body. I have running a MD for 10ns. However, after 5ns part of 
protein will running out of the box and be located at other part of the water 
box. And the whole structure seems ver strange. It seems that it was caused by 
the mass translation but  I have used the comm_mode=Linear. Any suggestions?


-- 
Zhen Chen,
Department of Bioprocess and Biosystem Engineering,
Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany
Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de



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  Own a website.Get an unlimited package.Pay next to nothing.*Go to 
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Re: [gmx-users] protein running out of box

[Justin A. Lemkul]

sheerychen wrote:
Hello, every body. I have running a MD for 10ns. However, after 5ns part 
of protein will running out of the box and be located at other part of 
the water box. And the whole structure seems ver strange. It seems that 
it was caused by the mass translation but  I have used the 
comm_mode=Linear. Any suggestions?




What you are seeing is a normal consequence of periodicity.  There is no "side" 
in an infinite system:


http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions

-Justin


--
Zhen Chen,
Department of Bioprocess and Biosystem Engineering,
Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany
Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de 






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--


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


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[gmx-users] protein running out of box

[sheerychen]

Hello, every body. I have running a MD for 10ns. However, after 5ns part of
protein will running out of the box and be located at other part of the
water box. And the whole structure seems ver strange. It seems that it was
caused by the mass translation but  I have used the comm_mode=Linear. Any
suggestions?

-- 
Zhen Chen,
Department of Bioprocess and Biosystem Engineering,
Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany
Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.c...@tuhh.de
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Re: [gmx-users] problem with FeS cluster

[Justin A. Lemkul]

subarna thakur wrote:

Hi
I have gone through the material you have earlier mentioned but  I am 
still in dark and not sure where to start. Should I make chages in the 
relevent .rtp file to incorporate the atoms of the FE-S cluster?


If you derive your own parameters, you can either make an .rtp entry for the 
cluster, or simply generate an .itp file by hand.  Either way will work, but no 
matter what, it is not a trivial task to derive the appropriate parameters. 
Making and .rtp entry/.itp file is simple, proving the validity of your 
parameters is not.


-Justin


Subarna


*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Wednesday, 3 June, 2009 4:46:37 PM
*Subject:* Re: [gmx-users] problem with FeS cluster



subarna thakur wrote:
 > Hello user
 > Can anybody please tell me how to prepare a topology file for the 
FES4 cluster incorporated in a protein
 > 

I passed along some useful information to you yesterday.  There is no 
easy answer.  To do so would involve a large amount of work, in any 
case, if it is even possible to model this species using a standard MM 
force field.


-Justin

 > Subarna
 >
 > 
 > Cricket on your mind? Visit the ultimate cricket website. Enter now! 


 >
 >
 > 
 >
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-- 

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


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--


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


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Re: [gmx-users] Re: Re: Normal of the benzene and z axis.

[David van der Spoel]

Eudes Fileti wrote:
Dear David, thanks for the reply. 
In fact 3 carbons can provide me the normal 
vector of the molecule. But according to manual, 
g_sorient considers the angle formed by the triple 1 2 3, 
as the vector that goes from 2 to the midpoint of 1 and 3 
(which is the plan of the molecule). 
So how can I to build a index file for g_sorient to plot the
normal vector? 


g_sorient -h:

g_sorient analyzes solvent orientation around solutes. It calculates two
angles between the vector from one or more reference positions to the first
atom of each solvent molecule:
theta1: the angle with the vector from the first atom of the solvent 
molecule

to the midpoint between atoms 2 and 3.
theta2: the angle with the normal of the solvent plane, defined by the same
three atoms, or when the option -v23 is set the angle with the vector 
between

atoms 2 and 3.
The reference can be a set of atoms or the center of mass of a set of atoms.
The group of solvent atoms should consist of 3 atoms per solvent molecule.
Only solvent molecules between -rmin and -rmax are considered for -o and -no
each frame.




Sorry if the question is obvious and I can't to see.
Bests
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4437-0196


 

Message: 5
Date: Wed, 3 Jun 2009 09:08:43 -0300
From: Eudes Fileti mailto:fil...@ufabc.edu.br>>
Subject: [gmx-users] Re: Normal of the benzene and z axis.
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID:
   <65e289a20906030508y708e2633rddba6dc6c8f16...@mail.gmail.com
<mailto:65e289a20906030508y708e2633rddba6dc6c8f16...@mail.gmail.com>>
Content-Type: text/plain; charset="windows-1252"

Thanks for the reply.
But I have tried use g_sorient tool and I could
not see what the sequence of index give me a normal
vector of the molecule of benzene.
There another tool for this analysis?
Bests
eef
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4437-0196
http://fileti.ufabc.edu.br


On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti mailto:fil...@ufabc.edu.br>> wrote:

 > Dear gmx users;How can I calculate the angle distribution forthe
angle
 > between the normal of the benzene and z axis?
 > Bests
 > eef
 > ___
 > Eudes Eterno Fileti
 > Centro de Ciências Naturais e Humanas
 > Universidade Federal do ABC — CCNH
 > Av. dos Estados, 5001
 > Santo André - SP - Brasil
 > CEP 09210-971
 > +55.11.4437-0196
 > http://fileti.ufabc.edu.br
 >
-- next part --
An HTML attachment was scrubbed...
URL:

http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/31b76231/attachment-0001.html

--

Eudes Fileti wrote:
 > Thanks for the reply.
 > But I have tried use g_sorient tool and I could
 > not see what the sequence of index give me a normal
 > vector of the molecule of benzene.
three carbons in the ring.
 > There another tool for this analysis?
 > Bests
 > eef
 > ___
 > Eudes Eterno Fileti
 > Centro de Ciências Naturais e Humanas
 > Universidade Federal do ABC — CCNH
 > Av. dos Estados, 5001
 > Santo André - SP - Brasil
 > CEP 09210-971
 > +55.11.4437-0196
 > http://fileti.ufabc.edu.br
 >
 >
 > On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti mailto:fil...@ufabc.edu.br>
 > <mailto:fil...@ufabc.edu.br <mailto:fil...@ufabc.edu.br>>> wrote:
 >
 > Dear gmx users;
 > How can I calculate the angle distribution for
 > the angle between the normal of the benzene and z axis?
 > Bests
 > eef
 > ___
 > Eudes Eterno Fileti
 > Centro de Ciências Naturais e Humanas
 > Universidade Federal do ABC — CCNH
 > Av. dos Estados, 5001
 > Santo André - SP - Brasil
 > CEP 09210-971
 > +55.11.4437-0196
 > http://fileti.ufabc.edu.br
 >





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Re: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)

[Nicolas Sapay]

Shay Amram a écrit :


Dear GROMACS users,

I have been trying to expand a membrane by a non-integer multiplier 
(for example X1.5). This can be done using


*genbox -cs Membrane.gro -o Expanded_membrane.gro –box 1.5X 1.5Y Z***

This has worked very good with _homogenous_ membranes, and only very 
short equilibrium times were required to re-equilibrate the membrane 
(~10-20ns).


Now I am trying to deal the same way with _heterogeneous_ membrane 
(POPG/POPE mixture, Mikko Karttunen et. al).


When trying to invoke the above command to the POPG/POPE membrane I 
get a membrane with different compositions of lipids in the upper and 
lower leaflets.


This happens (so I suspect) because the arrangement of lipids in each 
leaflet is somewhat different so that the molecules that "get' to be 
multiplied do not conserve the


same ratio of different lipids as in the original structure (which has 
ratio of 1:3 POPG/POPE).


Is there a way to multiply the membrane by a _non-integer_ number AND 
somehow conserve the ratio of different lipid species too?


Or at the very least, to have both upper and lower leaflets identical 
after multiplication? (This, too, would help immensely).


This is quite a difficult task unfortunately. Personally, I create a 
membrane patch larger than the one I want (e.g. 2x 2y 1z), load the gro 
file into VMD, then cut a patch the size/composition I need. That means 
doing selections like:


   set sel [atomselect top "same resid as (x<... and x>... and y<...
   and y>...)"]

Checking the number of lipids in each layer:

   [atomselect top "resname DOPG and name P1 and z>... and (same resid
   as (x<... and x>... and y<... and y>...))"] num
   [atomselect top "resname DOPG and name P1 and z<... and (same resid
   as (x<... and x>... and y<... and y>...))"] num

Completing the selection by manually adding the residues I need:

   set sel [atomselect top "same resid as (x<... and x>... and y<...
   and y>...) or resid ..."]

Saving the coordinates:

   animate write pdb sel $sel

This is a tidy task and some equilibration is still required after that. 
Basic knowledge of TCL/VMD scripting languages may be required to 
facilitate/automate the work.


Nicolas


Thanks,

-Shay



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[gmx-users] Re: Re: Normal of the benzene and z axis.

[Eudes Fileti]

Dear David, thanks for the reply.
In fact 3 carbons can provide me the normal
vector of the molecule. But according to manual,
g_sorient considers the angle formed by the triple 1 2 3,
as the vector that goes from 2 to the midpoint of 1 and 3
(which is the plan of the molecule).
So how can I to build a index file for g_sorient to plot the
normal vector?
Sorry if the question is obvious and I can't to see.
Bests
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4437-0196
>
>
>  
>
> Message: 5
> Date: Wed, 3 Jun 2009 09:08:43 -0300
> From: Eudes Fileti 
> Subject: [gmx-users] Re: Normal of the benzene and z axis.
> To: gmx-users@gromacs.org
> Message-ID:
><65e289a20906030508y708e2633rddba6dc6c8f16...@mail.gmail.com>
> Content-Type: text/plain; charset="windows-1252"
>
> Thanks for the reply.
> But I have tried use g_sorient tool and I could
> not see what the sequence of index give me a normal
> vector of the molecule of benzene.
> There another tool for this analysis?
> Bests
> eef
> ___
> Eudes Eterno Fileti
> Centro de Ciências Naturais e Humanas
> Universidade Federal do ABC — CCNH
> Av. dos Estados, 5001
> Santo André - SP - Brasil
> CEP 09210-971
> +55.11.4437-0196
> http://fileti.ufabc.edu.br
>
>
> On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti  wrote:
>
> > Dear gmx users;How can I calculate the angle distribution forthe angle
> > between the normal of the benzene and z axis?
> > Bests
> > eef
> > ___
> > Eudes Eterno Fileti
> > Centro de Ciências Naturais e Humanas
> > Universidade Federal do ABC — CCNH
> > Av. dos Estados, 5001
> > Santo André - SP - Brasil
> > CEP 09210-971
> > +55.11.4437-0196
> > http://fileti.ufabc.edu.br
> >
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/31b76231/attachment-0001.html
>
> --
>
> Eudes Fileti wrote:
> > Thanks for the reply.
> > But I have tried use g_sorient tool and I could
> > not see what the sequence of index give me a normal
> > vector of the molecule of benzene.
> three carbons in the ring.
> > There another tool for this analysis?
> > Bests
> > eef
> > ___
> > Eudes Eterno Fileti
> > Centro de Ciências Naturais e Humanas
> > Universidade Federal do ABC — CCNH
> > Av. dos Estados, 5001
> > Santo André - SP - Brasil
> > CEP 09210-971
> > +55.11.4437-0196
> > http://fileti.ufabc.edu.br
> >
> >
> > On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti  > <mailto:fil...@ufabc.edu.br>> wrote:
> >
> > Dear gmx users;
> > How can I calculate the angle distribution for
> > the angle between the normal of the benzene and z axis?
> > Bests
> > eef
> > ___
> > Eudes Eterno Fileti
> > Centro de Ciências Naturais e Humanas
> > Universidade Federal do ABC — CCNH
> > Av. dos Estados, 5001
> > Santo André - SP - Brasil
> > CEP 09210-971
> > +55.11.4437-0196
> > http://fileti.ufabc.edu.br
> >
>
>
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Re: [gmx-users] Re: Normal of the benzene and z axis.

[David van der Spoel]

Eudes Fileti wrote:

Thanks for the reply.
But I have tried use g_sorient tool and I could
not see what the sequence of index give me a normal
vector of the molecule of benzene.

three carbons in the ring.

There another tool for this analysis?
Bests
eef
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4437-0196
http://fileti.ufabc.edu.br


On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti > wrote:


Dear gmx users;
How can I calculate the angle distribution for
the angle between the normal of the benzene and z axis?
Bests
eef
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4437-0196
http://fileti.ufabc.edu.br





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--
David.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se

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[gmx-users] Re: Normal of the benzene and z axis.

[Eudes Fileti]

Thanks for the reply.
But I have tried use g_sorient tool and I could
not see what the sequence of index give me a normal
vector of the molecule of benzene.
There another tool for this analysis?
Bests
eef
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4437-0196
http://fileti.ufabc.edu.br


On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti  wrote:

> Dear gmx users;How can I calculate the angle distribution forthe angle
> between the normal of the benzene and z axis?
> Bests
> eef
> ___
> Eudes Eterno Fileti
> Centro de Ciências Naturais e Humanas
> Universidade Federal do ABC — CCNH
> Av. dos Estados, 5001
> Santo André - SP - Brasil
> CEP 09210-971
> +55.11.4437-0196
> http://fileti.ufabc.edu.br
>
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Re: [gmx-users] problem with FeS cluster

[subarna thakur]

Hi
I have gone through the material you have earlier mentioned but  I am still in 
dark and not sure where to start. Should I make chages in the relevent .rtp 
file to incorporate the atoms of the FE-S cluster?
Subarna





From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Wednesday, 3 June, 2009 4:46:37 PM
Subject: Re: [gmx-users] problem with FeS cluster



subarna thakur wrote:
> Hello user
> Can anybody please tell me how to prepare a topology file for the FES4 
> cluster incorporated in a protein
>  

I passed along some useful information to you yesterday.  There is no easy 
answer.  To do so would involve a large amount of work, in any case, if it is 
even possible to model this species using a standard MM force field.

-Justin

> Subarna
> 
> 
> Cricket on your mind? Visit the ultimate cricket website. Enter now! 
> 
> 
> 
> 
> 
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-- 

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


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  Own a website.Get an unlimited package.Pay next to nothing.*Go to 
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Re: [gmx-users] g_dist: extract distances between any two atom pairs

[Justin A. Lemkul]

Joern Lenz wrote:

Dear Gromacs Users,


I need to extract all possible distances between any two atom pairs of a small 
hexa- to dodecamer from a trajectory. The same is necessary for all dihedral 
angles of this protein. Now I wonder if this is possible without defining all 
of them manually in the ndx file and call g_dist for each of them ? Is there 
a short answer on that ? Maybe I missed the answer to that question in the 
forum ?!




That level of detail might just require some iterative calls to g_dist and 
g_angle, unfortunately.  Scripts are your friend, here.  Also, g_mdmat might be 
useful, but it plots minimum distances between *residue* pairs, not atom pairs. 
 Much more convenient than repeated calls to g_dist, however :)


-Justin


greetings,
joern
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--


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


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Re: [gmx-users] problem with FeS cluster

[Justin A. Lemkul]

subarna thakur wrote:

Hello user
Can anybody please tell me how to prepare a topology file for the FES4 
cluster incorporated in a protein
 


I passed along some useful information to you yesterday.  There is no easy 
answer.  To do so would involve a large amount of work, in any case, if it is 
even possible to model this species using a standard MM force field.


-Justin


Subarna


Cricket on your mind? Visit the ultimate cricket website. Enter now! 






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--


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


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Re: [gmx-users] problem in inflategro

[Justin A. Lemkul]

Samik Bhattacharya wrote:
hi i am simulating a membrane protein where i am facing some 
difficulties in running the inflategro.pl available at 
http://moose.bio.ucalgary.ca. i cant understand what should be the input 
of areaperlipid.dat file?  where can i find that file ? or i've to make 
it myself? also contents of the same file is not very claer to me... pls 
a little help will be very encouraging. Thanking you


The areaperlipid.dat is output, a way of assessing progress of the 
inflating/shrinking process.


-Justin


Shamik



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--


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


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Re: [gmx-users] lincs warning

[XAvier Periole]

On Jun 3, 2009, at 10:48 AM, Erik Marklund wrote:


XAvier Periole skrev:


On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote:


Hi XAvier,
Do you use virtual sites? I've seen this when I used virtual sites,

No virtual sites.
large time steps and a system that probably wasn't equilibrated  
enough.

time step 2 fs and a system totally equilibrated, nothing there.

I would have considered this if the warning were reproduced when
restarting the simulation.

It seems more that it is a loss of accuracy due to communication
between CPUs ?

If you use dynamic load balancing then you are sacrificing binary  
reproducibility. Because of this, and the chaotic nature of MD, the  
error will likely not occur at the same point in your continuation.  
Still, the source of the error persists and is what demands  
attention I'd say.
Well starting from a cpt file, I would expect reproducibility at the  
difference that the

decomposition over CPUs might be refreshed.

It might be but I am still favoring a communication issue.

I am now testing the effect of using -rdd and -rcon on the LINCS  
warnings.

XAvier.


Ran.

XAvier Periole wrote:


Dears,

I am experiencing some problems running a few proteins in water
(GROMOS43a1/SPC)
with gmx-4.0.4 using 32 CPUs.

After some ns lincs warnings appear and eventually the simulation
crashes dues
to too many lincs warnings.

When restarting the simulation feeding "-cpi md.cpt" to mdrun the
simulation restarts
fine and no lincs warning are reported on the same portion of the
simulation. The
simulation runs again for some ns and the same happens: new lincs
warning appear
and eventually the simulation crashes again.

Any explanation for this? Any solution?

Best,
XAvier.

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--
---
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Laboratory of Molecular Biophysics,
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://xray.bmc.uu.se/molbiophys

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Re: [gmx-users] lincs warning

[XAvier Periole]

On Jun 3, 2009, at 10:58 AM, Giovanni Bussi wrote:


Dear Xavier,

With the default flag for pbc (periodic_molecules=no) you may end up
in lincs problem if an atom of the protein becomes too close to the
image of another atom of the protein.

If this is your case, use periodic_molecules=yes, or enlarge the  
solvation cell.
Thanks, I have however a very large water box and no problem there I  
believe.


Hope this helps,

Giovanni



On Wed, Jun 3, 2009 at 10:48 AM, Erik Marklund  
 wrote:

XAvier Periole skrev:


On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote:


Hi XAvier,
Do you use virtual sites? I've seen this when I used virtual sites,


No virtual sites.


large time steps and a system that probably wasn't equilibrated  
enough.


time step 2 fs and a system totally equilibrated, nothing there.

I would have considered this if the warning were reproduced when
restarting the simulation.

It seems more that it is a loss of accuracy due to communication
between CPUs ?


If you use dynamic load balancing then you are sacrificing binary
reproducibility. Because of this, and the chaotic nature of MD, the  
error
will likely not occur at the same point in your continuation.  
Still, the

source of the error persists and is what demands attention I'd say.


XAvier.


Ran.

XAvier Periole wrote:


Dears,

I am experiencing some problems running a few proteins in water
(GROMOS43a1/SPC)
with gmx-4.0.4 using 32 CPUs.

After some ns lincs warnings appear and eventually the simulation
crashes dues
to too many lincs warnings.

When restarting the simulation feeding "-cpi md.cpt" to mdrun the
simulation restarts
fine and no lincs warning are reported on the same portion of the
simulation. The
simulation runs again for some ns and the same happens: new lincs
warning appear
and eventually the simulation crashes again.

Any explanation for this? Any solution?

Best,
XAvier.

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--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
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://xray.bmc.uu.se/molbiophys

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Re: [gmx-users] lincs warning

[Giovanni Bussi]

Dear Xavier,

With the default flag for pbc (periodic_molecules=no) you may end up
in lincs problem if an atom of the protein becomes too close to the
image of another atom of the protein.

If this is your case, use periodic_molecules=yes, or enlarge the solvation cell.

Hope this helps,

Giovanni



On Wed, Jun 3, 2009 at 10:48 AM, Erik Marklund  wrote:
> XAvier Periole skrev:
>>
>> On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote:
>>
>>> Hi XAvier,
>>> Do you use virtual sites? I've seen this when I used virtual sites,
>>
>> No virtual sites.
>>>
>>> large time steps and a system that probably wasn't equilibrated enough.
>>
>> time step 2 fs and a system totally equilibrated, nothing there.
>>
>> I would have considered this if the warning were reproduced when
>> restarting the simulation.
>>
>> It seems more that it is a loss of accuracy due to communication
>> between CPUs ?
>>
> If you use dynamic load balancing then you are sacrificing binary
> reproducibility. Because of this, and the chaotic nature of MD, the error
> will likely not occur at the same point in your continuation. Still, the
> source of the error persists and is what demands attention I'd say.
>>
>> XAvier.
>>
>>> Ran.
>>>
>>> XAvier Periole wrote:

 Dears,

 I am experiencing some problems running a few proteins in water
 (GROMOS43a1/SPC)
 with gmx-4.0.4 using 32 CPUs.

 After some ns lincs warnings appear and eventually the simulation
 crashes dues
 to too many lincs warnings.

 When restarting the simulation feeding "-cpi md.cpt" to mdrun the
 simulation restarts
 fine and no lincs warning are reported on the same portion of the
 simulation. The
 simulation runs again for some ns and the same happens: new lincs
 warning appear
 and eventually the simulation crashes again.

 Any explanation for this? Any solution?

 Best,
 XAvier.

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>>> ___
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>
>
> --
> ---
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> er...@xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
>
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[gmx-users] g_dist: extract distances between any two atom pairs

[Joern Lenz]

Dear Gromacs Users,


I need to extract all possible distances between any two atom pairs of a small 
hexa- to dodecamer from a trajectory. The same is necessary for all dihedral 
angles of this protein. Now I wonder if this is possible without defining all 
of them manually in the ndx file and call g_dist for each of them ? Is there 
a short answer on that ? Maybe I missed the answer to that question in the 
forum ?!

greetings,
joern
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Re: [gmx-users] lincs warning

[Erik Marklund]

XAvier Periole skrev:


On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote:


Hi XAvier,
Do you use virtual sites? I've seen this when I used virtual sites,

No virtual sites.

large time steps and a system that probably wasn't equilibrated enough.

time step 2 fs and a system totally equilibrated, nothing there.

I would have considered this if the warning were reproduced when
restarting the simulation.

It seems more that it is a loss of accuracy due to communication
between CPUs ?

If you use dynamic load balancing then you are sacrificing binary 
reproducibility. Because of this, and the chaotic nature of MD, the 
error will likely not occur at the same point in your continuation. 
Still, the source of the error persists and is what demands attention 
I'd say.

XAvier.


Ran.

XAvier Periole wrote:


Dears,

I am experiencing some problems running a few proteins in water
(GROMOS43a1/SPC)
with gmx-4.0.4 using 32 CPUs.

After some ns lincs warnings appear and eventually the simulation
crashes dues
to too many lincs warnings.

When restarting the simulation feeding "-cpi md.cpt" to mdrun the
simulation restarts
fine and no lincs warning are reported on the same portion of the
simulation. The
simulation runs again for some ns and the same happens: new lincs
warning appear
and eventually the simulation crashes again.

Any explanation for this? Any solution?

Best,
XAvier.

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--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
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://xray.bmc.uu.se/molbiophys

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[gmx-users] problem with FeS cluster

[subarna thakur]

Hello user
Can anybody please tell me how to prepare a topology file for the FES4 cluster 
incorporated in a protein

Subarna


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RE: [gmx-users] .itp file for an electrode

[Kukol, Andreas]

It is not very difficult to construct a topology (itp-file) for one atom. You 
may look at the definitions of sodium or chloride in the .rtp file for the 
force field you want to use and adapt them to your needs.

Then you need the atom coordinates of the two parallel lattices, which you can 
make with genconf starting from a one atom coordinate file.

Andreas


---

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Negar Ashari Astani
Sent: 03 June 2009 09:22
To: gmx-users@gromacs.org
Subject: [gmx-users] .itp file for an electrode

Hello everbody

I'm trying to repeat a simulation which is reported in a paper. I'm going to 
model an electrode according to this exact method reported in this paper "the 
electrodes were modeled as two parallel XY square lattices made of charged 
Lennard-Jones spheres with radii 0.11 nm. Surface charge densities on the 
electrodes  were varied  by the partial  charge of the lattice spheres."
I'm looking for the .itp file for a metalic electrode.
Does anyone by any chance have such a file?

Thank you all so much

--
Negar Ashari Astani
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[gmx-users] .itp file for an electrode

[Negar Ashari Astani]

Hello everbody

I'm trying to repeat a simulation which is reported in a paper. I'm going to
model an electrode according to this exact method reported in this paper
"the electrodes were modeled as two parallel XY square lattices made of
charged Lennard-Jones spheres with radii 0.11 nm. Surface charge densities
on the electrodes  were varied  by the partial  charge of the lattice
spheres."
I'm looking for the .itp file for a metalic electrode.
Does anyone by any chance have such a file?

Thank you all so much

-- 
Negar Ashari Astani
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Re: [gmx-users] lincs warning

[XAvier Periole]

On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote:


Hi XAvier,
Do you use virtual sites? I've seen this when I used virtual sites,

No virtual sites.
large time steps and a system that probably wasn't equilibrated  
enough.

time step 2 fs and a system totally equilibrated, nothing there.

I would have considered this if the warning were reproduced when
restarting the simulation.

It seems more that it is a loss of accuracy due to communication
between CPUs ?

XAvier.


Ran.

XAvier Periole wrote:


Dears,

I am experiencing some problems running a few proteins in water
(GROMOS43a1/SPC)
with gmx-4.0.4 using 32 CPUs.

After some ns lincs warnings appear and eventually the simulation
crashes dues
to too many lincs warnings.

When restarting the simulation feeding "-cpi md.cpt" to mdrun the
simulation restarts
fine and no lincs warning are reported on the same portion of the
simulation. The
simulation runs again for some ns and the same happens: new lincs
warning appear
and eventually the simulation crashes again.

Any explanation for this? Any solution?

Best,
XAvier.

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Re: [gmx-users] lincs warning

[Ran Friedman]

Hi XAvier,
Do you use virtual sites? I've seen this when I used virtual sites,
large time steps and a system that probably wasn't equilibrated enough.
Ran.

XAvier Periole wrote:
>
> Dears,
>
> I am experiencing some problems running a few proteins in water
> (GROMOS43a1/SPC)
> with gmx-4.0.4 using 32 CPUs.
>
> After some ns lincs warnings appear and eventually the simulation
> crashes dues
> to too many lincs warnings.
>
> When restarting the simulation feeding "-cpi md.cpt" to mdrun the
> simulation restarts
> fine and no lincs warning are reported on the same portion of the
> simulation. The
> simulation runs again for some ns and the same happens: new lincs
> warning appear
> and eventually the simulation crashes again.
>
> Any explanation for this? Any solution?
>
> Best,
> XAvier.
>
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Re: [gmx-users] lincs warning

[XAvier Periole]

On Jun 3, 2009, at 9:51 AM, Mark Abraham wrote:


XAvier Periole wrote:

Dears,
I am experiencing some problems running a few proteins in water  
(GROMOS43a1/SPC)

with gmx-4.0.4 using 32 CPUs.
After some ns lincs warnings appear and eventually the simulation  
crashes dues

to too many lincs warnings.
When restarting the simulation feeding "-cpi md.cpt" to mdrun the  
simulation restarts
fine and no lincs warning are reported on the same portion of the  
simulation. The
simulation runs again for some ns and the same happens: new lincs  
warning appear

and eventually the simulation crashes again.
Any explanation for this? Any solution?


Check out 4.0.5 release notes? Check out 4.0.5?

Yes. Nothing that seem to matter to these lincs warnings!


Mark
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[gmx-users] Fwd: problem with FES4 cluster

[Tsjerk Wassenaar]

Subarna,

I am not a helpdesk or mailing list, if I had had the answer, I would
have replied on the mailing list already. Then, if you feel it is
appropriate to send a mail to someone you don't know, at least take
the effort to write a complete message.

Tsjerk


-- Forwarded message --
From: subarna thakur 
Date: Wed, Jun 3, 2009 at 9:34 AM
Subject: problem with FES4 cluster
To: tsje...@gmail.com



Hi
I am facing a problem with a protein with Ferro sulphur cluster
(FS4),I am unable to construct the .gro file with pdb2gmx command. How
do i construct the topology file of the ligand and where do I add the
appropriate definitions for the bonds, angles, dihedrals, pairs, etc.



Subarna Thkaur

Ph.D Student

University of North Bengal



Cricket on your mind? Visit the ultimate cricket website. Enter now!


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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RE: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)

[Shay Amram]

By some fluke one of the layers consists of the lipid ratio I require (while
the other does not).

I will try your suggestion regarding to horizontal flip of that layer.

Thanks!

-Shay

 

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: Tuesday, June 02, 2009 23:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)

 

 

 

Shay Amram wrote:

> Dear GROMACS users,

> 

>  

> 

> I have been trying to expand a membrane by a non-integer multiplier (for 

> example X1.5). This can be done using

> 

>  

> 

> *genbox -cs Membrane.gro -o Expanded_membrane.gro -box 1.5X 1.5Y Z***

> 

>  

> 

> This has worked very good with _homogenous_ membranes, and only very 

> short equilibrium times were required to re-equilibrate the membrane 

> (~10-20ns).

> 

> Now I am trying to deal the same way with _heterogeneous_ membrane 

> (POPG/POPE mixture, Mikko Karttunen et. al).

> 

>  

> 

> When trying to invoke the above command to the POPG/POPE membrane I get 

> a membrane with different compositions of lipids in the upper and lower 

> leaflets.

> 

> This happens (so I suspect) because the arrangement of lipids in each 

> leaflet is somewhat different so that the molecules that "get' to be 

> multiplied do not conserve the

> 

> same ratio of different lipids as in the original structure (which has 

> ratio of 1:3 POPG/POPE).

> 

>  

 

If you have an excess of POPE, you can (either manually, or by using a
script) 

randomly choose some POPE to be converted to (or replaced with) POPG by some


clever means.  This is not a trivial task.

 

> 

> Is there a way to multiply the membrane by a _non-integer_ number AND 

> somehow conserve the ratio of different lipid species too?

> 

 

The output is dependent upon the configuration of the input and the box
size, so 

no, there is no straightforward, automatic, way of doing so given the 

constraints of your box dimensions.

 

> Or at the very least, to have both upper and lower leaflets identical 

> after multiplication? (This, too, would help immensely).

> 

>  

 

If you can construct a satisfactory monolayer, you can manipulate its 

coordinates (i.e. horizontal flip and translation) to create a bilayer.  You


would have to do plenty of equilibration after doing so, of course.

 

-Justin

 

> 

> Thanks,

> 

> -Shay

> 

>  

> 

>  

> 

> 

> 

> 

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-- 



 

Justin A. Lemkul

Ph.D. Candidate

ICTAS Doctoral Scholar

Department of Biochemistry

Virginia Tech

Blacksburg, VA

jalemkul[at]vt.edu | (540) 231-9080

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 



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Re: [gmx-users] lincs warning

[Mark Abraham]

XAvier Periole wrote:


Dears,

I am experiencing some problems running a few proteins in water 
(GROMOS43a1/SPC)

with gmx-4.0.4 using 32 CPUs.

After some ns lincs warnings appear and eventually the simulation 
crashes dues

to too many lincs warnings.

When restarting the simulation feeding "-cpi md.cpt" to mdrun the 
simulation restarts
fine and no lincs warning are reported on the same portion of the 
simulation. The
simulation runs again for some ns and the same happens: new lincs 
warning appear

and eventually the simulation crashes again.

Any explanation for this? Any solution?


Check out 4.0.5 release notes? Check out 4.0.5?

Mark
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[gmx-users] lincs warning

[XAvier Periole]

Dears,

I am experiencing some problems running a few proteins in water  
(GROMOS43a1/SPC)

with gmx-4.0.4 using 32 CPUs.

After some ns lincs warnings appear and eventually the simulation  
crashes dues

to too many lincs warnings.

When restarting the simulation feeding "-cpi md.cpt" to mdrun the  
simulation restarts
fine and no lincs warning are reported on the same portion of the  
simulation. The
simulation runs again for some ns and the same happens: new lincs  
warning appear

and eventually the simulation crashes again.

Any explanation for this? Any solution?

Best,
XAvier.

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