Re: [gmx-users] make_hole

[Mark Abraham]

varsha gautham wrote:

Dear all,

When i look into the gromacs contributions couldnt locate
mdrun_make_hole.tar.gz ..Is this a seperate file or is it coming with
gromacs 3.14 only?it will be helpful if somebody send me a link to
download mdrun_make_hole.tar.gz?


I found the file in the GROMACS contributions section in under 10 
seconds with a Google search :-)


In any case this utility is for making holes in the lipid, and you want 
a hole in the water.


Mark
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[gmx-users] (no subject)

[Q. Y. HUAN]

Hi all,

Is it right if running energy minimization using 4 nodes?

thanks for any comment

QIU YI HUAN




  
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Re: [gmx-users] Insertion of polymer into the bilayer

[Mark Abraham]

varsha gautham wrote:

Dear all,

I want to insert polymer in the aqueous phase of the bilayer.when i
read through the mailing list i found that this can be done in three
ways

1.By using genbox command

genbox -cp polymer.pdb -cs bilayer.pdb -o merged.pdb

this results in the insertion of polymer molecules to the centre of
the bilayer.what has to be done if i want to insert that just above
the aqueous phase of the bilayer.


As I said three days ago, you can do this through "judicious use of 
editconf" having "read the man pages for genbox and editconf thoroughly" 
:-) See http://www.gromacs.org/pipermail/gmx-users/2009-February/039886.html



2.If this can be done with vmd using move-> then save cordinates, then
tell me clearly how it can be done.

3.If this  can be done with making a hole and inserting the polymer
into this hole by means of  perl script.May i know where it is
avilable?


Mark
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[gmx-users] make_hole

[varsha gautham]

Dear all,

When i look into the gromacs contributions couldnt locate
mdrun_make_hole.tar.gz ..Is this a seperate file or is it coming with
gromacs 3.14 only?it will be helpful if somebody send me a link to
download mdrun_make_hole.tar.gz?

-varsha
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Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

[Omer Markovitch]

Why not create "dummy" topologies, without charges/vdw ?
Another option, which I am not sure of its effect, is, perhaps, to take
extremely small cutoffs.
--Omer.


> Lee Soin wrote:
>
>> I'm trying to rule out the effect of electrostatic or Van der Waals
>> interactions while performing a simulation. Do you mean that I should modify
>> the code and re-compile?
>>
>>
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[gmx-users] energy minimization

[Q. Y. HUAN]

Hi all,

Is it right if running energy minimization using 4 nodes?

thanks for any comments




  
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[gmx-users] Insertion of polymer into the bilayer

[varsha gautham]

Dear all,

I want to insert polymer in the aqueous phase of the bilayer.when i
read through the mailing list i found that this can be done in three
ways

1.By using genbox command

genbox -cp polymer.pdb -cs bilayer.pdb -o merged.pdb

this results in the insertion of polymer molecules to the centre of
the bilayer.what has to be done if i want to insert that just above
the aqueous phase of the bilayer.

2.If this can be done with vmd using move-> then save cordinates, then
tell me clearly how it can be done.

3.If this  can be done with making a hole and inserting the polymer
into this hole by means of  perl script.May i know where it is
avilable?

Thanks for giving your  valuble time to read this mail

-varsha
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[gmx-users] energy minimization with 4 nodes

[Q. Y. HUAN]

Hi all,

Is it right if running energy minimization using 4 nodes?

thanks for any comment

QIU YI HUAN



  
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Re: [gmx-users] energy minimization with 4 nodes

[Mark Abraham]

Q. Y. HUAN wrote:

Hi all,

Is it right if running energy minimization using 4 nodes?


Yes.

Mark
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[gmx-users] energy minimization with 4 nodes

[Q. Y. HUAN]

Hi all,

Is it right if running energy minimization using 4 nodes?

thanks for any comment

QIU YI HUAN



  
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[gmx-users] obtaining gromacs for ubuntu (was Re: gmx-users Digest, Vol 58, Issue 125 (akalabya bissoyi))

[chris . neale]

Dear akalabya,

First some general suggestions on using this mailing list:
1. Please pick a relevant title as your subject
2. Please don't include an entire digest in your post, it is irrelevant
3. Please take some more time to format your question. "plz help me"  
doesn't actually invoke a strong desire to spend time on your problem.


As for your actual question, gromacs is not a standard part of ubuntu,  
and probably does not come standard with any linux distribution. You  
can use apt-get to download a binary in some cases, but it is best for  
you to download the source and compile it yourself.


http://www.gromacs.org/index.php?option=com_content&task=view&id=79&Itemid=98

Chris.

-- original message --

hello everybody
thank you for u suggestion,  as i am new to Linux. so i am facing problem in
find out my working directory.
what is the universal path location of gromac in ubantu 8.10  where i can
type my command for execute the programme.
plz help me regarding finding working directory.

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Re: [gmx-users] Re: gmx-users Digest, Vol 58, Issue 125

[Justin A. Lemkul]

akalabya bissoyi wrote:

hello everybody
thank you for u suggestion,  as i am new to Linux. so i am facing 
problem in find out my working directory.


"Working directory" refers to whatever directory you are in.

what is the universal path location of gromac in ubantu 8.10  where i 
can type my command for execute the programme.


If you installed via Synaptic, then things will be all over the place - 
executables probably in /usr/bin, libraries in /usr/lib, topologies in 
/usr/share/gromacs/top, etc.


There is no single command to execute Gromacs, it is a software package.  As I 
advised before, read the manual and search for tutorials (there are some linked 
on wiki.gromacs.org - start there!).


Get some reference materials on learning Linux before trying to learn both Linux 
and Gromacs at the same time.  For a new user to both, it can be frustrating and 
unproductive.


-Justin


plz help me regarding finding working directory.

On Tue, Feb 24, 2009 at 2:41 AM, <mailto:gmx-users-requ...@gromacs.org>> wrote:


Send gmx-users mailing list submissions to
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When replying, please edit your Subject line so it is more specific
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Today's Topics:

  1. gromac running in ubantu 8.10 (akalabya bissoyi)
  2. Re: gromac running in ubantu 8.10 (Justin A. Lemkul)
  3. Turning off electrostatic or Van der Waals interactions (Lee Soin)
  4. Re: Turning off electrostatic or Van der Waalsinteractions
 (Justin A. Lemkul)
  5. Re: Turning off electrostatic or Van der Waalsinteractions
 (Lee Soin)
  6. Re: Turning off electrostatic or Van der  Waals   interactions
 (Justin A. Lemkul)
  7. analysis using Gromacs tools  (oguz gurbulak)


--

Message: 1
Date: Mon, 23 Feb 2009 06:37:30 -0800
From: akalabya bissoyi mailto:bissoyi.akala...@gmail.com>>
Subject: [gmx-users] gromac running in ubantu 8.10
To: gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>, gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
Message-ID:
   mailto:f166b2e50902230637i10031f2ck2e89ce4ef457a...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"

hello everybody

i have install gromac in my ubantu8.10 through synaptic package but
after
install how to run the programme, where to put the input file ,how
to run
the programme.
plz anybody help me.
 thank u have nice day

--
akalabya
N.I.T.Rourkela
-- next part --
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--

Message: 2
Date: Mon, 23 Feb 2009 09:41:08 -0500
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] gromac running in ubantu 8.10
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <49a2b584.60...@vt.edu <mailto:49a2b584.60...@vt.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



akalabya bissoyi wrote:
 > hello everybody
 >
 > i have install gromac in my ubantu8.10 through synaptic package but
 > after install how to run the programme, where to put the input
file ,how
 > to run the programme.

1. Read the manual.
2. Search Google for "Gromacs tutorial"
3. Visit wiki.gromacs.org <http://wiki.gromacs.org> and read the
tutorial information and FAQ's there

-Justin

 > plz anybody help me.
 >  thank u have nice day
 >
 > --
 > akalabya
 > N.I.T.Rourkela
 >
 >
 >

 >
 > ___
 > gmx-users mailing listgmx-users@gromacs.org
<mailto:gmx-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
<mailto

[gmx-users] akalabya bissoyi has invited you to open a Google mail account

[akalabya bissoyi]

I've been using Gmail and thought you might like to try it out. Here's
an invitation to create an account.

---

akalabya bissoyi has invited you to open a free Gmail account.

To accept this invitation and register for your account, visit
http://mail.google.com/mail/a-65f584377c-de962af40c-cf5edfb3c5

Once you create your account, akalabya bissoyi will be notified with
your new email address so you can stay in touch with Gmail!

If you haven't already heard about Gmail, it's a new search-based webmail
service that offers:

- Over 2,700 megabytes (two gigabytes) of free storage
- Built-in Google search that instantly finds any message you want
- Automatic arrangement of messages and related replies into
  "conversations"
- Powerful spam protection using innovative Google technology
- No large, annoying ads--just small text ads and related pages that are
  relevant to the content of your messages

To learn more about Gmail before registering, visit:
http://mail.google.com/mail/help/benefits.html

And, to see how easy it can be to switch to a new email service, check
out our new switch guide: http://mail.google.com/mail/help/switch/

We're still working every day to improve Gmail, so we might ask for your
comments and suggestions periodically.  We hope you'll like Gmail.  We
do.  And, it's only going to get better.

Thanks,

The Gmail Team

(If clicking the URLs in this message does not work, copy and paste them
into the address bar of your browser).
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[gmx-users] Re: gmx-users Digest, Vol 58, Issue 125

[akalabya bissoyi]

hello everybody
thank you for u suggestion,  as i am new to Linux. so i am facing problem in
find out my working directory.
what is the universal path location of gromac in ubantu 8.10  where i can
type my command for execute the programme.
plz help me regarding finding working directory.

On Tue, Feb 24, 2009 at 2:41 AM,  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. gromac running in ubantu 8.10 (akalabya bissoyi)
>   2. Re: gromac running in ubantu 8.10 (Justin A. Lemkul)
>   3. Turning off electrostatic or Van der Waals interactions (Lee Soin)
>   4. Re: Turning off electrostatic or Van der Waalsinteractions
>  (Justin A. Lemkul)
>   5. Re: Turning off electrostatic or Van der Waalsinteractions
>  (Lee Soin)
>   6. Re: Turning off electrostatic or Van der  Waals   interactions
>  (Justin A. Lemkul)
>   7. analysis using Gromacs tools  (oguz gurbulak)
>
>
> --
>
> Message: 1
> Date: Mon, 23 Feb 2009 06:37:30 -0800
> From: akalabya bissoyi 
> Subject: [gmx-users] gromac running in ubantu 8.10
> To: gmx-users-requ...@gromacs.org, gmx-users@gromacs.org
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> hello everybody
>
> i have install gromac in my ubantu8.10 through synaptic package but after
> install how to run the programme, where to put the input file ,how to run
> the programme.
> plz anybody help me.
>  thank u have nice day
>
> --
> akalabya
> N.I.T.Rourkela
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/15c5dae0/attachment-0001.html
>
> --
>
> Message: 2
> Date: Mon, 23 Feb 2009 09:41:08 -0500
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] gromac running in ubantu 8.10
> To: Discussion list for GROMACS users 
> Message-ID: <49a2b584.60...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> akalabya bissoyi wrote:
> > hello everybody
> >
> > i have install gromac in my ubantu8.10 through synaptic package but
> > after install how to run the programme, where to put the input file ,how
> > to run the programme.
>
> 1. Read the manual.
> 2. Search Google for "Gromacs tutorial"
> 3. Visit wiki.gromacs.org and read the tutorial information and FAQ's
> there
>
> -Justin
>
> > plz anybody help me.
> >  thank u have nice day
> >
> > --
> > akalabya
> > N.I.T.Rourkela
> >
> >
> > 
> >
> > ___
> > 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
> Graduate Research Assistant
> 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: Mon, 23 Feb 2009 23:26:40 +0800
> From: Lee Soin 
> Subject: [gmx-users] Turning off electrostatic or Van der Waals
>interactions
> To: gmx-users@gromacs.org
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi!
> Is there an option to turn off electrostatic or Van der Waals interactions
> in GROMACS?
>
> --
> Sun Li
> Department of Physics
> Nanjing University, China
> -- next part --
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Re: [gmx-users] analysis using Gromacs tools

[Mark Abraham]

oguz gurbulak wrote:

Dear All,

 

I'm planning to use Gromacs  for analysis with Amber trajectory files ( 
mdcrd, rst files ). And I found a script that converts Amber mdcrd files 
to *Gromacs-compatible .xtc *files. I want to learn that if 
*Gromacs-compatible .xtc *files are enough to perform an analysis 
 using Gromacs tools ? 


"Analysis" is too vague a description to get a useful answer. Some 
GROMACS analysis tools will be fine with just your trajectory file, some 
will require atom names that could come from a PDB or .tpr file, some 
will require atom types and/or connectivity that must come from a .tpr 
file. This goes for AMBER too!


or Will I have to have some other files for analysis 
 in Gromacs ?  I’m 


Maybe.

Mark
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[gmx-users] analysis using Gromacs tools

[chris . neale]

You will require a .tpr file for many analysis tools. In some cases,  
you can get away with a .ndx file. Check g_thistool -h to see what is  
mandatory input. You can make a .ndx file if you have a .pdb using  
make_ndx -f my.pdb -o my.ndx and then select your groups. If you need  
a .tpr file, then you will need a gromacs .top topology file to run  
your .pdb and .top through grompp and generate the .tpr. Generating  
your .top may be simple if you have a simple system. Try downloading  
the amber forcefield that is formatted for gromacs and running your  
.pdb through pdb2gmx while selecting that amber ff in order to  
generate a .top file.


Note that if you need a .tpr file this is all going to require that  
you learn how to use gromacs and will not be completed in one afternoon.


The gromacs manual is quite good.

Chris.


-- original message --

Dear All,

I'm planning to use Gromacs  for analysis with Amber trajectory files  
( mdcrd, rst files ). And I found a script that converts Amber mdcrd  
files to Gromacs-compatible .xtc files. I want to learn that if  
Gromacs-compatible .xtc files are enough to perform an analysis using  
Gromacs tools ? or Will I have to have some other files for analysis  
in Gromacs ?  I?m waiting for your suggestions and helps.


Thank you very much for your attention.

Sincerely


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[gmx-users] analysis using Gromacs tools

[Adrien Delmont]

Dear All,
 
I want to use Gromacs  for analysis with Amber trajectory files ( mdcrd, rst 
files ). And I found a script ( trajectory_converter_v1.5.sh ) that converts 
Amber mdcrd files to Gromacs-compatible .xtc files. Does this script work 
well ? Also  I want to learn that if Gromacs-compatible .xtc files are enough 
to perform an analysis using Gromacs tools ? or Will I have to have some other 
files for analysis in Gromacs ?  I’m waiting for your suggestions and helps.
 
Sincerely


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[gmx-users] analysis using Gromacs tools

[oguz gurbulak]

Dear All,
 
I'm planning to use Gromacs  for analysis with Amber trajectory files ( mdcrd, 
rst files ). And I found a script that converts Amber mdcrd files to 
Gromacs-compatible .xtc files. I want to learn that if Gromacs-compatible .xtc 
files are enough to perform an analysis using Gromacs tools ? or Will I have to 
have some other files for analysis in Gromacs ?  I’m waiting for your 
suggestions and helps.
 
Thank you very much for your attention.
 
Sincerely


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Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

[Justin A. Lemkul]

Lee Soin wrote:
I'm trying to rule out the effect of electrostatic or Van der Waals 
interactions while performing a simulation. Do you mean that I should 
modify the code and re-compile?




No, I mean use the free energy options in the .mdp file.  You may be able to use 
a B-state in the topology with dummy atoms to accomplish what you want to do.


-Justin


2009/2/23 Justin A. Lemkul mailto:jalem...@vt.edu>>



Lee Soin wrote:

Hi!
Is there an option to turn off electrostatic or Van der Waals
interactions in GROMACS?


Look into the free energy code; if this is not your intent, be more
specific with what you are trying to do.

-Justin

-- 
Sun Li

Department of Physics
Nanjing University, China




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--
Sun Li
Department of Physics
Nanjing University, China


--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

[Lee Soin]

I'm trying to rule out the effect of electrostatic or Van der Waals
interactions while performing a simulation. Do you mean that I should modify
the code and re-compile?

2009/2/23 Justin A. Lemkul 

>
>
> Lee Soin wrote:
>
>> Hi!
>> Is there an option to turn off electrostatic or Van der Waals interactions
>> in GROMACS?
>>
>>
> Look into the free energy code; if this is not your intent, be more
> specific with what you are trying to do.
>
> -Justin
>
>  --
>> Sun Li
>> Department of Physics
>> Nanjing University, China
>>
>>
>> 
>>
>> ___
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>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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-- 
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Department of Physics
Nanjing University, China
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Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

[Justin A. Lemkul]

Lee Soin wrote:

Hi!
Is there an option to turn off electrostatic or Van der Waals 
interactions in GROMACS?




Look into the free energy code; if this is not your intent, be more specific 
with what you are trying to do.


-Justin


--
Sun Li
Department of Physics
Nanjing University, China




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Department of Biochemistry
Virginia Tech
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[gmx-users] Turning off electrostatic or Van der Waals interactions

[Lee Soin]

Hi!
Is there an option to turn off electrostatic or Van der Waals interactions
in GROMACS?

-- 
Sun Li
Department of Physics
Nanjing University, China
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Re: [gmx-users] gromac running in ubantu 8.10

[Justin A. Lemkul]

akalabya bissoyi wrote:

hello everybody
 
i have install gromac in my ubantu8.10 through synaptic package but 
after install how to run the programme, where to put the input file ,how 
to run the programme.


1. Read the manual.
2. Search Google for "Gromacs tutorial"
3. Visit wiki.gromacs.org and read the tutorial information and FAQ's there

-Justin


plz anybody help me.
 thank u have nice day 


--
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N.I.T.Rourkela




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Department of Biochemistry
Virginia Tech
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[gmx-users] gromac running in ubantu 8.10

[akalabya bissoyi]

hello everybody

i have install gromac in my ubantu8.10 through synaptic package but after
install how to run the programme, where to put the input file ,how to run
the programme.
plz anybody help me.
 thank u have nice day

-- 
akalabya
N.I.T.Rourkela
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Re: [gmx-users] About position restraint specification

[Justin A. Lemkul]

Lee Soin wrote:

There's also an option "freezegrps". When should this be used?



Freeze groups: Manual section 3.3
Restraints: section 4.3

Note the fundamental difference between "fixed" and "harmonically restrained."

-Justin



2009/2/23 Justin A. Lemkul mailto:jalem...@vt.edu>>



Lee Soin wrote:

Hello, all!
Which option in .mdp file is used to specify position restraint
and the corresponding force constant?


In your topology, you should have something like:

#ifdef POSRES
#include "posre.itp"
#endif

The posre.itp file contains force constants; in the .mdp file you
can "define = -DPOSRES"

-Justin

-- 
Sun Li

Department of Physics
Nanjing University, China




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Justin A. Lemkul
Graduate Research Assistant
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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--
Sun Li
Department of Physics
Nanjing University, China


--


Justin A. Lemkul
Graduate Research Assistant
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] About position restraint specification

[Lee Soin]

There's also an option "freezegrps". When should this be used?

2009/2/23 Justin A. Lemkul 

>
>
> Lee Soin wrote:
>
>> Hello, all!
>> Which option in .mdp file is used to specify position restraint and the
>> corresponding force constant?
>>
>>
> In your topology, you should have something like:
>
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> The posre.itp file contains force constants; in the .mdp file you can
> "define = -DPOSRES"
>
> -Justin
>
>  --
>> Sun Li
>> Department of Physics
>> Nanjing University, China
>>
>>
>> 
>>
>> ___
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>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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-- 
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Department of Physics
Nanjing University, China
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Re: [gmx-users] About position restraint specification

[Justin A. Lemkul]

Lee Soin wrote:

Hello, all!
Which option in .mdp file is used to specify position restraint and the 
corresponding force constant?




In your topology, you should have something like:

#ifdef POSRES
#include "posre.itp"
#endif

The posre.itp file contains force constants; in the .mdp file you can "define = 
-DPOSRES"


-Justin


--
Sun Li
Department of Physics
Nanjing University, China




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Department of Biochemistry
Virginia Tech
Blacksburg, VA
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] About position restraint specification

[Lee Soin]

Hello, all!
Which option in .mdp file is used to specify position restraint and the
corresponding force constant?

-- 
Sun Li
Department of Physics
Nanjing University, China
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Re: [gmx-users] protein structure prediction

[José Carlos Calvo Tudela]

Per Larsson escribió:


23 feb 2009 kl. 12.55 skrev Mark Abraham:


José Carlos Calvo Tudela wrote:
can I use the GROMACS software to get the energy of a protein 
conformation?


Yes, but your question is not well-formed. Only energy differences 
can have meaning.


Up to now I am using TINKER library (analyze program). Is there any 
similar software in GROMACS?


I don't know.


If I'm not mistaken, the energy you get from analyse.x  program in 
Tinker is the potential energy for a protein in is current 
conformation, given a particular force-field.


In that case, you might be able to get the same from Gromacs if you do 
a simulation with 0 steps, ie without any integration, and then look 
at the potential energy terms in the log file (or do many steps, and 
look at the energy before the first step)

Ok, thank you very much. I will try this


Cheers
/Per




Mark
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--
José Carlos Calvo Tudela
Miembro del Departamento de Arquitectura y Tecnología de Computadores 
(http://atc.ugr.es)
y del Equipo de Desarrollo Web de la Universidad de Granada
Universidad de Granada (http://www.ugr.es)


Contacto: jcca...@atc.ugr.es  
 http://atc.ugr.es/~jccalvo
 34 958 240588   
 646 74 25 54


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Re: [gmx-users] protein structure prediction

[Per Larsson]

23 feb 2009 kl. 12.55 skrev Mark Abraham:


José Carlos Calvo Tudela wrote:
can I use the GROMACS software to get the energy of a protein  
conformation?


Yes, but your question is not well-formed. Only energy differences  
can have meaning.


Up to now I am using TINKER library (analyze program). Is there any  
similar software in GROMACS?


I don't know.


If I'm not mistaken, the energy you get from analyse.x  program in  
Tinker is the potential energy for a protein in is current  
conformation, given a particular force-field.


In that case, you might be able to get the same from Gromacs if you do  
a simulation with 0 steps, ie without any integration, and then look  
at the potential energy terms in the log file (or do many steps, and  
look at the energy before the first step)


Cheers
/Per




Mark
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Re: [gmx-users] protein structure prediction

[José Carlos Calvo Tudela]

So,

In my software I make a pdb file with a certain conformation of the 
protein, then I need to know the energy of the conformation (CHARMM, 
AMBER,...), because I perform a minimization process. Is that possible? 
which program can do it in GROMACS?


Thanks

Jose Carlos

Mark Abraham escribió:

José Carlos Calvo Tudela wrote:
can I use the GROMACS software to get the energy of a protein 
conformation?


Yes, but your question is not well-formed. Only energy differences can 
have meaning.


Up to now I am using TINKER library (analyze program). Is there any 
similar software in GROMACS?


I don't know.

Mark
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--
José Carlos Calvo Tudela
Miembro del Departamento de Arquitectura y Tecnología de Computadores 
(http://atc.ugr.es)
y del Equipo de Desarrollo Web de la Universidad de Granada
Universidad de Granada (http://www.ugr.es)


Contacto: jcca...@atc.ugr.es  
 http://atc.ugr.es/~jccalvo
 34 958 240588   
 646 74 25 54


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Re: [gmx-users] protein structure prediction

[Mark Abraham]

José Carlos Calvo Tudela wrote:

can I use the GROMACS software to get the energy of a protein conformation?


Yes, but your question is not well-formed. Only energy differences can 
have meaning.


Up to now I am using TINKER library (analyze program). Is there any 
similar software in GROMACS?


I don't know.

Mark
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[gmx-users] protein structure prediction

[José Carlos Calvo Tudela]

can I use the GROMACS software to get the energy of a protein conformation?

Up to now I am using TINKER library (analyze program). Is there any 
similar software in GROMACS?


Thank you very much

Best regards

Jose Carlos

--
José Carlos Calvo Tudela
Miembro del Departamento de Arquitectura y Tecnología de Computadores 
(http://atc.ugr.es)
y del Equipo de Desarrollo Web de la Universidad de Granada
Universidad de Granada (http://www.ugr.es)


Contacto: jcca...@atc.ugr.es  
 http://atc.ugr.es/~jccalvo
 34 958 240588   
 646 74 25 54


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[gmx-users] structure factor

[Alexander Malafeev]

Hello, I try to calculate structure factor for coarse-grained system with
g_rdf, but I get error

> Fatal error:
>
> Error: atom (B1) not in list (5 types checked)!

It is possible to calculate structure factor for coarse-grained model with
g_rdf? And how I can do it?
Thanks in advance.
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Re: [gmx-users] MD parameters for DPPC bilayer

[Justin A. Lemkul]

Nikit sharan wrote:

dear users,

Can anyone send me the Md parameters(.mdp file) for dppc molecule with
12lipids and 3655 water molecules that worked without any errors like
"pressure scaling not more than 1%" and more?It will be very helpful
as i will check out that with my mdp file.



Your previous .mdp file looked reasonable, except perhaps 2 things you may 
consider:

1. "nstcheckpoint" does not exist.
2. You could try increasing your cutoff's to, for example, 1.4 nm.

-Justin


Thanks in advance
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Virginia Tech
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Re: [gmx-users] segmentation fault after mdrun

[Justin A. Lemkul]

Nikit sharan wrote:

Dear justin,

As you suggested i have changed the coloumb type to PME and set
pme_order to 5 as  said in the mailing list as it will increase the


Try an even number.


accuracy.But then the simulation is not getting completed.Its taking
hours together.Normally what's the running time for a lipid bilayer?I


Timings will be dependent on your hardware, especially the communication between 
nodes in a cluster.


-Justin


dint find anything wrong with the topology as it is downloaded from
tielman's website.it is also well equilibriated.Kindly give me your
suggestions.My mdp.file is below:


title= Yo
cpp  = cpp
include  =
define   =
integrator   = md
tinit= 0
dt   = 0.005
nsteps   = 5
init_step= 0
comm-mode= Linear
nstcomm  = 1
comm-grps= system
nstxout  = 200
nstvout  = 0
nstfout  = 0
nstcheckpoint= 1000
nstlog   = 100
nstenergy= 100
nstxtcout= 1000
xtc-precision= 1000
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.0
domain-decomposition = no
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.0
epsilon-r= 1
vdw-type = Cut-off
rvdw-switch  = 0
rvdw = 1.0
DispCorr = EnerPres
table-extension  = 1
fourierspacing   = 0.12
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
tau_p= 0.5 0.5 0.5
compressibility  = 4.5e-5 4.5e-5 4.5e-5
ref_p= 1.0 1.0 1.0
andersen_seed= 815131
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Justin A. Lemkul
Graduate Research Assistant
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] mdrun halting

[Justin A. Lemkul]

varsha gautham wrote:

Dear all,

The production run of DPPC bilayer with 128 lipids and 3655 water and
some solvent molecules is halting without completion.As justin
suggested ,i changed the columb type from cut-off to PME.It keeps on
running for hours together.The system is well equilibriated and i
found no issues or warnings with starting structure.But still i dont
know why the production run is not getting completed.I hereby attached
mdp file.Please suggest me which parameter do i need to correct,



Is there some output to the log that contains an error message?  If so, please 
post it.


-Justin


--
title   = cla
cpp = cpp; the c pre-processor
constraints = all-bonds
integrator  = md
dt  = 0.002 ; ps !
nsteps  = 2500 ; total 50 ps.
nstcomm = 1
nstxout = 2500 ; collect data every 1 ps
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist   = 1.4
coulombtype = PME
rcoulomb= 1.4
rvdw= 1.4
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = berendsen
tau_t   = 0.1 0.1
tc-grps = DPPC SOL
ref_t   = 300 300
; Pressure coupling is on
Pcoupl  = berendsen
pcoupltype  = isotropic
tau_p   = 0.5
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp= 300.0
gen_seed= 173529

thanks in advance.

-varsha
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Justin A. Lemkul
Graduate Research Assistant
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] MD parameters for DPPC bilayer

[Nikit sharan]

dear users,

Can anyone send me the Md parameters(.mdp file) for dppc molecule with
12lipids and 3655 water molecules that worked without any errors like
"pressure scaling not more than 1%" and more?It will be very helpful
as i will check out that with my mdp file.

Thanks in advance
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Re: [gmx-users] How to define new residue in GROMACS?

[Tsjerk Wassenaar]

Hi Yiming Chen,

In this case there's no need to add GTP as a building block. Have a
look at John Kerrigan's drug - enzyme tutorial to see how to include a
prodrg topology in your simulation:

http://wiki.gromacs.org/index.php/Tutorials

Also, do note the caution regarding non-standard groups in your system
(and mixing force fields):

http://wiki.gromacs.org/index.php/Parameterization

Finally, don't use the gmx force field; it's deprecated.

Cheers,

Tsjerk

On Mon, Feb 23, 2009 at 10:32 AM, Yiming Chen
 wrote:
> For example, I want to add GTP as residue current force field, and after
> that pdb2gmx will be able to recognize GTP molecule.
>
> At first, I created GTP.pdb:
>
> REMARK   This PDB file is created by CS Chem3D
>
> REMARK
>
> COMPND   Untitled-1.pdb
>
> HETATM1  C   UNK 0  -0.561   0.002  -1.145
>C
> HETATM2  C   UNK 0   0.328  -1.116  -1.641
>C
> HETATM3  C   UNK 0   1.149  -1.405  -0.410
>C
> HETATM4  C   UNK 0   1.361   0.002   0.113
>C
> HETATM5  C   UNK 0   2.929  -0.248   3.300
>C
> HETATM6  C   UNK 0   5.299  -0.874   2.006
>C
> HETATM7  C   UNK 0   0.958   0.191   2.581
>C
> HETATM8  C   UNK 0   4.131  -0.512   4.102
>C
> HETATM9  C   UNK 0   3.049  -0.325   1.915
>C
> HETATM   10  H   UNK 0   7.349  -1.394   2.036
>H
> HETATM   11  H   UNK 0   6.594  -1.285   0.394
>H
> HETATM   12  H   UNK 0  -1.494  -0.383  -0.678
>H
> HETATM   13  H   UNK 0   0.972  -0.803  -2.494
>H
> HETATM   14  H   UNK 0   0.603  -2.041   0.322
>H
> HETATM   15  H   UNK 0   2.165   0.515  -0.468
>H
> HETATM   16  H   UNK 0   2.947  -2.013   0.015
>H
> HETATM   17  H   UNK 0   0.178  -2.926  -2.340
>H
> HETATM   18  H   UNK 0  -0.106   0.431   2.504
>H
> HETATM   19  H   UNK 0   6.160  -1.008   3.934
>H
> HETATM   20  N   UNK 0   1.777  -0.040   1.517
>N
> HETATM   21  N   UNK 0   1.651   0.064   3.691
>N
> HETATM   22  N   UNK 0   4.234  -0.642   1.256
>N
> HETATM   23  N   UNK 0   5.281  -0.814   3.397
>N
> HETATM   24  N   UNK 0   6.507  -1.212   1.437
>N
> HETATM   25  O   UNK 0   0.158   0.696  -0.141
>O
> HETATM   26  O   UNK 0   2.362  -2.026  -0.746
>O
> HETATM   27  O   UNK 0  -0.417  -2.236  -2.037
>O
> HETATM   28  O   UNK 0   4.142  -0.481   5.335
>O
> HETATM   29  O   UNK 0  -0.826   0.950  -2.157
>O
> HETATM   30  O   UNK 0  -5.338   2.374  -0.127
>O-1-
> HETATM   31  O   UNK 0  -3.230   0.072  -2.587
>O
> HETATM   32  O   UNK 0  -2.156   1.936  -4.009
>O-1-
> HETATM   33  O   UNK 0  -5.619   0.198  -1.738
>O
> HETATM   34  O   UNK 0  -4.404   2.410  -2.384
>O
> HETATM   35  O   UNK 0  -5.108   0.603  -4.028
>O-1-
> HETATM   36  O   UNK 0  -3.544   3.985  -0.564
>O
> HETATM   37  O   UNK 0  -3.027   1.592  -0.529
>O-1-
> HETATM   38  O   UNK 0  -1.402  -0.335  -4.284
>O
> HETATM   39  P   UNK 0  -1.939   0.652  -3.302
>P1+
> HETATM   40  P   UNK 0  -4.624   0.851  -2.639
>P1+
> HETATM   41  P   UNK 0  -4.060   2.614  -0.833
>P1+
> END
>
> Then I submitted GTP.pdb to
> http://davapc1.bioch.dundee.ac.uk/prodrg/index.html, and obtained
> DRGGMX.ITP:
>
> I don't know how to convert .itp file to .rtp file, and how to add new
> residue to current .rtp files. Could any one help me? Thank you!
>
> ___
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>



-- 
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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] Oscillating Electrical Field

[David van der Spoel]

Benjamin Hall wrote:

Hi

I'm trying to create an oscillating electrical field in my simulation, 
and I was hoping that someone who had successfully done this in the past 
could please offer some advice on the choice of parameters in my mdp. 
Eventually, I would like to create a system with oscillating fields 
across both x and y, pi/2 radians out of phase in order to cause a body 
in my simulation to rotate by aligning its charge distribution to the 
field. At the moment, I would just like to find out a couple of things 
about exactly which parameters to use.


I've looked at the source code from src/mdlib/sim_util.c and tried out a 
few combinations, and as far as I can see you need to enter parameters 
for the x axis (as an example) in both E_x and E_xt, representing the 
maximum field strength. E_x values are chosen as described in the 
manual. E_xt takes three values- the first value has to be 1 (to 
generate an oscillating field), the second value a number related to the 
frequency of the wave, and the third value a measure of phase so that 
you can vary the starting values of the field. Other values are ignored.


My first question is have I interpreted these values correctly? Also, 
the code refers to t, which I assume to be the time. What is the units 
of t, and does to cosine function expect radians or degrees? Also, there 
seems to be an optional term which causes the waves to decrease 
exponentially over time-


Ext[m] = cos(Et[m].a[0]*(t-t0))*exp(-sqr(t-t0)/(2.0*sqr(Et[m].a[2])));

can I turn this off or ignore it if I want to specify a phase?


I think your guesses are mostly correct. But what's more, mdrun will 
output an xvg file containing the applied field such that you can use 
trial and error.




Many thanks in advance

Ben

Benjamin A. Hall
Structural Bioinformatics & Computational Biochemistry Unit / OCISB
University of Oxford
http://sbcb.bioch.ox.ac.uk/hall.php
+44 (0)1865 613304
benjamin.h...@bioch.ox.ac.uk







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Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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Re: [gmx-users] segmentation fault after mdrun

[Carsten Kutzner]

On Feb 23, 2009, at 9:22 AM, Nikit sharan wrote:


Dear justin,

As you suggested i have changed the coloumb type to PME and set
pme_order to 5 as  said in the mailing list as it will increase the

Hi Nikit,

I think pme_order should be an even number in gromacs. You might
want to try with order = 6 then.

Carsten



--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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[gmx-users] How to define new residue in GROMACS?

[Yiming Chen]

For example, I want to add GTP as residue current force field, and after
that pdb2gmx will be able to recognize GTP molecule.

At first, I created GTP.pdb:

REMARK   This PDB file is created by CS Chem3D

REMARK

COMPND   Untitled-1.pdb

HETATM1  C   UNK 0  -0.561   0.002  -1.145
   C
HETATM2  C   UNK 0   0.328  -1.116  -1.641
   C
HETATM3  C   UNK 0   1.149  -1.405  -0.410
   C
HETATM4  C   UNK 0   1.361   0.002   0.113
   C
HETATM5  C   UNK 0   2.929  -0.248   3.300
   C
HETATM6  C   UNK 0   5.299  -0.874   2.006
   C
HETATM7  C   UNK 0   0.958   0.191   2.581
   C
HETATM8  C   UNK 0   4.131  -0.512   4.102
   C
HETATM9  C   UNK 0   3.049  -0.325   1.915
   C
HETATM   10  H   UNK 0   7.349  -1.394   2.036
   H
HETATM   11  H   UNK 0   6.594  -1.285   0.394
   H
HETATM   12  H   UNK 0  -1.494  -0.383  -0.678
   H
HETATM   13  H   UNK 0   0.972  -0.803  -2.494
   H
HETATM   14  H   UNK 0   0.603  -2.041   0.322
   H
HETATM   15  H   UNK 0   2.165   0.515  -0.468
   H
HETATM   16  H   UNK 0   2.947  -2.013   0.015
   H
HETATM   17  H   UNK 0   0.178  -2.926  -2.340
   H
HETATM   18  H   UNK 0  -0.106   0.431   2.504
   H
HETATM   19  H   UNK 0   6.160  -1.008   3.934
   H
HETATM   20  N   UNK 0   1.777  -0.040   1.517
   N
HETATM   21  N   UNK 0   1.651   0.064   3.691
   N
HETATM   22  N   UNK 0   4.234  -0.642   1.256
   N
HETATM   23  N   UNK 0   5.281  -0.814   3.397
   N
HETATM   24  N   UNK 0   6.507  -1.212   1.437
   N
HETATM   25  O   UNK 0   0.158   0.696  -0.141
   O
HETATM   26  O   UNK 0   2.362  -2.026  -0.746
   O
HETATM   27  O   UNK 0  -0.417  -2.236  -2.037
   O
HETATM   28  O   UNK 0   4.142  -0.481   5.335
   O
HETATM   29  O   UNK 0  -0.826   0.950  -2.157
   O
HETATM   30  O   UNK 0  -5.338   2.374  -0.127
   O-1-
HETATM   31  O   UNK 0  -3.230   0.072  -2.587
   O
HETATM   32  O   UNK 0  -2.156   1.936  -4.009
   O-1-
HETATM   33  O   UNK 0  -5.619   0.198  -1.738
   O
HETATM   34  O   UNK 0  -4.404   2.410  -2.384
   O
HETATM   35  O   UNK 0  -5.108   0.603  -4.028
   O-1-
HETATM   36  O   UNK 0  -3.544   3.985  -0.564
   O
HETATM   37  O   UNK 0  -3.027   1.592  -0.529
   O-1-
HETATM   38  O   UNK 0  -1.402  -0.335  -4.284
   O
HETATM   39  P   UNK 0  -1.939   0.652  -3.302
   P1+
HETATM   40  P   UNK 0  -4.624   0.851  -2.639
   P1+
HETATM   41  P   UNK 0  -4.060   2.614  -0.833
   P1+
END

Then I submitted GTP.pdb to
http://davapc1.bioch.dundee.ac.uk/prodrg/index.html, and obtained
DRGGMX.ITP:

I don't know how to convert .itp file to .rtp file, and how to add new
residue to current .rtp files. Could any one help me? Thank you!
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[gmx-users] segmentation fault after mdrun

[Nikit sharan]

Dear justin,

As you suggested i have changed the coloumb type to PME and set
pme_order to 5 as  said in the mailing list as it will increase the
accuracy.But then the simulation is not getting completed.Its taking
hours together.Normally what's the running time for a lipid bilayer?I
dint find anything wrong with the topology as it is downloaded from
tielman's website.it is also well equilibriated.Kindly give me your
suggestions.My mdp.file is below:


title= Yo
cpp  = cpp
include  =
define   =
integrator   = md
tinit= 0
dt   = 0.005
nsteps   = 5
init_step= 0
comm-mode= Linear
nstcomm  = 1
comm-grps= system
nstxout  = 200
nstvout  = 0
nstfout  = 0
nstcheckpoint= 1000
nstlog   = 100
nstenergy= 100
nstxtcout= 1000
xtc-precision= 1000
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.0
domain-decomposition = no
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.0
epsilon-r= 1
vdw-type = Cut-off
rvdw-switch  = 0
rvdw = 1.0
DispCorr = EnerPres
table-extension  = 1
fourierspacing   = 0.12
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
tau_p= 0.5 0.5 0.5
compressibility  = 4.5e-5 4.5e-5 4.5e-5
ref_p= 1.0 1.0 1.0
andersen_seed= 815131
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