Re: [gmx-users]D Gsol from g_sas calculation

[David van der Spoel]

limei zhang wrote:

Hi to all,



I did surface calculation on a protein either with or without 
Cu-binding, using g_sas with exactly the same parameter setting. For the 
delta solvation energy from the output file (the the 5th column in the 
output file with a label of D Gsol), non-Cu bound protein gives all 0, 
but the Cu-protein gives values from 0- 4 KJ/mol/nm^2. Could anyone tell 
me how the delta solvation free energy is calculated?  Particularly, 
what is the delta solvation free energy relative to?



The program spits out a reference to an Eisenberg paper. Please check 
the code as well. In my hands the results are close to useless.




Thanks very much,



Limei

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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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[gmx-users] Re: Removal of pbc for analysis

[alkasrivastava]

Hi All,

I am doing a 5 peptide simulation, and i want to analyze some of the basic
properties like radius of gyration, distance between peptides etc. but i
wanted to do it in a situation when all my peptides are inside the box.
Due to pbc i am getting artifacts. i tried all the -pbc option (inbox,
whole, nojump, etc) as well as all the -center option and a combination of
both for converting trajectory by trjconv  but i am not getting what i
want. I want all of my peptides to be present in the box and that to in
whole form not broken so that my analysis give me a true reflection of
what is happening. If anyone can help me.

Thanks
ALKA

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[gmx-users] Zinc (Zn) parameters

[Ramon Crehuet]

Dear Gromacs users,
I am planing to do MD of an enzyme that has a Zn in its active site. Up
to now I have used QM/MM or ONIOM approaches but now I need to perform a
long MD and would like to model the Zn with MM, preferably in OPLS.
I know that there are three possible approaches: Bonded, nonbonded and
cationic dummy atom. I have seen a thread, where Maik Goette said that
onyl the bonded approach worked. I would like to know in more detail
what kind of problems could I encounter. What does "not work" imply?
Weeks of unreliable calculations...?
I would also be very grateful if people working in this area could send
me some reference publications, in particular of what can be done with
Gromacs. I have only found: "Zinc binding in proteins and solution: A
simple but accurate nonbonded representation" Roland H. Stote, Martin
Karplus, 1995.
Thanks in advance,
Ramon
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Re: [gmx-users] Re: Removal of pbc for analysis

[Justin A. Lemkul]

[EMAIL PROTECTED] wrote:

Hi All,

I am doing a 5 peptide simulation, and i want to analyze some of the basic
properties like radius of gyration, distance between peptides etc. but i
wanted to do it in a situation when all my peptides are inside the box.
Due to pbc i am getting artifacts. i tried all the -pbc option (inbox,
whole, nojump, etc) as well as all the -center option and a combination of
both for converting trajectory by trjconv  but i am not getting what i
want. I want all of my peptides to be present in the box and that to in
whole form not broken so that my analysis give me a true reflection of
what is happening. If anyone can help me.


Well, you're not mentioning how you're doing it (commands!), so otherwise we'd 
just shrug our shoulders and say, "you've tried everything, so I guess nothing 
works!"  Sorry to say that trjconv is one of the most difficult tools to provide 
help with, so without actually seeing the results of what you're doing, the best 
advice is to just keep playing with it.  Sometimes my fitting procedures have 
taken four or five iterations of different options!


I have done some simulations of multiple peptides/proteins and the like, and a 
simple -pbc nojump has always worked just fine.  Otherwise, try -pbc mol/res 
under GMX 3.3.3.  Centering probably won't work very well, since there are 
multiple peptides.


-Justin



Thanks
ALKA

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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] energy groups

[Justin A. Lemkul]

rams rams wrote:

Dear Users,

I have a question about separating a system into energy groups. In my 
system, I have a metal atom and a few residues close to the metal atom 
(catalytic center). I ran the simulation with out any restraints. In the 
most representative structure, the catalytic center is completely 
distorted. To keep the catalytic center as such I am trying to freeze a 
few of the atoms. For this, I created an index file with the required 
atoms to freeze and did added the following lines to my .mdp file:


energygrps_excl =  Test Test Test SOL
freezegrps  =  Test
freezedim   =  Y Y Y

(Test is the name of the group of atoms for which I made the index file 
and these are the atoms I am freezing)


my .mdp file also contains the following line:

energygrps   =  Protein, Na, SOL

Now, my question is:

The atoms which I defined in the energygrps_excl are present both in the 
excluding group as well as in the energygrps. So under which group they 
are exactly considered.


A note of etiquette - don't double post; it makes you look impatient.  Everyone 
here has important work they're doing, too, you know :-)


That said, if you don't know what you're doing, don't do it until you do :-)

What you've done is exclude nonbonded interactions within the atoms of the 
"Test" group (with respect to themselves), and between "Test" and the solvent. 
Interactions between "Test" and the rest of the protein, Na+, etc. are still 
included in the calculations.


Wouldn't it be simpler to just use position restraints?  Or investigate why your 
catalytic center is so distorted?  Maybe there is a larger problem with whatever 
you've done...


-Justin



With these, I made the tpr file with the follwing command and the 
simulation is running (though I didnt checked whether the freezed atom 
positions are fixed or not):


grompp -f .mdp -c .pdb -p .top -n .ndx -o .tpr

Ram. 
 





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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] How to do CGMD in GROMACS?

[Anirban Ghosh]

Hi All,
I am interested in doing Coarse Grained MD in GROMACS. Is there any module in 
GROMACS with which I can do this? Please tell me the procedure of doing CGMD in 
GROMACS. Thanks a lot.
Regards,

 
Anirban Ghosh
M.Tech Bioinformatics
University of Hyderabad


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Re: [gmx-users] Zinc (Zn) parameters

[Tsjerk Wassenaar]

Hi Ramon,

Zinc should be considered as one of those "exotic species"
(http://wiki.gromacs.org/index.php/Exotic_Species). It's almost
impossible to give a set of parameters which will work for all zinc
binding sites. Actually, it's best to parameterize based on the
environment. Now, if you have QM/MM calculations, I think it should be
possible to use these to fit parameters.
As for the literature, I believe I had some references to zinc
parameterization in our Proteins paper (TRAIL-DR5 complex) from
earlier this year.

Hope it helps,

Tsjerk

On Thu, Jul 17, 2008 at 12:15 PM, Ramon Crehuet <[EMAIL PROTECTED]> wrote:
> Dear Gromacs users,
> I am planing to do MD of an enzyme that has a Zn in its active site. Up
> to now I have used QM/MM or ONIOM approaches but now I need to perform a
> long MD and would like to model the Zn with MM, preferably in OPLS.
> I know that there are three possible approaches: Bonded, nonbonded and
> cationic dummy atom. I have seen a thread, where Maik Goette said that
> onyl the bonded approach worked. I would like to know in more detail
> what kind of problems could I encounter. What does "not work" imply?
> Weeks of unreliable calculations...?
> I would also be very grateful if people working in this area could send
> me some reference publications, in particular of what can be done with
> Gromacs. I have only found: "Zinc binding in proteins and solution: A
> simple but accurate nonbonded representation" Roland H. Stote, Martin
> Karplus, 1995.
> Thanks in advance,
> Ramon
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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] How to do CGMD in GROMACS?

[Justin A. Lemkul]

Read just about any of the papers from Marrink's group.

-Justin

Anirban Ghosh wrote:

Hi All,
 
I am interested in doing Coarse Grained MD in GROMACS. Is there any 
module in GROMACS with which I can do this? Please tell me the procedure 
of doing CGMD in GROMACS. Thanks a lot.
 
 
Regards,
 

 
 
*Anirban Ghosh*

*M.Tech Bioinformatics*
*University of Hyderabad*


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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] (no subject)

[alkasrivastava]

Hi all
I have installed gromacs 3.3.3 in one of my 32 machine fedora core 2.
so check i tried to to do speptide tutorial in
/usr/local/gromacs/share/gromacs/tutor/speptide

But when i m running grompp for position restraint with the command
grompp -f pr -o pr -c after_em -r after_em -p speptide

i get the following warning

 WARNING 1 [file aminoacids.dat, line 1]:
  T-Coupling group Protein has fewer than 10% of the atoms (191 out of
  2741)
  Maybe you want to try Protein and Non-Protein instead?

I tried to change SOL with non protein but getting the same warning. is it
ok to go further with this warning

When i did grompp for full MD with the command

grompp -v -f full -o full -c after_pr -p speptide

again i m getting the same warning

WARNING 1 [file aminoacids.dat, line 1]:
  T-Coupling group Protein has fewer than 10% of the atoms (191 out of
  2741)
  Maybe you want to try Protein and Non-Protein instead?


I tried to change SOL with non protein but getting the same warning.

I don't know what to do now and how can i overcome this, if anyone could
help me.

Thanks

ALKA



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Re: [gmx-users] (no subject)

[Per Larsson]

Check the information on the gromacs wiki about this:

 
http://wiki.gromacs.org/index.php/Errors#T-Coupling_group_XXX_has_fewer_than_10.25_of_the_atoms

Cheers
/Per


17 jul 2008 kl. 14.38 skrev [EMAIL PROTECTED]:


Hi all
I have installed gromacs 3.3.3 in one of my 32 machine fedora core 2.
so check i tried to to do speptide tutorial in
/usr/local/gromacs/share/gromacs/tutor/speptide

But when i m running grompp for position restraint with the command
grompp -f pr -o pr -c after_em -r after_em -p speptide

i get the following warning

WARNING 1 [file aminoacids.dat, line 1]:
 T-Coupling group Protein has fewer than 10% of the atoms (191 out of
 2741)
 Maybe you want to try Protein and Non-Protein instead?

I tried to change SOL with non protein but getting the same warning.  
is it

ok to go further with this warning

When i did grompp for full MD with the command

grompp -v -f full -o full -c after_pr -p speptide

again i m getting the same warning

WARNING 1 [file aminoacids.dat, line 1]:
 T-Coupling group Protein has fewer than 10% of the atoms (191 out of
 2741)
 Maybe you want to try Protein and Non-Protein instead?


I tried to change SOL with non protein but getting the same warning.

I don't know what to do now and how can i overcome this, if anyone  
could

help me.

Thanks

ALKA



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Re: [gmx-users] (no subject)

[Justin A. Lemkul]

For warnings/errors, etc. please check the archive and wiki before posting.  I 
just responded to a similar issue a few days ago:


http://www.gromacs.org/pipermail/gmx-users/2008-June/034786.html

-Justin

[EMAIL PROTECTED] wrote:

Hi all
I have installed gromacs 3.3.3 in one of my 32 machine fedora core 2.
so check i tried to to do speptide tutorial in
/usr/local/gromacs/share/gromacs/tutor/speptide

But when i m running grompp for position restraint with the command
grompp -f pr -o pr -c after_em -r after_em -p speptide

i get the following warning

 WARNING 1 [file aminoacids.dat, line 1]:
  T-Coupling group Protein has fewer than 10% of the atoms (191 out of
  2741)
  Maybe you want to try Protein and Non-Protein instead?

I tried to change SOL with non protein but getting the same warning. is it
ok to go further with this warning

When i did grompp for full MD with the command

grompp -v -f full -o full -c after_pr -p speptide

again i m getting the same warning

WARNING 1 [file aminoacids.dat, line 1]:
  T-Coupling group Protein has fewer than 10% of the atoms (191 out of
  2741)
  Maybe you want to try Protein and Non-Protein instead?


I tried to change SOL with non protein but getting the same warning.

I don't know what to do now and how can i overcome this, if anyone could
help me.

Thanks

ALKA



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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] How to do CGMD in GROMACS?

[Kia Balali-Mood]

Also check Prof. Marrink's website:
http://md.chem.rug.nl/~marrink/science.html

There are good instructions to get started, for both lipids (2004 FF) and
proteins (MArtini)
> 
> Message: 6
> Date: Thu, 17 Jul 2008 07:55:19 -0400
> From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] How to do CGMD in GROMACS?
> To: Discussion list for GROMACS users 
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 
> Read just about any of the papers from Marrink's group.
> 
> -Justin
> 
> Anirban Ghosh wrote:
> > Hi All,
> >  
> > I am interested in doing Coarse Grained MD in GROMACS. Is there any 
> > module in GROMACS with which I can do this? Please tell me the procedure 
> > of doing CGMD in GROMACS. Thanks a lot.
> >  
> >  
> > Regards,
> >  
> > 
> >  
> >  
> > *Anirban Ghosh*
> > *M.Tech Bioinformatics*
> > *University of Hyderabad*
macs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to [EMAIL PROTECTED]
> > 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
> 
> 

-- 
Kia Balali-Mood, PhD, CBiol, MIBiol
Postdoctoral Researcher, Department of Biochemistry, 
Oxford University, OX1 3QU, UK
http://sansom.biop.ox.ac.uk/kia/ , tel. +44 (0)1865 275 (380 or 275)

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[gmx-users] [Fwd: questions about surface tension]

[David van der Spoel]

 Original Message 
Subject: questions about surface tension
Date: Thu, 17 Jul 2008 21:27:28 +0800
From: Li Yang <[EMAIL PROTECTED]>
To: David van der Spoel <[EMAIL PROTECTED]>

Dir Sir

I must apologize if I've disturbed you.

I have been learning the molecular dynamics simulation. And now，I'm
interesting at the surface tension calculations.I have some questions
about it:

1. For the formula, \gamma_m=(P_N - P_L) * L_z / 2, is it only
available for a flat surface, like a lipid bilayer in water ?  For
example, the surface fluctuation of lipid bilayer often occur in the
simulation, sometimes, the surface is not flat but bending, in such a
case, is the formula still available? What about the vesicle?

2. In my system, there are a bilayer patch and a NP of ~10nm, they are
all in water. At the beginning (state 1), NP and the bilayer don't
contact each other. After some nanoseconds runtime, NP adsorbs on the
surface of the bilayer (state 2). Finally(state 3), the NP embeds into
the inner of the lipid bilayer.

In this case, how can I measure the changing surface tension of the
LIPID BILAYER during the simulation?  Is the formula above available for
my system?
In state 1, is that meaning there are four interface in the system? What
about the case (state 2,3) that the NP contacting the bilayer ? 

I hope I've describe my questions clearly. Any suggestion or recommended
reference will be appreciated.

Thank you very much, wait for your reply.

Sincerely

Li Yang 

Li Yang
[EMAIL PROTECTED]
　　2008-07-17

-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] how to measure the surface tension of membrane by inclusion

[Li Yang]

Hi

I have some questions about the surface tension calculations:

1. For the formula, \gamma_m=(P_N - P_L) * L_z / 2, is it only 
available for a flat surface, like a lipid bilayer in water ?  For example, the 
surface fluctuation of lipid bilayer often occur in the simulation, sometimes, 
the surface is not flat but bending, in such a case, is the formula still 
available? What about the vesicle?

2. In my system, there are a bilayer patch and a NP of ~10nm, they are 
all in water. At the beginning (state 1), NP and the bilayer don't contact each 
other. After some nanoseconds runtime, NP adsorbs on the surface of the bilayer 
(state 2). Finally(state 3), the NP embeds into the inner of the lipid bilayer. 

In this case, how can I measure the changing surface tension during the 
simulation?  Is the formula above available for my system?
In state 1, is that meaning there are four interface in the system? What about 
the case (state 2,3) that the NP contacting the bilayer ?

I hope I've describe my questions clearly. Any suggestion or recommended 
reference will be appreciated.

Thank you very much.

Sincerely


Li Yang
[EMAIL PROTECTED]
　　2008-07-17
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[gmx-users] Constraint Pulling - Oscillating Forces

[VENKATESH HARIHARAN]

Hello,

I am running constraint pulling on a peptide chain.  After the run, the
pull.pdo file outputs the time, along with the force (in kJ/(mol nm)).  The
problem is that the forces are oscillating between almost 1000 pN.  I tried to
reduce the constraint tolerance, but it does not help that much. Any
suggestions on reducing hte oscillations of force?  Thanks.

__

Venkatesh Hariharan
Pennsylvania State University
Schreyer Honors College
Undergraduate - Bioengineering

"You must be the change you wish to see in the world."
--Mohandas Karamchand Gandhi


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[gmx-users] CHARMM FF

[Roland Schulz]

Hi all,

who has the CHARMM FF working with Gromacs? I heard that Erik's group has
something working. Is this correct? My impression is that all force terms
are supported in the CVS version including CMAP. But obviously converting
the files in the itp format is not trivial. Which converters do you use?
I think it would be great to extend the CHARMM FF page
http://wiki.gromacs.org/index.php/CHARMM to be in a similar way as the Amber
FF site is, so that not everyone is reinventing the wheel. I'm welcome to
help in that effort.

Of course in the long run it should be done by the new pbd2gmx but my
impression is that it will still take quite a long time.

Roland
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[gmx-users] Re: CHARMM FF

[Erik Lindahl]

Hi Roland,
We have it working with pdb2gmx, but not CMAP yet, but we're working on
integrating that. I'll see what I can do about pushing things into CVS when
I'm back from vacation in two weeks!

Cheers,

Erik

On Thu, Jul 17, 2008 at 6:57 PM, Roland Schulz <[EMAIL PROTECTED]> wrote:

> Hi all,
>
> who has the CHARMM FF working with Gromacs? I heard that Erik's group has
> something working. Is this correct? My impression is that all force terms
> are supported in the CVS version including CMAP. But obviously converting
> the files in the itp format is not trivial. Which converters do you use?
> I think it would be great to extend the CHARMM FF page
> http://wiki.gromacs.org/index.php/CHARMM to be in a similar way as the
> Amber FF site is, so that not everyone is reinventing the wheel. I'm welcome
> to help in that effort.
>
> Of course in the long run it should be done by the new pbd2gmx but my
> impression is that it will still take quite a long time.
>
> Roland
>
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[gmx-users] Re: gmx-users Digest, Vol 51, Issue 70

[Alan]

Hi Erik,

Despite ffamber seems more developed for GMX, can you tell us if
pdb2gmx (for next release) is also working for amber or we still need
to tweak the pdb input file (Nxxx and Cxxx terms, CYN etc.)?

Many thanks in advance,
Alan

> Date: Thu, 17 Jul 2008 21:49:56 +0200
> From: "Erik Lindahl" <[EMAIL PROTECTED]>
> Subject: [gmx-users] Re: CHARMM FF
> To: "Roland Schulz" <[EMAIL PROTECTED]>
> Cc: gmx-users@gromacs.org
> Message-ID:
><[EMAIL PROTECTED]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Roland,
> We have it working with pdb2gmx, but not CMAP yet, but we're working on
> integrating that. I'll see what I can do about pushing things into CVS when
> I'm back from vacation in two weeks!
>
> Cheers,
>
> Erik
>
> On Thu, Jul 17, 2008 at 6:57 PM, Roland Schulz <[EMAIL PROTECTED]> wrote:
>
>> Hi all,
>>
>> who has the CHARMM FF working with Gromacs? I heard that Erik's group has
>> something working. Is this correct? My impression is that all force terms
>> are supported in the CVS version including CMAP. But obviously converting
>> the files in the itp format is not trivial. Which converters do you use?
>> I think it would be great to extend the CHARMM FF page
>> http://wiki.gromacs.org/index.php/CHARMM to be in a similar way as the
>> Amber FF site is, so that not everyone is reinventing the wheel. I'm welcome
>> to help in that effort.
>>
>> Of course in the long run it should be done by the new pbd2gmx but my
>> impression is that it will still take quite a long time.
>>
>> Roland
>>

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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[gmx-users] Re: CHARMM FF

[Alan]

Hi Erik,

Despite ffamber seems more developed for GMX, can you tell us if
pdb2gmx (for next release) is also working for amber or we still need
to tweak the pdb input file (Nxxx and Cxxx terms, CYN etc.)?

Many thanks in advance,
Alan

> Date: Thu, 17 Jul 2008 21:49:56 +0200
> From: "Erik Lindahl" <[EMAIL PROTECTED]>
> Subject: [gmx-users] Re: CHARMM FF
> To: "Roland Schulz" <[EMAIL PROTECTED]>
> Cc: gmx-users@gromacs.org
> Message-ID:
><[EMAIL PROTECTED]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Roland,
> We have it working with pdb2gmx, but not CMAP yet, but we're working on
> integrating that. I'll see what I can do about pushing things into CVS when
> I'm back from vacation in two weeks!
>
> Cheers,
>
> Erik
>
> On Thu, Jul 17, 2008 at 6:57 PM, Roland Schulz <[EMAIL PROTECTED]> wrote:
>
>> Hi all,
>>
>> who has the CHARMM FF working with Gromacs? I heard that Erik's group has
>> something working. Is this correct? My impression is that all force terms
>> are supported in the CVS version including CMAP. But obviously converting
>> the files in the itp format is not trivial. Which converters do you use?
>> I think it would be great to extend the CHARMM FF page
>> http://wiki.gromacs.org/index.php/CHARMM to be in a similar way as the
>> Amber FF site is, so that not everyone is reinventing the wheel. I'm welcome
>> to help in that effort.
>>
>> Of course in the long run it should be done by the new pbd2gmx but my
>> impression is that it will still take quite a long time.
>>
>> Roland
>>

--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Re: [gmx-users] CHARMM FF

[Nicolas]

We also have a implementation of CHARMM(27) for Gromacs, but without 
CMAP as well. The main limitation is the computational cost due to the 
CHARMM TIP3P water model (it cannot be treated by the special code 
dedicated to water). IIRW the Gromacs 4 publication, the authors said 
there is no particular to difficulty to makes the water loop working for 
CHARMM TIP3P...  Is it planed to implement that into the CVS version?


Nicolas

Roland Schulz a écrit :

Hi all,

who has the CHARMM FF working with Gromacs? I heard that Erik's group 
has something working. Is this correct? My impression is that all 
force terms are supported in the CVS version including CMAP. But 
obviously converting the files in the itp format is not trivial. Which 
converters do you use?
I think it would be great to extend the CHARMM FF page 
http://wiki.gromacs.org/index.php/CHARMM to be in a similar way as the 
Amber FF site is, so that not everyone is reinventing the wheel. I'm 
welcome to help in that effort.


Of course in the long run it should be done by the new pbd2gmx but my 
impression is that it will still take quite a long time.


Roland


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begin:vcard
fn:Nicolas Sapay
n:Sapay;Nicolas
org:University of Calgary;Biological department
adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada
email;internet:[EMAIL PROTECTED]
title:Research Assistant
tel;work:403-220-6869
x-mozilla-html:TRUE
url:http://moose.bio.ucalgary.ca/
version:2.1
end:vcard

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Re: Re: [gmx-users] (no subject)

[JMandumpal]

  
I think, setting tc groups = system will solve this issue.

On Thu, 17 Jul 2008 Justin A.Lemkul wrote :
>For warnings/errors, etc. please check the archive and wiki before posting.  I 
>just responded to a similar issue a few days ago:
>
>http://www.gromacs.org/pipermail/gmx-users/2008-June/034786.html
>
>-Justin
>
>[EMAIL PROTECTED] wrote:
>>Hi all
>>I have installed gromacs 3.3.3 in one of my 32 machine fedora core 2.
>>so check i tried to to do speptide tutorial in
>>/usr/local/gromacs/share/gromacs/tutor/speptide
>>
>>But when i m running grompp for position restraint with the command
>>grompp -f pr -o pr -c after_em -r after_em -p speptide
>>
>>i get the following warning
>>
>>  WARNING 1 [file aminoacids.dat, line 1]:
>>   T-Coupling group Protein has fewer than 10% of the atoms (191 out of
>>   2741)
>>   Maybe you want to try Protein and Non-Protein instead?
>>
>>I tried to change SOL with non protein but getting the same warning. is it
>>ok to go further with this warning
>>
>>When i did grompp for full MD with the command
>>
>>grompp -v -f full -o full -c after_pr -p speptide
>>
>>again i m getting the same warning
>>
>>WARNING 1 [file aminoacids.dat, line 1]:
>>   T-Coupling group Protein has fewer than 10% of the atoms (191 out of
>>   2741)
>>   Maybe you want to try Protein and Non-Protein instead?
>>
>>
>>I tried to change SOL with non protein but getting the same warning.
>>
>>I don't know what to do now and how can i overcome this, if anyone could
>>help me.
>>
>>Thanks
>>
>>ALKA
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[gmx-users] Biomolecular Modelling Retreat 8-12th September 2008

[Itamar Kass]

Stradbroke Island, Brisbane Australia


A small school/retreat on classical molecular dynamics simulation 
techniques will be held from the 8th to the 12th of September 2008. The 
retreat has been organized as a satellite setting the WATOC (World 
Organization for Theoretically Orientated Chemists) conference to be 
held 14-19th of Sept., Sydney, Australia.


The retreat is primarily targeted at PhD and postdoctoral students who 
are using or want to use simulations in their studies.  It is aimed more 
at people who want to learn more about how to use MD as opposed to 
people who are already expert.


The lectures include Wilfred van Gunsteren (ETH, Zurich), Siewert-Jan 
Marrink (University of Groningen), Volker Knecht (MPI, Berlin) and Alan 
Mark (university of Queensland). The school will cover both the basics 
of MD simulations as well as a range of more specialized topics such as 
simulations of membrane systems, peptide folding and free energy 
calculations.


The retreat will be held at University of Queensland's Morton Bay 
research station which is on Stradbroke Island just off the coast from 
Brisbane which has enabled us to keep the cost quite low. It is timed to 
end in time for the students to attend the young scientists forum of 
WATOC in Sydney.

More details can be found at:

http://compbio.chemistry.uq.edu.au/MDschool/Main.html

--

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Molecular Dynamics Group
| School of Molecular and Microbial Sciences (SMMS)
| Chemistry Building (#68)
| The University of Queensland
| St. Lucia Campus, Brisbane, QLD 4067
| Australia
|
| Tel: +61 7 3365 9175
| Fax: +61 7 3365 3872
| E-mail: [EMAIL PROTECTED]
| Web page: http://compbio.chemistry.uq.edu.au/md/ikass/


Unless stated otherwise, this e-mail represents only the views of the Sender 
and not the views of The University of Queensland

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