Re: [gmx-users] Ionic liquids

[Jones de Andrade]

Hi.

I would not agree with the fact that the approach isn't good.

The dialkylimidazolium cation class has a lot of interest on it, which
leaded to the development of force field for them rather than others.

It doesn't mean that there isn't force field for the [EtNH3]+ [NO3]- IL, but
means that there is no obvious reason for someone avoid those ions at a
first glance.

But, in fact, one should avoid the chlorine as counter-ion because it leads
to ILs with a slight larger melting point. There are better options.

On the other hand, a lot depends on the literature. I would expect that
there would be more studies for the interaction of enzimes with
dialkylimidazolium cation based ILs than any other class. BUT, I can be
deadly wrong on this point.

Back to the beggining: having 10 thousand water molecules, with 3 atoms only
and usually rigid, is much simpler than 10 thousand cations with about 25
atoms in a fully flexible structure, in a box which *must* have the same
number of countercharges, with anions of at least 5 atoms (which can
sometimes be made rigid). The computational cost of such a simulation would
rise in a amazingly way when compared to usual aqueous simulations.

Best regards and good luck!

Sincerally yours,

Jones

On 8/22/07, SeungPyo Hong <[EMAIL PROTECTED]> wrote:
>
> Sorry for late respond~
> I totally agree with you.
> Frankly, I don't have any idea about that kind of idea.
> I just help the guy to do what he want to do.
> Anyhow, as Mark said, I think some experiment is required to get a
> meaningful result.
>
> First I warn you that this is not a good approach at all.
> He want to simulate [EtNH3]+ [NO3]-.
> I think that the structure of the is relatively simple and thus made their
> structure with WebMO(Gaussian).
> Then to get the groamcs topology, I use PRODRG server.
> The partial charge of them are corrected to same as Gaussian result.
>
> Then I placed them in a lattice with a same interval.
> And run MD simulation with only solvent.
> By doing this I can get a solvent coordinate in a box.
>
> Using this solvent coordinate and topology, you can run MD.
> But PRODRG does not give an accurate information and thus be careful.
>
> Good luck
>
> On 8/16/07, Sampo Karkola <[EMAIL PROTECTED]> wrote:
> >
> > Hi,
> >
> > nice to hear that someone else is also interested in doing MD in room
> > temperature ionic liquids. What kind of ions do you use? Bmim chlorides
> > perhaps, or do you have a larger counterion to bmim? Or a completely
> > different cation? As Mark pointed out, if you do not have a properly
> > parameterised  force field for ILs, the results probably are not
> > reliable, but I still would like to hear how did you define the
> > parameters and how the mdruns performed.
> >
> > Regards,
> >
> > Sampo
> >
> > __
> > Sampo Karkola
> > Doctoral student
> >
> > Laboratory of Organic Chemistry
> > Department of Chemistry
> > POBox 55, FIN-00014
> > University of Helsinki
> > Finland
> >
> > tel. +358 9 19150369
> > fax. +358 9 19150366
> > [EMAIL PROTECTED]
> >
> > SeungPyo Hong wrote:
> > >
> > > On 8/16/07, *Mark Abraham* < [EMAIL PROTECTED]
> > > > wrote:
> > >
> > > Sampo Karkola wrote:
> > >  > Dear all,
> > >  >
> > >  > I was wondering if there are any parameters defined for ionic
> > > liquids?
> > >  > Some enzymes have retained their activity when the solvent has
> > been a
> > >  > mixture of water and ionic liquids and it would be interesting
> > to
> > > study
> > >  > the actual catalytical reactions in such a solvent.
> > >
> > > I don't know how you can mix an ionic liquid and water and not get
> > a
> > > really hot aqueous solution that would smash an enzyme :-)
> > >
> > >  > I'm not an expert on the ionic liquids field or in simulating
> > > reactions,
> > >  > but ionic liquids have been used in eg. microwave-assisted
> > synthesis
> > >  > with promising results. If one wants to study the reactions
> > that take
> > >  > place in ionic liquids, with or without an enzyme catalysing
> > it, are
> > >  > there any well-known procedures to follow? Is Gromacs the
> > correct
> > > tool
> > >  > for that? I'm not going to study such reactions, at least not
> > at the
> > >  > moment, but I'd just like to know how/if they can be done.
> > >
> > > If you distort the solvent too far from pure water, the
> > parameterization
> > > process of these force fields will no longer be valid for studying
> > the
> > > systems you want. Parameterizing new force fields for these
> > solvents is
> > > probably not a worthwhile undertaking, and definitely not one to
> > do
> > > lightly.
> > >
> > > Mark
> > > ___
> > > gmx-users mailing listgmx-users@gromacs.org
> > > 
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > 

Re: [gmx-users] Ionic liquids

[Sampo Karkola]

Hi and thanks for sharing,

as pointed out earlier in this list, there is a published force field 
for ILs to be used in gromacs. Maybe that would be a good starting point 
for you, too. If I remember correct, they did not have the same ions, 
but they had the most common ones.


I am not going to do any simulations with ILs, I'm just curious to see 
the development around ILs.


Regards,

Sampo

__
Sampo Karkola
Doctoral student

Laboratory of Organic Chemistry
Department of Chemistry
POBox 55, FIN-00014
University of Helsinki
Finland

tel. +358 9 19150369
fax. +358 9 19150366
[EMAIL PROTECTED]

SeungPyo Hong wrote:

Sorry for late respond~
I totally agree with you.
Frankly, I don't have any idea about that kind of idea.
I just help the guy to do what he want to do.
Anyhow, as Mark said, I think some experiment is required to get a 
meaningful result.


First I warn you that this is not a good approach at all.
He want to simulate [EtNH3]+ [NO3]-.
I think that the structure of the is relatively simple and thus made 
their structure with WebMO(Gaussian).

Then to get the groamcs topology, I use PRODRG server.
The partial charge of them are corrected to same as Gaussian result.

Then I placed them in a lattice with a same interval.
And run MD simulation with only solvent.
By doing this I can get a solvent coordinate in a box.

Using this solvent coordinate and topology, you can run MD.
But PRODRG does not give an accurate information and thus be careful.

Good luck

On 8/16/07, *Sampo Karkola* <[EMAIL PROTECTED] 
> wrote:


Hi,

nice to hear that someone else is also interested in doing MD in room
temperature ionic liquids. What kind of ions do you use? Bmim chlorides
perhaps, or do you have a larger counterion to bmim? Or a completely
different cation? As Mark pointed out, if you do not have a properly
parameterised  force field for ILs, the results probably are not
reliable, but I still would like to hear how did you define the
parameters and how the mdruns performed.

Regards,

Sampo

__
Sampo Karkola
Doctoral student

Laboratory of Organic Chemistry
Department of Chemistry
POBox 55, FIN-00014
University of Helsinki
Finland

tel. +358 9 19150369
fax. +358 9 19150366
[EMAIL PROTECTED] 

SeungPyo Hong wrote:
 >
 > On 8/16/07, *Mark Abraham* < [EMAIL PROTECTED]

 > >> wrote:
 >
 > Sampo Karkola wrote:
 >  > Dear all,
 >  >
 >  > I was wondering if there are any parameters defined for ionic
 > liquids?
 >  > Some enzymes have retained their activity when the solvent
has been a
 >  > mixture of water and ionic liquids and it would be
interesting to
 > study
 >  > the actual catalytical reactions in such a solvent.
 >
 > I don't know how you can mix an ionic liquid and water and
not get a
 > really hot aqueous solution that would smash an enzyme :-)
 >
 >  > I'm not an expert on the ionic liquids field or in simulating
 > reactions,
 >  > but ionic liquids have been used in eg. microwave-assisted
synthesis
 >  > with promising results. If one wants to study the
reactions that take
 >  > place in ionic liquids, with or without an enzyme
catalysing it, are
 >  > there any well-known procedures to follow? Is Gromacs the
correct
 > tool
 >  > for that? I'm not going to study such reactions, at least
not at the
 >  > moment, but I'd just like to know how/if they can be done.
 >
 > If you distort the solvent too far from pure water, the
parameterization
 > process of these force fields will no longer be valid for
studying the
 > systems you want. Parameterizing new force fields for these
solvents is
 > probably not a worthwhile undertaking, and definitely not one
to do
 > lightly.
 >
 > Mark
 > ___
 > 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
 > < 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 [EMAIL PROTECTED]

 > >.
 > Can't post? Read
http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Ionic liquids

[SeungPyo Hong]

Sorry for late respond~
I totally agree with you.
Frankly, I don't have any idea about that kind of idea.
I just help the guy to do what he want to do.
Anyhow, as Mark said, I think some experiment is required to get a
meaningful result.

First I warn you that this is not a good approach at all.
He want to simulate [EtNH3]+ [NO3]-.
I think that the structure of the is relatively simple and thus made their
structure with WebMO(Gaussian).
Then to get the groamcs topology, I use PRODRG server.
The partial charge of them are corrected to same as Gaussian result.

Then I placed them in a lattice with a same interval.
And run MD simulation with only solvent.
By doing this I can get a solvent coordinate in a box.

Using this solvent coordinate and topology, you can run MD.
But PRODRG does not give an accurate information and thus be careful.

Good luck

On 8/16/07, Sampo Karkola <[EMAIL PROTECTED]> wrote:
>
> Hi,
>
> nice to hear that someone else is also interested in doing MD in room
> temperature ionic liquids. What kind of ions do you use? Bmim chlorides
> perhaps, or do you have a larger counterion to bmim? Or a completely
> different cation? As Mark pointed out, if you do not have a properly
> parameterised  force field for ILs, the results probably are not
> reliable, but I still would like to hear how did you define the
> parameters and how the mdruns performed.
>
> Regards,
>
> Sampo
>
> __
> Sampo Karkola
> Doctoral student
>
> Laboratory of Organic Chemistry
> Department of Chemistry
> POBox 55, FIN-00014
> University of Helsinki
> Finland
>
> tel. +358 9 19150369
> fax. +358 9 19150366
> [EMAIL PROTECTED]
>
> SeungPyo Hong wrote:
> >
> > On 8/16/07, *Mark Abraham* <[EMAIL PROTECTED]
> > > wrote:
> >
> > Sampo Karkola wrote:
> >  > Dear all,
> >  >
> >  > I was wondering if there are any parameters defined for ionic
> > liquids?
> >  > Some enzymes have retained their activity when the solvent has
> been a
> >  > mixture of water and ionic liquids and it would be interesting to
> > study
> >  > the actual catalytical reactions in such a solvent.
> >
> > I don't know how you can mix an ionic liquid and water and not get a
> > really hot aqueous solution that would smash an enzyme :-)
> >
> >  > I'm not an expert on the ionic liquids field or in simulating
> > reactions,
> >  > but ionic liquids have been used in eg. microwave-assisted
> synthesis
> >  > with promising results. If one wants to study the reactions that
> take
> >  > place in ionic liquids, with or without an enzyme catalysing it,
> are
> >  > there any well-known procedures to follow? Is Gromacs the correct
> > tool
> >  > for that? I'm not going to study such reactions, at least not at
> the
> >  > moment, but I'd just like to know how/if they can be done.
> >
> > If you distort the solvent too far from pure water, the
> parameterization
> > process of these force fields will no longer be valid for studying
> the
> > systems you want. Parameterizing new force fields for these solvents
> is
> > probably not a worthwhile undertaking, and definitely not one to do
> > lightly.
> >
> > Mark
> > ___
> > 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 [EMAIL PROTECTED]
> > .
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > What a coincidence!
> > A student in the biology major come to me he want to do simulation with
> > ionic liquid.
> > I have much doubt about that kind of simulation but becase he is eager
> > to do it.
> > I try to make the solvent by placing the molecules in lattice and run MD
> > under pressure coupling.
> > Though I am also a beginner in this field, I am not sure of the
> > plausiblity of this method but it seems to be OK to me.
> >
> > --
> > --
> > 'God used beautiful mathematics in creating the world.'
> > -Paul Dirac
> > 'But he created too many object.'
> > -Seungpyo Hong
> >
> > Seungpyo Hong
> > Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon
> Korea
> > Tel. (82)-18-372-2468
> > [EMAIL PROTECTED] 
> > [EMAIL PROTECTED] 
> >
> >
> > 
> >
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www

[gmx-users] How to make grids in lipid bilayer (to measure contour length)

[Hwankyu Lee]

Dear gmx-users,

I'm trying to calculate contour length of huge lipid bilayer with 
undulation (non-projected area per lipid). In order to calculate that 
accurately, I would like to measure contour length in local areas of 
bilayer by making lots of grids in lipid bilayer.  I'm wondering if 
there is a tool or way to make grids in lipid bilayer in the .xtc 
trajectories.


Thank you for your help in advance.

best,
Hwankyu.

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RE: [gmx-users] Residue abbreviation list with explanations

[Dallas B. Warren]

> And what is my current issue is? What should I replace the residue
name with?

Ultimately, what ever you want to.  From the name of the file, it seems
like it is formaldehyde, which is a small molecule, and from the link I
provide you the residue name used for it is FLH.  So, convention wise,
that is probably the best name to use for it.

But, that is not going to solve your problem, since you are attempting
to use pdb2gmx to generate your topology.  And that is not going to work
because FLH will not be in the residue database, as is noted at the link
that was provided to you
(http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in
_residue_topology_database)

I would suggest you actually READ what is at URL above.  Funny enough,
on the second line it actually mentions formaldehyde, take note of what
it actually says.  Plus also take notice of the second paragraph.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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[gmx-users] Can I convert Amber (.prepin) into Gromacs (.itp) topology?

[SeungPyo Hong]

Dear gmx-user,
Until yesterday, I believe in PRODRG server.
But when I inspect the result carefully, I found it does not make sense at
all!
Of course, its because I did not modify the input and just thought all the
process will be done automatically.

Anyhow, I also found that partial charge is not plausible even after I get
the plausible structure by adding some options in it.
So, I tried amber's antechamber, and get .prepin file and the partial charge
in it seems to be reasonable.

Then, I want to convert .prepin file into .itp file.
Is there a software doing that work?

Or, is gromacs has tool that generate topology parameters like antechamber
in amber?

Thank you for reading.

-- 
--
'God used beautiful mathematics in creating the world.'
-Paul Dirac
'But he created too many objects.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
[EMAIL PROTECTED]
[EMAIL PROTECTED]
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[gmx-users] Re: Gromacs for AMD Opteron

[Erik Lindahl]

Hi,

We've supported x86-64 since 2002 or so. There are already handcoded  
x86-64 kernels in the correspodning x86_64_sse directory.


This is just a matter of your system not being recognized correctly  
as x86-64, but ia32 for some reason. First make sure that you are  
really setting -m64 in CFLAGS prior to running configure, and if that  
doesn't work you could try to update the config.sub and config.guess  
from ftp.gnu.org.


In any case - when you run configure one of the very first lines  
should echo the system type. That should be x86-64 and not ia32 when  
your compiler flags are set correctly.


Cheers,

Erik

On Aug 21, 2007, at 8:43 PM, Mithun Sridharan wrote:


Dear Sirs,

I'm Mithun Sridharan and am employed at Sun Microsystems in Germany.
I am working on porting Gromacs to Solaris x64 platforms and am  
currently facing issues in compiling the sources.
The compilation works well for 32 bit with GCC as well as Sun  
Studio 12 processors.


However, on compiling with -m64 (for a 64-bit space), the  
compilation fails for the file nb_kernel330_ia32_sse.s.
This file contains the assembler intrinsics and I would like to  
create a similar fole for AMD Opteron based processors as well as  
for SPARC.
I would like to know how these assembler files were generated. Was  
it compiled with -S flag from a C-program or was it manually done  
by hand?


I am also wondering why the make takes this specific file (32-bit  
file spec) for 64 bit compilation!
Another observation is that there is no such file for AMD  
platforms. Am I to understand that the AMD platforms are not  
supported?


If not, are there plans to support AMD platform in the future? I've  
seen good benchmark results on Opteron as Intel processors.


Please let me know if you are interested in the AMD port of the  
software.
I'd be glad if you could answer the queries for me to direct  
efforts on such a port.


Thanks a lot in advance.

-Mithun




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RE: [gmx-users] Step size too small

[Sheyore Omovie]

Thanks guys.
Both Tom's and Mark's suggestions will fix the problem. The reason it did not 
work before now in my case, was that the molecules were almost overlying 
(almost same coordinates in structure file), thus the inf values I got.
I created some distance between them along one axis and was able to move on 
with EM and simulation.
Rgds
John
> From: [EMAIL PROTECTED]> Subject: Re: [gmx-users] Step size too small> Date: 
> Mon, 20 Aug 2007 10:07:09 +0200> To: gmx-users@gromacs.org> > > 17 aug 2007 
> kl. 21.46 skrev TJ Piggot:> > > Hi,> >> > I do not think that what Per 
> suggests is the problem, if you look > > at the potential energy after the 
> minimisation this value is huge > > (and the other two values are inf!). The 
> problem is most likely > > with your topology. As you say the two molecules 
> have been > > successfully minimised on their own so I would suggest that 
> your > > problem is with either how you edit the .top file or the distance > 
> > restraint between the molecules. For my protein that has more than > > one 
> identical chains pdb2gmx does not recognise them as one if you > > provide 
> different chain identifiers in the pdb file, so doing this > > should 
> hopefully stop you having to edit the .top file.> >> > Yes. Just removing 
> bonds in the top-file is not a good solution. > Breaking bonds changes the 
> electronic structure of the molecule, > which in turn is represented by 
> different atom types, so you would > need to change them as well, depending 
> on the force field. Have you > tried the -nomerge option for pdb2gmx?> > 
> /Erik> > > Hope this helps> >> > Tom> >> > --On 17 August 2007 19:02 +0200 
> Per Larsson <[EMAIL PROTECTED]> > > wrote:> >> >> Hello!> >>> >>> >> Check 
> out> >> http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small. > >> 
> 2C_or_no_chan> >> ge_in_energy._Converged_to_machine_precision. > >> 
> 2C_but_not_to_the_requested_> >> precision> >>> >>> >> Cheers> >> /Per> >>> 
> >>> >>> >> 17 aug 2007 kl. 18.28 skrev Sheyore Omovie:> >>> >> Dear 
> gmx-users,> >>> >> I have 2 molecules in a box, as usual pdb2gmx saw them as 
> one. i > >> edited> >> the .top file to remove the bonds created between the 
> two > >> molecules, I> >> also added a distance restraint btw the molecules. 
> (The 2 > >> structures have> >> been separately minimized). However, I get 
> the ff message for EM run:> >>> >> Stepsize too small, or no change in 
> energy.> >> Converged to machine precision,> >> but not to the requested 
> precision Fmax < 1000> >>> >> Double precision normally gives you higher 
> accuracy.> >>> >> Steepest Descents converged to machine precision in 15 
> steps,> >> but did not reach the requested Fmax < 1000.> >> Potential Energy 
> = 1.0246325e+20> >> Maximum force = inf on atom 1> >> Norm of force = inf I 
> would appreciate any advice > >> on how> >> to fix this.> >> Rgds> >> John> 
> >>> >>> >> __> >> See what 
> you’re getting into?before you go there See it!> >> 
> ___> >> gmx-users mailing list 
> 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 [EMAIL PROTECTED]> >> Can't post? Read 
> http://www.gromacs.org/mailing_lists/users.php> >>> >>> >> >> >> > 
> --> > TJ Piggot> > [EMAIL PROTECTED]> > University of 
> Bristol, UK.> >> > ___> > 
> gmx-users mailing list 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 [EMAIL PROTECTED]> > Can't post? Read 
> http://www.gromacs.org/mailing_lists/users.php> > 
> ___> 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> [EMAIL PROTECTED] 
> http://xray.bmc.uu.se/molbiophys> > > 
> ___> gmx-users mailing list 
> 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 [EMAIL PROTECTED]> Can't post? Read 
> http://www.gromacs.org/mailing_lists/users.php
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Re: [gmx-users] Residue abbreviation list with explanations

[Sagittarius]

And this is what I found there:
   
  
see if there is a different name being used for the residue in the residue 
database and rename as appropriate, 

Mark Abraham <[EMAIL PROTECTED]> wrote:  Sagittarius wrote:
> Dear Gromacs users,
> 
> Could you please help me to find a Residue abbreviation list web site.
> I need to replace UNK below with something meaningful.
> 
> formaldehyde.pdb looks like this:
> COMPND UNNAMED 
> REMARK 1 PDB to MMOD atom-numbering translation table; the mmod numbers
> REMARK 1 pertain to the .dat file from which this file was created,
> REMARK 1 not to one created from this file:
> REMARK 1 PDB: 1 2 3 4 
> REMARK 1 MMOD: 1 2 3 4 /
> HETATM 1 C01 UNK 0 0.000 0.302 0.000 0.00 0.00 0
> HETATM 2 O02 UNK 0 0.000 1.510 0.000 0.00 0.00 0
> HETATM 3 H03 UNK 0 -0.960 -0.262 0.000 0.00 0.00 0
> HETATM 4 H04 UNK 0 0.960 -0.262 0.000 0.00 0.00 0
> CONECT 1 3 4
> CONECT 1 2
> CONECT 1 2
> CONECT 2 1
> CONECT 2 1
> CONECT 3 1
> CONECT 4 1
> END

Um no, you don't need a residue abbreviation list. See 
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

Mark
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RE: [gmx-users] Residue abbreviation list with explanations

[Sagittarius]

And what is my current issue
is? What should I replace the residue name with?


"Dallas B. Warren" <[EMAIL PROTECTED]> wrote:  > > Could you please help me to 
find a Residue abbreviation list web
site. 

If you want to find out what people are calling a particular molecule or
residue, best place to look is the PDB Database. If it is a small
molecule, then http://alpha2.bmc.uu.se/hicup/ is a good place to look.

However, as indicated previously, this is not what your current issue
is.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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Re: [gmx-users] RE : long-term drift and crash

[Stéphane Téletchéa]

BON Michael a écrit :

Hi,

Sorry fot no answering accurately.
Here is new insight for understanding my problem.

In fact, even simulations of pure water (tip4p and tip4p_ew) don't work !
And those simulations crash with a strange periodic pattern : still using 
g_msd, I observe
on the msd plot sudden jumps that occur exactly every 10.000 ps ! By "jump" I 
mean a violent
increase of the slope of the curve that lasts a short time, which is exactly 
0.1 ps each time in my case. The curve is linear with the correct diffusion 
constant otherwise. I observe such jumps between 10.0 and 10.1 ps, 20 and 20.1 
ps 30 and 30.1 ps, and so on, and each time the jumps have a higher magnitude 
than the previous one, till the simulation crashes.

I don't see anything in my parameters that could explain such a periodicity of 
10.000 ps. I tried to half the timestep, and it halved the duration of the 
jump, which thus became 0.05, but it didn't changed the periodicity of 10 ps. 
Changing tau_t had no consequence.

Here are again my parameters for water simulation : 
constraints = all-bonds



dt = 0.002


I think you should either use
- constraints = h-bonds,   dt = 0.002
or
- constraints = all-bonds, dt = 0.004
but not a combination of both.

Constraining all-bonds is *merely only* for getting a bigger time step 
for md, but for regular simulations, i would definitely only constrain 
h-bonds and use dt=0.002.


Cheers,
Stéphane

--
Stéphane Téletchéa, PhD.  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
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[gmx-users] Can the g_sas in the gmx3.3.1 give correct resarea and atomarea?

[Hu Zhongqiao]

I calculated SASA using g_sas for three proteins with -r and -oa and
found that the atom area for one protein is considerably larger than two
others. I dont know it is due to the nature of different proteins or
something incorrect for the command g_sas itself. And I checked the
mailing list and found that Berk once said in 2003
 
"The -r and -oa (resarea and atomarea) output of g_sas has always been
incorrect."
 
I want to ask if g_sas for the gmx3.3.1 can give correct resarea and
atomarea. 
 
Thanks in advance,
 
Zhongqiao Hu
 
Department of Chemical and Biomolecular Engineering
National University of Singapore
 
 
 
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[gmx-users] RE : long-term drift and crash

[BON Michael]

Hi,

Sorry fot no answering accurately.
Here is new insight for understanding my problem.

In fact, even simulations of pure water (tip4p and tip4p_ew) don't work !
And those simulations crash with a strange periodic pattern : still using 
g_msd, I observe
on the msd plot sudden jumps that occur exactly every 10.000 ps ! By "jump" I 
mean a violent
increase of the slope of the curve that lasts a short time, which is exactly 
0.1 ps each time in my case. The curve is linear with the correct diffusion 
constant otherwise. I observe such jumps between 10.0 and 10.1 ps, 20 and 20.1 
ps 30 and 30.1 ps, and so on, and each time the jumps have a higher magnitude 
than the previous one, till the simulation crashes.

I don't see anything in my parameters that could explain such a periodicity of 
10.000 ps. I tried to half the timestep, and it halved the duration of the 
jump, which thus became 0.05, but it didn't changed the periodicity of 10 ps. 
Changing tau_t had no consequence.

Here are again my parameters for water simulation : 
constraints = all-bonds
constraint_algorithm = Lincs
lincs_order = 4
integrator = md
dt = 0.002
nsteps = 100
comm_mode = none
coulomb_type = PME
fourier_spacing = 0.12
optimize_fft = yes
vdwtype = cut-off
rcoulomb = 1.2
rvdw = 1.2
rlist = 1.2
DispCorr= EnerPres
nstlist = 1
ns_type = grid
pbs = xyz
tcoupl = berendsen
tc-grps = System
tau_t = 0.5
ref_t = 300
pcoupl = no
gen_vel = yes
gen_temp = 300

I am still using AMBER99, and the include files ffamber_tip4p.itp and 
ffamber_tip4p_ew.itp, in double precision. With g_energy,  everything looks 
normal, I even find an average potential energy of 41.23 kJ/mol per tip4p water 
molecule, which is a published value. What is going on ?!

Thanks for your time and help,
Michael Bon

Message: 2
Date: Sat, 18 Aug 2007 12:34:02 +1000
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Re : long-term drift and crash
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

BON Michael wrote:
> The same bugs occurs during the NPT equilibration stage that I did after the 
> energy minimization (with l-bgfs, till convergence), the average pressure 
> being now -0.5 bar (over the 200 ps the simulation ran before it crashed).
> Still the same things : everything I plot with g_energy is normal, the msd 
> plot oscillates more and more, I see nothing special on the last 
> configuration just before the crash).

Actually that link suggests some NVT to fix temperatures and NPT to fix 
box size. It sounds like your system is fragile and you should be doing 
both of these... or at least telling us that you're doing both of these.

Mark


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Re: [gmx-users] nstlist with vdw only

[Erik Lindahl]

Hi,

On Aug 21, 2007, at 8:08 AM, Nicolas Schmidt wrote:

Would't this mean, that molecules could suddenly appear and lead to  
a discontinuity in the LJ-potential?
Or in what way should I modify the r_vdw according to what rlist? I  
wanna end with a cut-off of the LJ-potentail around 1.75nm.




Certainly - but there will be a discountinuity even with nstlist=1  
unless you use switch or shift modifications to the interaction.


For perfect energy conservation you should pick rlist slightly larger  
than rvdw (depends on your charge group size and nstlist, but start  
with 0.2-0.3 nm), and apply switch or shift.


However, there will be a bit of performance price to pay for that.

Personally, I think energy conservation is overrated. There's nothing  
wrong with it, but energy conservation per se doesn't mean anything.  
You could use the potential V=sin(r) for Lennard-Jones interaction  
and still get conservation if it is switched smoothly to zero at the  
cutoff distance.


The goal in most applications is to improve the accuracy of free  
energy, diffusion coefficients, or other observables, and then it is  
sometimes better to focus on the sampling and let thermostats take  
care of the drifts in energy.



Cheers,

Erik

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Re: [gmx-users] PME or SPME?

[Erik Lindahl]

And the reason for this is that nobody has really used lagrangian- 
interpolation PME since smooth PME appeared in 1995 :-)


Cheers,

Erik

On Aug 21, 2007, at 4:47 AM, Mark Abraham wrote:


Jones de Andrade wrote:

Hi all.
Well, I have some kind of a "didatic" doubt: Ok, from what I can  
understand up to now, PME uses lagrande interpolation for the  
genaration of the grid, while SPME uses cardinal B-splines to do so.
Is it correct? And if, so, gromacs implements PME or SPME (the  
manual states PME, but also states B-splines)?


SPME. The GROMACS manual refers to the algorithm in ref 10 of the  
manual as PME, even though it is a modification of the original  
algorithm in ref 9, and that modification is often referred to as  
"smooth PME".


Mark
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