date:20090526

Re: [gmx-users] Lennard-Jones 9-6 potential problems

2009-05-26 Thread Mark Abraham


zhangjianguo2002 wrote:
 
 
   Firstly, thanks Berk and David van der Spoel for your replies. Maybe 
I have not explain my problems clearly, there is only one type of 
particle,namely one full-atom benzene molecule is replaced by one 
coarse-grained benzene particle,so there in no non-bonded interactions 
between different types and comb-rule may not work.
in the [ defaults ] section of the ITP file, the defaults power for the 
repulsion term is 12, if I change it to 9, is that enough  if I want to 
use LJ-9-6 potential? is there still anything needed to be changed?


The text on manual page 112 says this works, but table 5.3 on page 106 
doesn't mention it. One or the other needs updating.


Mark
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Re: [gmx-users] Lennard-Jones 9-6 potential problems

2009-05-26 Thread David van der Spoel

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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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RE: [gmx-users] Lennard-Jones 9-6 potential problems

2009-05-26 Thread zhangjianguo2002

 
 
   Firstly, thanks Berk and David van der Spoel for your replies. Maybe I have 
not explain my problems clearly, there is only one type of particle,namely one 
full-atom benzene molecule is replaced by one coarse-grained benzene 
particle,so there in no non-bonded interactions between different types and 
comb-rule may not work.
in the [ defaults ] section of the ITP file, the defaults power for the 
repulsion term is 12, if I change it to 9, is that enough  if I want to use 
LJ-9-6 potential? is there still anything needed to be changed? 
 
Best regards!




>Hi,
>
>I forgot about this feature.
>Your problem is indeed that you used comb-rule=1,
>you have to use 2 or 3 to make this work.
>And indeed you should use user tables filled with the 9-6 potential.
>
>Gromacs could actually easily support p-6 tables with any value for p,
>by storing p in the tpr file and automatically using tables when p!=12.
>
>Berk
>
>> Date: Tue, 26 May 2009 09:45:22 +0200
>> From: sp...@xray.bmc.uu.se
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Lennard-Jones 9-6 potential problems
>> 
>> zhangjianguo2002 wrote:
>> > Hi everyone!
>> >   Have anyone used the Lennard-Jones 9-6 potential for  coarse-grained 
>> > models? when I use it, I get a very different result from  that is got 
>> > from the same Lennard-Jones 9-6 potential  formed a potential table,the 
>> > latter's results are comparable to the experiments. when I use LJ-9-6 
>> > potential,the ITP file  is as following:
>> >  
>> >   [ defaults ]
>> > ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
>> >1 1   no  1.0 1.0 9
>> 
>> Even if this may generate the correct parameters (please use gmxdump to 
>> check your tpr file) you still have to provide a user table to mdrun and 
>> to set vdw-type = user in your mdp file. You may need to change the 
>> nbfunc to three as well. Check source code in src/kernel/convparm to see 
>> what is going on.  I don't think this is documented anywhere, is it?
>> 
>> 
>> > 
>> > [ atomtypes ]
>> > ;   name  bond_typemasscharge   ptype  sigma  epsilon
>> >  opls_001   Cx  6  78.01900A0.5052.95;
>> > 
>> >  [ moleculetype ]
>> > ; Name nrexcl
>> > Phenyl  1
>> > [ atoms ]
>> > ;   nr  type  resnr resid  atom  cgnr   charge mass
>> >  1 opls_001 1  Phenyl C1 10.000  78.0190 
>> > 
>> >  other files ,such as mdp file and top file ,are all the same as normal 
>> > LJ-12-6 potential, are these correct if I want to use LJ-9-6 potential? 
>> > Do I still need to change something? Thanks very much for your kindness!
>> > 
>> > 
>> > 
>> > 
>> > ´©Ô½µØÕð´ø ¼ÍÄîãë´¨µØÕðÒ»ÖÜÄê 
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>> > 
>> > 
>> > 
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>> -- 
>> 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.
>> sp...@xray.bmc.uu.sespoel@gromacs.org   http://folding.bmc.uu.se
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[gmx-users] Shared library version binary on CYGWIN

2009-05-26 Thread Makoto Yoneya

Dear Mark and GROMACS users:

Mark wrote.
> You can't build DLLs since the cygwin build tools are unix-style, and 
> the GROMACS build strategy is unix-specific. --enable-shared also 
> probably won't work for unix-style shared libraries, because the dynamic 
> linker is probably the Windows ld.exe, which can't deal with unix-style 
> shared libraries.

Thanks a lot for the comment.

> It would be possible to make GROMACS write proper DLLs using the cygwin 
> dlltool functionality, but nobody has ever cared enough to do it. I'd 
> struggle to imagine a useful Windows environment where providing 100MB 
> of statically-linked executables was a serious problem. 

I found the libtool within gromacs source (both 3.3.3 and 4.0.4) is not as
new as that of e.g. fftw-3.2.1 (which use the libtool-2.2.6).
I'm wondering if the libtool version was updated to the newer one,
then the DLLs could be generated properly, because fftw-3.2.1 can
build DLL on cygwin if it configured with --enable-shared.
I'd tried that with gromacs a little but no success as I have no detailed
knowledge on GNU autotools.

> For a course, 
> you won't even need the whole executable set. mdrun, grompp, editconf, 
> pdb2gmx, genion, g_energy, trjconv and maybe one or two more analysis 
> tools to suit the course should do it.

You're right.
That may be a practical solution in the current situation.

Kind Regards.

Makoto Yoneya, Dr.
AIST, Japan

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Re: [gmx-users] gmxtest

2009-05-26 Thread Mark Abraham


Mark Abraham wrote:

Simba Xiao wrote:

Dear all,

Does your GMX 4 past the gmxtest package in the gmx wiki ?

My Gromacs 4.0.4 can not pass all the test. The test  tip4p, ti4pflex 
and some kernel issues failed.


That's normal at the moment, unfortunately. Future releases of gmxtest 
will probably fix the non-kernel issues, and GROMACS > 4.0.5 will fix 
the kernel issues.


Sorry, I mis-remembered something. The kernel issues were caused by a 
hard-to-provoke bug in 3.3.x which provided the reference trajectories. 
GROMACS 4.0.x are fine, but the test fails because of the flawed 
reference values. See bugzilla 313 for details.


Mark

I use standard packages and everything looks find. The simulation 
result are good and identical  to gromacs 3.3.3.


But, still it annoys me with the test result.

Can somebody tell how much the test matters and can somebody tell 
something more than the wiki tells (It dose not explain much).


Well, it does explain things, but not such that a new GROMACS user can 
get a useful result from existing versions of gmxtest. I'll upgrade the 
wiki documentation if/when a gmxtest re-release happens.


Mark
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Re: [gmx-users] gmxtest

2009-05-26 Thread Mark Abraham


Simba Xiao wrote:

Dear all,

Does your GMX 4 past the gmxtest package in the gmx wiki ?

My Gromacs 4.0.4 can not pass all the test. The test  tip4p, ti4pflex 
and some kernel issues failed.


That's normal at the moment, unfortunately. Future releases of gmxtest 
will probably fix the non-kernel issues, and GROMACS > 4.0.5 will fix 
the kernel issues.


I use standard packages and everything looks find. The simulation result 
are good and identical  to gromacs 3.3.3.


But, still it annoys me with the test result.

Can somebody tell how much the test matters and can somebody tell 
something more than the wiki tells (It dose not explain much).


Well, it does explain things, but not such that a new GROMACS user can 
get a useful result from existing versions of gmxtest. I'll upgrade the 
wiki documentation if/when a gmxtest re-release happens.


Mark
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Re: [gmx-users] Shared library version binary on CYGWIN

2009-05-26 Thread Mark Abraham


Makoto Yoneya wrote:
Dear GROMACS users: 


I'd like to get small sized shared library version GROMACS binary on
windows-PC with CYGWIN (to use in some course).
Even configured with "--enable-shared", the compiled binary set looks
not the shared library version (no DLLs and the total binary set
size was over 100MB).


You can't build DLLs since the cygwin build tools are unix-style, and 
the GROMACS build strategy is unix-specific. --enable-shared also 
probably won't work for unix-style shared libraries, because the dynamic 
linker is probably the Windows ld.exe, which can't deal with unix-style 
shared libraries.


It would be possible to make GROMACS write proper DLLs using the cygwin 
dlltool functionality, but nobody has ever cared enough to do it. I'd 
struggle to imagine a useful Windows environment where providing 100MB 
of statically-linked executables was a serious problem. For a course, 
you won't even need the whole executable set. mdrun, grompp, editconf, 
pdb2gmx, genion, g_energy, trjconv and maybe one or two more analysis 
tools to suit the course should do it.


Mark


Actually the compiled GROMACS binary correctly runs.
The problem was just the GROMACS was not shared library version I'd
expected.
I'd tried both gromacs-3.3.3 and gromacs-4.0.4 but the situations were same
(with ./configure --enable-shared --without-x and appropriate CPPFLAGS and
LDFLAGS).
So, my question was just how to get the shared library version on CYGWIN
with 
DLLs (like cyggmx-4.dll, cygmd-4.dll etc.).

Could someone kindly give me info?

Thank you for advance.

Makoto Yoneya, Dr.
AIST, Japan

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[gmx-users] gmxtest

2009-05-26 Thread Simba Xiao

Dear all,

Does your GMX 4 past the gmxtest package in the gmx wiki ?

My Gromacs 4.0.4 can not pass all the test. The test  tip4p, ti4pflex and
some kernel issues failed.

I use standard packages and everything looks find. The simulation result are
good and identical  to gromacs 3.3.3.

But, still it annoys me with the test result.

Can somebody tell how much the test matters and can somebody tell something
more than the wiki tells (It dose not explain much).

Great thanks!
S.

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Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

2009-05-26 Thread Mark Abraham


Stefano Meliga wrote:

Hi again,

I've tryed to perform the same preprocessing and EM steps without 
distance constraints and the situation improves a lot.
I get no warnings in the steepest descent EM and only one molecule 
cannot be set in the conjugate gradient EM.

Can you see the reason?


Yes. You're not doing EM. "t = 0.011 ps:" is a big clue. Choose your 
integrator in your .mdp file better.


Also, as Justin suggests, please be careful with the 
constraint/restraint terminology.


Mark


Thanks,
Stefano.

Stefano Meliga ha scritto:

Hi everybody,

I neutralized my system with the commands:

$grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro -p
4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr
$grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb -nname
CL-
(adding the atoms to the solution SOL)

I renamed the files to keep track of the different topology files:

mv 4AKEallHsol_pre.top 4AKEallHion.top
mv "#4AKEallHsol_pre.top.1#" 4AKEallHsol_pre.top

I run an all-bonds position restraint steepest descent EM:

$grxdir/grompp -f 4AKEprePREMsteep.mdp -po 4AKE_PREMsteep.mdp -c
4AKEallHion.gro -p 4AKEallHion.top -pp 4AKEallHion_out.top -o
4AKEallHion.tpr
$grxdir/mdrun -s 4AKEallHion.tpr -o 4AKE_PREMsteep.trr -c
4AKE_PREMsteep.gro -e 4AKE_PREMsteep.edr -g 4AKE_PREMsteep.log -v

mdrun exits successfully but displays the warning:
t = 0.011 ps: Water molecule starting at atom 17223 can not be settled.
Check for bad contacts and/or reduce the timestep.

In the gro file atom 17223 is an oxigen of the solution

Going further with my simulation i run a all-bonds position restrained
conjugate gradient EM:

$grxdir/grompp -f 4AKEprePREMcg.mdp -po 4AKE_PREMcg.mdp -c
4AKE_PREMsteep.gro -p 4AKEallHion_out.top -pp 4AKEallH_PREMsteep.top
-o 4AKEallH_PREMsteep.tpr
$grxdir/mdrun -s 4AKEallH_PREMsteep.tpr -o 4AKE_PREMcg.trr -c
4AKE_PREMcg.gro -e 4AKE_PREMcg.edr -g 4AKE_PREMcg.log -v

but get the fatal error:

Source code file: constr.c, line: 136

Fatal error:
Too many LINCS warnings (2200)

And some of this warnings are again solution's molecules that cannot 
be set.

May the problem be related to the ions added to neutralise the system?
mdrun was not showing this problem with the non-neutral system in
input.

Thanks a lot,
Stefano

  

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[gmx-users] Shared library version binary on CYGWIN

2009-05-26 Thread Makoto Yoneya

Dear GROMACS users: 

I'd like to get small sized shared library version GROMACS binary on
windows-PC with CYGWIN (to use in some course).
Even configured with "--enable-shared", the compiled binary set looks
not the shared library version (no DLLs and the total binary set
size was over 100MB).
Actually the compiled GROMACS binary correctly runs.
The problem was just the GROMACS was not shared library version I'd
expected.
I'd tried both gromacs-3.3.3 and gromacs-4.0.4 but the situations were same
(with ./configure --enable-shared --without-x and appropriate CPPFLAGS and
LDFLAGS).
So, my question was just how to get the shared library version on CYGWIN
with 
DLLs (like cyggmx-4.dll, cygmd-4.dll etc.).
Could someone kindly give me info?

Thank you for advance.

Makoto Yoneya, Dr.
AIST, Japan

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Re: [gmx-users] Viscosity using periodic perturbation method

2009-05-26 Thread Yanmei Song

Dear Herk:

Thank you so much for your help!

Maybe the way I asked make it confusing. I read your paper: " Determing the
shear viscosity of model liquids from molecular dynamics simulations"  You
used NVT. My question is which one is better? NPT or NVT? Or you can use
either of them.

"Strictly speaking it might be incorrect, but since pressure scaling is
usually less than 1%
it will not affect your results significantly."

So technically we should use NVT for the periodic perturbation method,
right? Thanks!

On Tue, May 26, 2009 at 12:03 AM, Berk Hess  wrote:

>  Hi,
>
> Yes, you can use NPT, the code takes care of this properly.
> Strictly speaking it might be incorrect, but since pressure scaling is
> usually less than 1%
> it will not affect your results significantly.
>
> Berk.
>
> --
> Date: Mon, 25 May 2009 15:19:10 -0700
> From: yson...@asu.edu
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Viscosity using periodic perturbation method
>
>
> Dear users:
>
> I was trying to calculate the viscosity of liquid system using periodic
> perturbation method. Does this method require NVT ensemble simulation in
> stead of NPT ? Because I read some literature on periodic perturbation
> method. they all used NVT.  I did not found any information about this on
> the manual. Can I use NPT Non-equilibrium MD in order to use periodic
> perturbation method? Thanks in advance!
> --
> Yanmei Song
> Ph.D. Candidate
> Department of Chemical Engineering
> Arizona State University
>
> --
> Express yourself instantly with MSN Messenger! MSN 
> Messenger
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-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

2009-05-26 Thread Justin A. Lemkul




Stefano Meliga wrote:

Hi again,

I've tryed to perform the same preprocessing and EM steps without 
distance constraints and the situation improves a lot.
I get no warnings in the steepest descent EM and only one molecule 
cannot be set in the conjugate gradient EM.

Can you see the reason?



Were you constraining bond lengths or using position restraints?  You've 
combined the terminology (restraints and constraints are separate ideas in Gromacs).


LINCS warnings and related problems are discussed extensively in the list 
archive (with potential solutions!) as well as on the wiki:


http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings

If the problem arises only after adding ions, inspect the location of ion 
insertion.  Since it is random, ions may have been placed in an unfavorable 
location, causing them (or a nearby water molecule) to go careening through the 
simulation cell.  That happened to me once :)


-Justin


Thanks,
Stefano.

Stefano Meliga ha scritto:

Hi everybody,

I neutralized my system with the commands:

$grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro -p
4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr
$grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb -nname
CL-
(adding the atoms to the solution SOL)

I renamed the files to keep track of the different topology files:

mv 4AKEallHsol_pre.top 4AKEallHion.top
mv "#4AKEallHsol_pre.top.1#" 4AKEallHsol_pre.top

I run an all-bonds position restraint steepest descent EM:

$grxdir/grompp -f 4AKEprePREMsteep.mdp -po 4AKE_PREMsteep.mdp -c
4AKEallHion.gro -p 4AKEallHion.top -pp 4AKEallHion_out.top -o
4AKEallHion.tpr
$grxdir/mdrun -s 4AKEallHion.tpr -o 4AKE_PREMsteep.trr -c
4AKE_PREMsteep.gro -e 4AKE_PREMsteep.edr -g 4AKE_PREMsteep.log -v

mdrun exits successfully but displays the warning:
t = 0.011 ps: Water molecule starting at atom 17223 can not be settled.
Check for bad contacts and/or reduce the timestep.

In the gro file atom 17223 is an oxigen of the solution

Going further with my simulation i run a all-bonds position restrained
conjugate gradient EM:

$grxdir/grompp -f 4AKEprePREMcg.mdp -po 4AKE_PREMcg.mdp -c
4AKE_PREMsteep.gro -p 4AKEallHion_out.top -pp 4AKEallH_PREMsteep.top
-o 4AKEallH_PREMsteep.tpr
$grxdir/mdrun -s 4AKEallH_PREMsteep.tpr -o 4AKE_PREMcg.trr -c
4AKE_PREMcg.gro -e 4AKE_PREMcg.edr -g 4AKE_PREMcg.log -v

but get the fatal error:

Source code file: constr.c, line: 136

Fatal error:
Too many LINCS warnings (2200)

And some of this warnings are again solution's molecules that cannot 
be set.

May the problem be related to the ions added to neutralise the system?
mdrun was not showing this problem with the non-neutral system in
input.

Thanks a lot,
Stefano

  

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--


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


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[gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

2009-05-26 Thread Stefano Meliga


Hi again,

I've tryed to perform the same preprocessing and EM steps without 
distance constraints and the situation improves a lot.
I get no warnings in the steepest descent EM and only one molecule 
cannot be set in the conjugate gradient EM.

Can you see the reason?

Thanks,
Stefano.

Stefano Meliga ha scritto:

Hi everybody,

I neutralized my system with the commands:

$grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro -p
4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr
$grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb -nname
CL-
(adding the atoms to the solution SOL)

I renamed the files to keep track of the different topology files:

mv 4AKEallHsol_pre.top 4AKEallHion.top
mv "#4AKEallHsol_pre.top.1#" 4AKEallHsol_pre.top

I run an all-bonds position restraint steepest descent EM:

$grxdir/grompp -f 4AKEprePREMsteep.mdp -po 4AKE_PREMsteep.mdp -c
4AKEallHion.gro -p 4AKEallHion.top -pp 4AKEallHion_out.top -o
4AKEallHion.tpr
$grxdir/mdrun -s 4AKEallHion.tpr -o 4AKE_PREMsteep.trr -c
4AKE_PREMsteep.gro -e 4AKE_PREMsteep.edr -g 4AKE_PREMsteep.log -v

mdrun exits successfully but displays the warning:
t = 0.011 ps: Water molecule starting at atom 17223 can not be settled.
Check for bad contacts and/or reduce the timestep.

In the gro file atom 17223 is an oxigen of the solution

Going further with my simulation i run a all-bonds position restrained
conjugate gradient EM:

$grxdir/grompp -f 4AKEprePREMcg.mdp -po 4AKE_PREMcg.mdp -c
4AKE_PREMsteep.gro -p 4AKEallHion_out.top -pp 4AKEallH_PREMsteep.top
-o 4AKEallH_PREMsteep.tpr
$grxdir/mdrun -s 4AKEallH_PREMsteep.tpr -o 4AKE_PREMcg.trr -c
4AKE_PREMcg.gro -e 4AKE_PREMcg.edr -g 4AKE_PREMcg.log -v

but get the fatal error:

Source code file: constr.c, line: 136

Fatal error:
Too many LINCS warnings (2200)

And some of this warnings are again solution's molecules that cannot be set.
May the problem be related to the ions added to neutralise the system?
mdrun was not showing this problem with the non-neutral system in
input.

Thanks a lot,
Stefano

  

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[gmx-users] solution molecules cannot be set by mdrun after neutralization

2009-05-26 Thread Stefano Meliga

Hi everybody,

I neutralized my system with the commands:

$grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro -p
4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr
$grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb -nname
CL-
(adding the atoms to the solution SOL)

I renamed the files to keep track of the different topology files:

mv 4AKEallHsol_pre.top 4AKEallHion.top
mv "#4AKEallHsol_pre.top.1#" 4AKEallHsol_pre.top

I run an all-bonds position restraint steepest descent EM:

$grxdir/grompp -f 4AKEprePREMsteep.mdp -po 4AKE_PREMsteep.mdp -c
4AKEallHion.gro -p 4AKEallHion.top -pp 4AKEallHion_out.top -o
4AKEallHion.tpr
$grxdir/mdrun -s 4AKEallHion.tpr -o 4AKE_PREMsteep.trr -c
4AKE_PREMsteep.gro -e 4AKE_PREMsteep.edr -g 4AKE_PREMsteep.log -v

mdrun exits successfully but displays the warning:
t = 0.011 ps: Water molecule starting at atom 17223 can not be settled.
Check for bad contacts and/or reduce the timestep.

In the gro file atom 17223 is an oxigen of the solution

Going further with my simulation i run a all-bonds position restrained
conjugate gradient EM:

$grxdir/grompp -f 4AKEprePREMcg.mdp -po 4AKE_PREMcg.mdp -c
4AKE_PREMsteep.gro -p 4AKEallHion_out.top -pp 4AKEallH_PREMsteep.top
-o 4AKEallH_PREMsteep.tpr
$grxdir/mdrun -s 4AKEallH_PREMsteep.tpr -o 4AKE_PREMcg.trr -c
4AKE_PREMcg.gro -e 4AKE_PREMcg.edr -g 4AKE_PREMcg.log -v

but get the fatal error:

Source code file: constr.c, line: 136

Fatal error:
Too many LINCS warnings (2200)

And some of this warnings are again solution's molecules that cannot be set.
May the problem be related to the ions added to neutralise the system?
mdrun was not showing this problem with the non-neutral system in
input.

Thanks a lot,
Stefano
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RE: [gmx-users] Normal Mode Analysis

2009-05-26 Thread Berk Hess


Hi,

But there is a '>' on line 18, at least in my mail.
I tested the patch and it worked for me.
Maybe something went wrong when cut and pasting the patch from the email?
I can mail you the whole file personally tomorrow, if required.

Berk

Date: Tue, 26 May 2009 14:47:52 +0200
Subject: Re: [gmx-users] Normal Mode Analysis
From: f.hoffga...@gmail.com
To: gmx-users@gromacs.org

Hi

thanks for your reply. I tried patching as you described it, but I got the 
error message:

patch:  `>' expected at line 18 of patch

Franzi

---
Franziska Hoffgaard
PhD Student

Bioinformatics & Theo. Biology Group
TU Darmstadt

2009/5/26 Berk Hess 






Hi,

I just saw that 4.0 uses a new mtx format which can also efficiently store 
sparse matrices.
Please try if my modified gmxdump for 4.0.5 works?
Store the data below in a file called fix and then do:
patch gmxdump.c fix


Berk

61a62,63 
> #include "sparsematrix.h"  
> #include "mtxio.h" 
364a367,402  

> static void list_mtx(char *fn) 
> {  
>   int  nrow,ncol,i,j,k;
>   real *full=NULL,value;   

>   gmx_sparsematrix_t * sparse=NULL;
>
>   gmx_mtxio_read(fn,&nrow,&ncol,&full,&sparse);
>

>   if (full == NULL) {
> snew(full,nrow*ncol);
> for(i=0;i   full[i] = 0;
> }
>
> for(i=0;inrow;i++) {
>   for(j=0;jndata[i];j++) {

> k = sparse->data[i][j].col;
> value = sparse->data[i][j].value;
> full[i*ncol+k] = value;
> full[k*ncol+i] = value;
>   }
> }
> gmx_sparsematrix_destroy(sparse);

>   }
>
>   printf("%d %d\n",nrow,ncol);
>   for(i=0; i for(j=0; j   printf(" %g",full[i*ncol+j]);
> }
> printf("\n");

>   }
>
>   sfree(full);
> }
>
381a420
> { efMTX, "-mtx", "hessian", ffOPTRD },
409a449,450
>   else if (ftp2bSet(efMTX,NFILE,fnm))
> list_mtx(ftp2fn(efMTX,NFILE,fnm));



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Re: [gmx-users] constant term in dihedral potential function

2009-05-26 Thread Mark Abraham


Kukol, Andreas wrote:

Dear all,

I included the following dihedral potential function in a topology:

V(phi2) = -5.865 + 7.470 [1+cos(phi2-180°)] + 3.99 [1+cos(2 phi2)] + 1.1 
[1+cos(3 phi2-180°)]

The problem is about representing the constant term -5.865. Using equation 4.61 
(Gromacs 4.0 manual):

V(phi) = k * (1 + cos (n phi - phis) )

I specified:

V = -5.865 * (1 + cos (0 - 90) ) = -5.865 with multiplicity n=0

That leads to the entry in the topology file:
 22232425 190 -5.685 0

This worked fine in Gromacs 3.3, but in Gromacs 4.05 I get the error message 
(from Grompp):

Fatal error:
Value of 'multiplicity' in Proper Dih. is 0, which is smaller than the minimum 
of 1

I wonder, if this is a bug in Gromacs 4.05, or if there is any better way to 
specify a constant term in a dihedral potential function.


This is only relevant if you're ever using the magnitude of the 
potential energy for something. d/dr of such a term is zero, of course, 
so there's no force contribution and thus it does not affect the 
dynamics at all.


Mark
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Re: [gmx-users] Normal Mode Analysis

2009-05-26 Thread Franzi Hoffgaard

Hi

thanks for your reply. I tried patching as you described it, but I got the
error message:

patch:  `>' expected at line 18 of patch

Franzi

---
Franziska Hoffgaard
PhD Student
Bioinformatics & Theo. Biology Group
TU Darmstadt

2009/5/26 Berk Hess 

>  Hi,
>
> I just saw that 4.0 uses a new mtx format which can also efficiently store
> sparse matrices.
> Please try if my modified gmxdump for 4.0.5 works?
> Store the data below in a file called fix and then do:
> patch gmxdump.c fix
>
> Berk
>
> 61a62,63
> > #include "sparsematrix.h"
> > #include "mtxio.h"
> 364a367,402
> > static void list_mtx(char *fn)
> > {
> >   int  nrow,ncol,i,j,k;
> >   real *full=NULL,value;
> >   gmx_sparsematrix_t * sparse=NULL;
> >
> >   gmx_mtxio_read(fn,&nrow,&ncol,&full,&sparse);
> >
> >   if (full == NULL) {
> > snew(full,nrow*ncol);
> > for(i=0;i >   full[i] = 0;
> > }
> >
> > for(i=0;inrow;i++) {
> >   for(j=0;jndata[i];j++) {
> > k = sparse->data[i][j].col;
> > value = sparse->data[i][j].value;
> > full[i*ncol+k] = value;
> > full[k*ncol+i] = value;
> >   }
> > }
> > gmx_sparsematrix_destroy(sparse);
> >   }
> >
> >   printf("%d %d\n",nrow,ncol);
> >   for(i=0; i > for(j=0; j >   printf(" %g",full[i*ncol+j]);
> > }
> > printf("\n");
> >   }
> >
> >   sfree(full);
> > }
> >
> 381a420
> > { efMTX, "-mtx", "hessian", ffOPTRD },
> 409a449,450
> >   else if (ftp2bSet(efMTX,NFILE,fnm))
> > list_mtx(ftp2fn(efMTX,NFILE,fnm));
>
>
> --
> Express yourself instantly with MSN Messenger! MSN 
> Messenger
>
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RE: [gmx-users] Normal Mode Analysis

2009-05-26 Thread Berk Hess


Hi,

I just saw that 4.0 uses a new mtx format which can also efficiently store 
sparse matrices.
Please try if my modified gmxdump for 4.0.5 works?
Store the data below in a file called fix and then do:
patch gmxdump.c fix

Berk

61a62,63 
> #include "sparsematrix.h"  
> #include "mtxio.h" 
364a367,402  
> static void list_mtx(char *fn) 
> {  
>   int  nrow,ncol,i,j,k;
>   real *full=NULL,value;   
>   gmx_sparsematrix_t * sparse=NULL;
>
>   gmx_mtxio_read(fn,&nrow,&ncol,&full,&sparse);
>
>   if (full == NULL) {
> snew(full,nrow*ncol);
> for(i=0;i   full[i] = 0;
> }
>
> for(i=0;inrow;i++) {
>   for(j=0;jndata[i];j++) {
> k = sparse->data[i][j].col;
> value = sparse->data[i][j].value;
> full[i*ncol+k] = value;
> full[k*ncol+i] = value;
>   }
> }
> gmx_sparsematrix_destroy(sparse);
>   }
>
>   printf("%d %d\n",nrow,ncol);
>   for(i=0; i for(j=0; j   printf(" %g",full[i*ncol+j]);
> }
> printf("\n");
>   }
>
>   sfree(full);
> }
>
381a420
> { efMTX, "-mtx", "hessian", ffOPTRD },
409a449,450
>   else if (ftp2bSet(efMTX,NFILE,fnm))
> list_mtx(ftp2fn(efMTX,NFILE,fnm));


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Re: [gmx-users] Normal Mode Analysis

2009-05-26 Thread Franzi Hoffgaard

Hi,

as I wrote in the first message, I tried renaming it with the extension .trj
and yielded segmentation faults. I also tried it with the extension .trr and
got the error message:

trn version: VERSION 4.0.4
---
Program gmxdump_d, VERSION 4.0.4
Source code file: trnio.c, line: 69

Fatal error:
Float size 3556. Maybe different CPU?
---

Both extensions didn't work.


There is just another little question that came into my mind. As I said I
performed the NMA with gromacs 3.2.1 and 4.0.x both with the same system and
setup. I would expect that the .mtx-files have similar sizes, but using
version 4.0.x the file-size is about 300 Mb and using the version 3.2.1 it
is about 7 Gb.

Franzi



2009/5/26 Berk Hess 

>  Hi,
>
> Try renaming it with the extension .trr iso .trj.
>
> Berk
>
> --
> Date: Tue, 26 May 2009 10:53:32 +0200
> From: f.hoffga...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Normal Mode Analysis
>
>
> Hi,
>
> I'm quite a new user of gromacs. I want to do an all-atom normal mode
> analysis of a small protein in water. As a result I would like to have the
> hessian matrix in a readable format, that I can use for further
> computations.
>
> As I have read in the manuals/tutorials/mailing-lists I minimized the whole
> system (at first with the steepest descent integrator for a couple of steps
> and later on with the l-bfgs integrator to become a maximum force close to
> zero). Afterwards I created the run input file (with the nm integrator)
> using the high precision trajectory from the minimization. This and the
> following call of mdrun worked fine. As a result I became the hessian.mtx.
>
> As I said I want the matrix in ASCII format, so I followed the instructions
> and renamed the file into hessian.trj and ran "gmxdump_d -f mat2.trj" and
> got a Segmentation fault.Trying gmxcheck also led to Segmentation fault. I
> tried same procedure but using trr instead of trj as file-ending. Both, for
> gmxcheck and gmxdump I yielded the following message:
>
> trn version: VERSION 4.0.4
> ---
> Program gmxdump_d, VERSION 4.0.4
> Source code file: trnio.c, line: 69
>
> Fatal error:
> Float size 3556. Maybe different CPU?
> ---
>
> I tried "g_traj -ox" as well without any result. This led me to the
> conclusion that the file is corrupt, but I just tried diagonalizing the
> hessian matrix using "g_nmeig" anyway. Surprisingly this yielded no error
> message and I ended up with the first 50 eigenvalues and -vectors. So
> despite my first assumption the file cannot be corrupt. Or am I wrong?
>
> The architecture/s I worked on are:
> 1. Suse Linux 10.3, 64 bit, Intel Processor, quad-core (gromacs 4.0.3)
> 2. Mac OS X 10.5 (Leopard), Intel Proc. 2 x quad-core (gromacs 4.0.4,
> gromacs 4.0.5)
>
> The results were on both architectures the same. But ...
>
> I read in a former email of this mailing list of a similar problem and that
> the problem did not occur in the gromacs version 3.2.1. So I uninstalled
> gromacs 4.0 and installed gromacs 3.2.1 and  performed the last stage of
> minimization and the computation of the hessian matrix. This binary file
> yielded no error using gmxdump and gmxcheck. (Input files for the l-bfgs and
> nm step were not changed.)
>
> So, my question is, is this a bug of the newer gromacs version/s or did I
> something wrong. As I would like to stick to a newer version of gromacs, I
> am wondering, what else (than downgrading) can I do to get the hessian
> matrix in a human readable format out of the normal mode analysis.
>
> Best regards, Franziska
>
> ---
> Franziska Hoffgaard
> PhD Student
> Bioinformatics & Theo. Biology Group
> TU Darmstadt
>
>
>
> --
> Express yourself instantly with MSN Messenger! MSN 
> Messenger
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RE: [gmx-users] Normal Mode Analysis

2009-05-26 Thread Berk Hess

Hi,

Try renaming it with the extension .trr iso .trj.

Berk

Date: Tue, 26 May 2009 10:53:32 +0200
From: f.hoffga...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Normal Mode Analysis

Hi,

I'm quite a new user of gromacs. I want to do an all-atom normal mode analysis 
of a small protein in water. As a result I would like to have the hessian 
matrix in a readable format, that I can use for further computations.

As I have read in the manuals/tutorials/mailing-lists I minimized the whole 
system (at first with the steepest descent integrator for a couple of steps and 
later on with the l-bfgs integrator to become a maximum force close to zero). 
Afterwards I created the run input file (with the nm integrator) using the high 
precision trajectory from the minimization. This and the following call of 
mdrun worked fine. As a result I became the hessian.mtx.

As I said I want the matrix in ASCII format, so I followed the instructions and 
renamed the file into hessian.trj and ran "gmxdump_d -f mat2.trj" and got a 
Segmentation fault.Trying gmxcheck also led to Segmentation fault. I tried same 
procedure but using trr instead of trj as file-ending. Both, for gmxcheck and 
gmxdump I yielded the following message:

trn version: VERSION 4.0.4
---
Program gmxdump_d, VERSION 4.0.4
Source code file: trnio.c, line: 69

Fatal error:
Float size 3556. Maybe different CPU?

---

I tried "g_traj -ox" as well without any result. This led me to the conclusion 
that the file is corrupt, but I just tried diagonalizing the hessian matrix 
using "g_nmeig" anyway. Surprisingly this yielded no error message and I ended 
up with the first 50 eigenvalues and -vectors. So despite my first assumption 
the file cannot be corrupt. Or am I wrong?

The architecture/s I worked on are:
1. Suse Linux 10.3, 64 bit, Intel Processor, quad-core (gromacs 4.0.3)
2. Mac OS X 10.5 (Leopard), Intel Proc. 2 x quad-core (gromacs 4.0.4, gromacs 
4.0.5)

The results were on both architectures the same. But ...

I read in a former email of this mailing list of a similar problem and that the 
problem did not occur in the gromacs version 3.2.1. So I uninstalled gromacs 
4.0 and installed gromacs 3.2.1 and  performed the last stage of minimization 
and the computation of the hessian matrix. This binary file yielded no error 
using gmxdump and gmxcheck. (Input files for the l-bfgs and nm step were not 
changed.)

So, my question is, is this a bug of the newer gromacs version/s or did I 
something wrong. As I would like to stick to a newer version of gromacs, I am 
wondering, what else (than downgrading) can I do to get the hessian matrix in a 
human readable format out of the normal mode analysis.

Best regards, Franziska

---
Franziska Hoffgaard
PhD Student
Bioinformatics & Theo. Biology Group
TU Darmstadt

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[gmx-users] Normal Mode Analysis

2009-05-26 Thread Franzi Hoffgaard

Hi,

I'm quite a new user of gromacs. I want to do an all-atom normal mode
analysis of a small protein in water. As a result I would like to have the
hessian matrix in a readable format, that I can use for further
computations.

As I have read in the manuals/tutorials/mailing-lists I minimized the whole
system (at first with the steepest descent integrator for a couple of steps
and later on with the l-bfgs integrator to become a maximum force close to
zero). Afterwards I created the run input file (with the nm integrator)
using the high precision trajectory from the minimization. This and the
following call of mdrun worked fine. As a result I became the hessian.mtx.

As I said I want the matrix in ASCII format, so I followed the instructions
and renamed the file into hessian.trj and ran "gmxdump_d -f mat2.trj" and
got a Segmentation fault.Trying gmxcheck also led to Segmentation fault. I
tried same procedure but using trr instead of trj as file-ending. Both, for
gmxcheck and gmxdump I yielded the following message:

trn version: VERSION 4.0.4
---
Program gmxdump_d, VERSION 4.0.4
Source code file: trnio.c, line: 69

Fatal error:
Float size 3556. Maybe different CPU?
---

I tried "g_traj -ox" as well without any result. This led me to the
conclusion that the file is corrupt, but I just tried diagonalizing the
hessian matrix using "g_nmeig" anyway. Surprisingly this yielded no error
message and I ended up with the first 50 eigenvalues and -vectors. So
despite my first assumption the file cannot be corrupt. Or am I wrong?

The architecture/s I worked on are:
1. Suse Linux 10.3, 64 bit, Intel Processor, quad-core (gromacs 4.0.3)
2. Mac OS X 10.5 (Leopard), Intel Proc. 2 x quad-core (gromacs 4.0.4,
gromacs 4.0.5)

The results were on both architectures the same. But ...

I read in a former email of this mailing list of a similar problem and that
the problem did not occur in the gromacs version 3.2.1. So I uninstalled
gromacs 4.0 and installed gromacs 3.2.1 and  performed the last stage of
minimization and the computation of the hessian matrix. This binary file
yielded no error using gmxdump and gmxcheck. (Input files for the l-bfgs and
nm step were not changed.)

So, my question is, is this a bug of the newer gromacs version/s or did I
something wrong. As I would like to stick to a newer version of gromacs, I
am wondering, what else (than downgrading) can I do to get the hessian
matrix in a human readable format out of the normal mode analysis.

Best regards, Franziska

---
Franziska Hoffgaard
PhD Student
Bioinformatics & Theo. Biology Group
TU Darmstadt
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RE: [gmx-users] constant term in dihedral potential function

2009-05-26 Thread Berk Hess


Hi,

I don't know how you currently supply your dihedral (multiple periodic dihedral 
terms?).
But you can supply the whole potential, including the constant term, using a 
Ryckaert-Bellemans dihedral.
The manual gives some conversion formulas.

Berk

> From: a.ku...@herts.ac.uk
> To: gmx-users@gromacs.org
> Date: Tue, 26 May 2009 09:29:36 +0100
> Subject: [gmx-users] constant term in dihedral potential function
> 
> Dear all,
> 
> I included the following dihedral potential function in a topology:
> 
> V(phi2) = -5.865 + 7.470 [1+cos(phi2-180°)] + 3.99 [1+cos(2 phi2)] + 1.1 
> [1+cos(3 phi2-180°)]
> 
> The problem is about representing the constant term -5.865. Using equation 
> 4.61 (Gromacs 4.0 manual):
> 
> V(phi) = k * (1 + cos (n phi - phis) )
> 
> I specified:
> 
> V = -5.865 * (1 + cos (0 - 90) ) = -5.865 with multiplicity n=0
> 
> That leads to the entry in the topology file:
>  22232425 190 -5.685 0
> 
> This worked fine in Gromacs 3.3, but in Gromacs 4.05 I get the error message 
> (from Grompp):
> 
> Fatal error:
> Value of 'multiplicity' in Proper Dih. is 0, which is smaller than the 
> minimum of 1
> 
> I wonder, if this is a bug in Gromacs 4.05, or if there is any better way to 
> specify a constant term in a dihedral potential function.
> 
> Many thanks
> Andreas
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[gmx-users] constant term in dihedral potential function

2009-05-26 Thread Kukol, Andreas

Dear all,

I included the following dihedral potential function in a topology:

V(phi2) = -5.865 + 7.470 [1+cos(phi2-180°)] + 3.99 [1+cos(2 phi2)] + 1.1 
[1+cos(3 phi2-180°)]

The problem is about representing the constant term -5.865. Using equation 4.61 
(Gromacs 4.0 manual):

V(phi) = k * (1 + cos (n phi - phis) )

I specified:

V = -5.865 * (1 + cos (0 - 90) ) = -5.865 with multiplicity n=0

That leads to the entry in the topology file:
 22232425 190 -5.685 0

This worked fine in Gromacs 3.3, but in Gromacs 4.05 I get the error message 
(from Grompp):

Fatal error:
Value of 'multiplicity' in Proper Dih. is 0, which is smaller than the minimum 
of 1

I wonder, if this is a bug in Gromacs 4.05, or if there is any better way to 
specify a constant term in a dihedral potential function.

Many thanks
Andreas
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RE: [gmx-users] Lennard-Jones 9-6 potential problems

2009-05-26 Thread Berk Hess


Hi,

I forgot about this feature.
Your problem is indeed that you used comb-rule=1,
you have to use 2 or 3 to make this work.
And indeed you should use user tables filled with the 9-6 potential.

Gromacs could actually easily support p-6 tables with any value for p,
by storing p in the tpr file and automatically using tables when p!=12.

Berk

> Date: Tue, 26 May 2009 09:45:22 +0200
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Lennard-Jones 9-6 potential problems
> 
> zhangjianguo2002 wrote:
> > Hi everyone!
> >   Have anyone used the Lennard-Jones 9-6 potential for  coarse-grained 
> > models? when I use it, I get a very different result from  that is got 
> > from the same Lennard-Jones 9-6 potential  formed a potential table,the 
> > latter's results are comparable to the experiments. when I use LJ-9-6 
> > potential,the ITP file  is as following:
> >  
> >   [ defaults ]
> > ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
> >1 1   no  1.0 1.0 9
> 
> Even if this may generate the correct parameters (please use gmxdump to 
> check your tpr file) you still have to provide a user table to mdrun and 
> to set vdw-type = user in your mdp file. You may need to change the 
> nbfunc to three as well. Check source code in src/kernel/convparm to see 
> what is going on.  I don't think this is documented anywhere, is it?
> 
> 
> > 
> > [ atomtypes ]
> > ;   name  bond_typemasscharge   ptype  sigma  epsilon
> >  opls_001   Cx  6  78.01900A0.5052.95;
> > 
> >  [ moleculetype ]
> > ; Name nrexcl
> > Phenyl  1
> > [ atoms ]
> > ;   nr  type  resnr resid  atom  cgnr   charge mass
> >  1 opls_001 1  Phenyl C1 10.000  78.0190 
> > 
> >  other files ,such as mdp file and top file ,are all the same as normal 
> > LJ-12-6 potential, are these correct if I want to use LJ-9-6 potential? 
> > Do I still need to change something? Thanks very much for your kindness!
> > 
> > 
> > 
> > 
> > ´©Ô½µØÕð´ø ¼ÍÄîãë´¨µØÕðÒ»ÖÜÄê 
> > 
> > 
> > 
> > 
> > 
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
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> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> -- 
> 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.
> sp...@xray.bmc.uu.se  sp...@gromacs.org   http://folding.bmc.uu.se
> ___
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> http://www.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Lennard-Jones 9-6 potential problems

2009-05-26 Thread David van der Spoel


zhangjianguo2002 wrote:

Hi everyone!
  Have anyone used the Lennard-Jones 9-6 potential for  coarse-grained 
models? when I use it, I get a very different result from  that is got 
from the same Lennard-Jones 9-6 potential  formed a potential table,the 
latter's results are comparable to the experiments. when I use LJ-9-6 
potential,the ITP file  is as following:
 
  [ defaults ]

; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
   1 1   no  1.0 1.0 9


Even if this may generate the correct parameters (please use gmxdump to 
check your tpr file) you still have to provide a user table to mdrun and 
to set vdw-type = user in your mdp file. You may need to change the 
nbfunc to three as well. Check source code in src/kernel/convparm to see 
what is going on.  I don't think this is documented anywhere, is it?





[ atomtypes ]
;   name  bond_typemasscharge   ptype  sigma  epsilon
 opls_001   Cx  6  78.01900A0.5052.95;

 [ moleculetype ]
; Name nrexcl
Phenyl  1
[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1 opls_001 1  Phenyl C1 10.000  78.0190 

 other files ,such as mdp file and top file ,are all the same as normal 
LJ-12-6 potential, are these correct if I want to use LJ-9-6 potential? 
Do I still need to change something? Thanks very much for your kindness!





?? ?? 






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--
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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[gmx-users] Re: Dynamics with DNA

2009-05-26 Thread Alan

Hey Tanos,

You must read some papers but my recommendations are:

GMX 4.0.5 and AMBER99SB forcefield. Look at
http://acpypi.googlecode.comwhere you can find info about how to add
amber forcefield to GMX.

Cheers,
Alan


Subject: [gmx-users] Dynamics with DNA
>
>   Hi folks !
>   Does someone knows how to perform Molecular dynamics simulations of
> DNA molecules using GROMACS 3.3.2 ? Is that possible ? With forcefield
> should I use ? If it is not possible with GROMACS does someone have a
> suggstions of which software colud be used ?
>   Best whises,
>   Tanos C. C. Franca.
>   Rio de Janeiro - RJ
>   Brazil
>
> --
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] Lennard-Jones 9-6 potential problems

2009-05-26 Thread zhangjianguo2002

Hi everyone!
  Have anyone used the Lennard-Jones 9-6 potential for  coarse-grained models? 
when I use it, I get a very different result from  that is got from the same 
Lennard-Jones 9-6 potential  formed a potential table,the latter's results are 
comparable to the experiments. when I use LJ-9-6 potential,the ITP file  is as 
following:
  
  [ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
   1 1   no  1.0 1.0 9

[ atomtypes ]
;   name  bond_typemasscharge   ptype  sigma  epsilon
 opls_001   Cx  6  78.01900A0.5052.95;

 [ moleculetype ]
; Name nrexcl
Phenyl  1
[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass 
 1 opls_001 1  Phenyl C1 10.000  78.0190  

 other files ,such as mdp file and top file ,are all the same as normal LJ-12-6 
potential, are these correct if I want to use LJ-9-6 potential? Do I still need 
to change something? Thanks very much for your kindness!

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[gmx-users] Re: oplsaa parametrization

2009-05-26 Thread Alan

Dear Rosa, here goes my little contribution to try to help you:
http://acpypi.googlecode.com.
For me, no doubt that antechamber is the best tool for getting the
topological information about small molecules (pls, read the wikis in ACPYPI
pages to know more).

The module to generate OPLS/AA is still experimental but if you take
information from MKTOP (which I intend to add to ACPYPI eventually) then you
can get something good enough, specially if you do your homework and read
the papers related to this matter.

Cheers,
Alan

Subject: [gmx-users] oplsaa parametrization
>
> Dear Users
> I m trying to simulate a structure (not a protein) which is not
> parametrized in oplsaa FF. I created the structure using PRODRG and
> included the results of *.itp from PRODRG to ffoplsaa.rtp file and tried
> to use available oplss_xxx for my atom type near to those ones already
> exists in *.atp. I also optimized my structure at RHF/6-31G* level and
> calculated the charge using resp. Then updated ffoplsaa.rtp using this
> calculated charge. By refering to the mailing list it seems that I need
> to modify bn.itp and nob.itp file as well (?!). I m just wonder if
> anybody use PRODRG how he/she parametrized FF. As I m new in GROMACS and
> any tutorial or procedure to follow will help me so much. Thank you in
> advance for any ideas or comments.
>
> Also when I use pdb2gmx, I have this warning; all CONECT records are
> ignored. However when I proceed with energy minization in vacuum the
> program doesnt complain and it can produce *.tpr file.
>
> Regards
> Rosa
>
> --
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: Hi: Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex

2009-05-26 Thread Tsjerk Wassenaar

Hi Nehme,

> Also, in our zinc finger models, the zinc plays a structural role and it is
> not implicated in DNA recognition. Furthermore, I will read your paper and
> the references. I looked in the Literature and from NMR studies/X-ray and MD
> done on zinc fingers containing a zinc ion coordinated to 4 cysteines. It
> seems that these cysteines are deprotonated and the remaining negative
> charges are stabilized by nearby positively charged side chains of arginines
> or lysines.

It's hard, although not impossible, to assess the protonation state of
such a center experimentally. Mind that crystal structures and NMR
structures also use force fields and predefined topologies to model
the structure. That means that you will only get out what you put in.
If you set some group to be deprotonated while it should be
protonated, this may be hard or even impossible to track down. You may
still get a reasonable fit to the experimental data. For such issues
Xray/NMR are not the best means. Note that I'm not saying you're
wrong, but you should justify your choices.

> I tried to use CHARMM forcefield, but every time I had the 4 cysteines
> protonated, the coordination bonds removed and the parameters for zinc not
> assigned.
> How can I solve this issue?
>

In Gromacs you can use the file specbond.dat to define special bonds.
Have a look at http://wiki.gromacs.org/index.php/specbond.dat and
search the archives for more information.

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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RE: [gmx-users] Viscosity using periodic perturbation method

2009-05-26 Thread Berk Hess


Hi,

Yes, you can use NPT, the code takes care of this properly.
Strictly speaking it might be incorrect, but since pressure scaling is usually 
less than 1%
it will not affect your results significantly.

Berk.

Date: Mon, 25 May 2009 15:19:10 -0700
From: yson...@asu.edu
To: gmx-users@gromacs.org
Subject: [gmx-users] Viscosity using periodic perturbation method

Dear users:

I was trying to calculate the viscosity of liquid system using periodic 
perturbation method. Does this method require NVT ensemble simulation in stead 
of NPT ? Because I read some literature on periodic perturbation method. they 
all used NVT.  I did not found any information about this on the manual. Can I 
use NPT Non-equilibrium MD in order to use periodic perturbation method? Thanks 
in advance!

-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University

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