Re: [gmx-users] Deshuffling a .gro file

[Yang Ye]

On 3/20/2007 10:03 PM, toma0052 wrote:

Hello,
 I am performing a simulation in parallel on four processors.  The
simulation seems to run fine, and outputs a shuffled *.gro file.  I would
like to change the order of atoms to what they were in the original input
*.gro file, but I am having some trouble.  I have seen some previous posts
on this, but I am still a bit confused. 


David van der Spoel wrote:
  
[...]


  

If your standard dsehuf.ndx for a system of N atoms starts with:
[ deshuf ]
0 1 4 6 7 etc.
you have to modify it to the old format:
1 N
deshuf N
0 1 4 6 7 etc.

You only have to change the top bit, not the actual numbers. An
alternative is to modify it to be:
[ deshuf ]
1 2 5 7 8 etc.

That wouldn't be too hard with a script either.




This says that I need to alter my deshuf.ndx file a bit, and then just do
editconf -f shuf.gro -n deshuf.ndx -o unshuf.gro  to obtain an unchuffled
*.gro file.  However, my deshuf.ndx file already began counting the atoms
at 1, i.e.:

[ DeShuffle ]
  1  2  3  4  5  6  7  8  9  10
  11  12  13  14  15  16  17  18  19  20
  21  22  23  24  25  26  27  28  29  30
  31  32  33  34  35  36  37  38  39  40
  41  42  43  44  45  46  47  48  49  50
...

So, everything already seems to be fine (other than the name in the
brackets, which didn't seem to matter if changed) with the deshuf.ndx file.
 When I do editconf -f shuf.gro -n deshuf.ndx -o unshuf.gro  though, my
*.gro file does not sort properly, although some sorting does take place. 
The atoms seem to be in the correct general order (The first series of

atoms are all DPPC, and the rest are all SOL) but the atom numbers are in
the wrong order (The order goes 1DPPC ... 44DPPC, 1257DPPC ... 1299DPPC,
2513DPPC ... etc whereas it should go from 1DPPC to 128DPPC and then begin
to number the SOL molecules at 129SOL).  Is this a problem with my input
into grompp?  I am using both -shuffle and -sort.  Is this incorrect?
How do I deshuffle my *.gro file to list the 128 DPPC molecules and then
the 3655 SOL molecules with atom numbers 1 to 17365?
  
Sorry that your description was not easy to be comprehend. Perhaps this 
is why this post was not followed.

I would like to offer some general principles here.
1. deshuf.ndx is definitely not ordered so you shall see some 
disordering in the later part of ndx file.
2. After deshuffling using editconf, it is normal for the resulting .gro 
to have noncontinuous numbering for molecule. It is more important to 
have the correct molecule type. For example, all your SOL shall be in 
one block with no other molecules embedded.



Yang Ye

Thank you,
Mike Tomasini

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[gmx-users] parinello-rahman coupling

[lorix]

Dear gmx-users,

I am a new one...
coming to the point...I am simulating in parallel different 
configurations and settings of a protein

around 300 residues large plus approximately 12000 water molecules.
I am simulating NPT with berendsen for P and T to equilibrate over 100 
ps and then the simulation

for several ns (5-20) with nose-hoover for T and parinello-rahman for P.
But in the last step I cannot find a value for tau_p to maintained and 
average of 1 bar.
Reducing the tau_p value (0.06, 0.05 and 0.01) I get many messages in 
the log file like:


Grid: 11 x 10 x 9 cells
Grid: 11 x 11 x 9 cells

and then the simulation stops randomly without any messages besides the 
lam-mpi ones.


does anyone have ideas?

thanks

loris...
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[gmx-users] Fwd: Drug - Enzyme Tutorial

[fulya caglar]

Note: forwarded message attached.
 
-
Finding fabulous fares is fun.
Let Yahoo! FareChase search your favorite travel sites to find flight and hotel 
bargains.--- Begin Message ---
Although I could run sucessfully speptide tutorial,while attempting the 
drug-enzyme tutorial  I am getting the following error message after the first 
mdrun command ( mdrun -s trp_em.tpr -o trp_em.trr -c trp_b4pr.pdb -g em.log –e 
em.edr);

 

- 

Warning: 1-4 interaction between 2100 and 2105 at distance 15.231 which is 
larger than the 1-4 table size 1.000 nm

These are ignored for the rest of the simulation

This usually means your system is exploding,

if not, you should increase table-extension in your mdp file

---

Program mdrun_mpi, VERSION 3.3.1

Source code file: nsgrid.c, line: 226

 

Range checking error:

Explanation: During neighborsearching, we assign each particle to a grid

based on its coordinates. If your system contains collisions or parameter

errors that give particles very high velocities you might end up with some

coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot

put these on a grid, so this is usually where we detect those errors.

Make sure your system is properly energy-minimized and that the potential

energy seems reasonable before trying again.

 

Variable ci has value -2147483648. It should have been within [ 0 .. 19488 ]

Please report this to the mailing list (gmx-users@gromacs.org)

 

---

 

   I would be very glad to know why I get this type of error.  Thanks very much.

 

   With thanks

 Sincerely Fulya

 
-
Food fight? Enjoy some healthy debate
in the Yahoo! Answers Food & Drink Q&A.--- End Message ---
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Re: [gmx-users] parinello-rahman coupling

[Tsjerk Wassenaar]

Hi Loris,

Enjoying the nice weather here, I'll just give a gentle reiteration of
previous remarks. What you observe is caused by the fact that you only
have a very small system from which you try to extract a macroscopic
property (i.e. defined only for large systems). The large fluctuations
are normal. It would be a good idea to read some general texts about
statistical mechanics and molecular dynamics and before posting a
question to the user list, it would also be good to browse through the
archives of this list, to see if the question you're about to ask has
already been answered (and trust me, this one has been, many times).

Good luck with your simulations,

Tsjerk

On 3/27/07, lorix <[EMAIL PROTECTED]> wrote:

Dear gmx-users,

I am a new one...
coming to the point...I am simulating in parallel different
configurations and settings of a protein
around 300 residues large plus approximately 12000 water molecules.
I am simulating NPT with berendsen for P and T to equilibrate over 100
ps and then the simulation
for several ns (5-20) with nose-hoover for T and parinello-rahman for P.
But in the last step I cannot find a value for tau_p to maintained and
average of 1 bar.
Reducing the tau_p value (0.06, 0.05 and 0.01) I get many messages in
the log file like:

Grid: 11 x 10 x 9 cells
Grid: 11 x 11 x 9 cells

and then the simulation stops randomly without any messages besides the
lam-mpi ones.

does anyone have ideas?

thanks

loris...
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--
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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[gmx-users] Fwd: How can I do the simulation of a protein with Tyr (SO3H)

[fulya caglar]

Note: forwarded message attached.
 
-
Bored stiff? Loosen up...
Download and play hundreds of games for free on Yahoo! Games.--- Begin Message ---
 
  Hi!
  I'm trying to do a simulation of a protein with bound sulfite ion (Tyr 
(SO3H)).After the first command ( pdb2gmx) I am getting the following error 
message : 
  
-
  Fatal error:
Residue 'SUL' not found in residue topology database
  
-

  I would be very glad to know why I get this type of error and what can I do 
about this.   

   With thanks

 Sincerely Fulya

 
-
TV dinner still cooling?
Check out "Tonight's Picks" on Yahoo! TV.--- End Message ---
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Re: [gmx-users] Fwd: Drug - Enzyme Tutorial

[Tsjerk Wassenaar]

Hi Fulya,

Did grompp give you any warnings? At what time did the error occur? At
the start of the simulation or later? Could you check the log file for
LINCS warnings, and try to track down the first occurrence? This would
help to be able to say some more than "your system is exploding".

Best,

Tsjerk

On 3/27/07, fulya caglar <[EMAIL PROTECTED]> wrote:



Note: forwarded message attached.

 
Finding fabulous fares is fun.
Let Yahoo! FareChase search your favorite travel sites to find flight and
hotel bargains.

-- Forwarded message --
From: fulya caglar <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Date: Mon, 26 Mar 2007 12:44:18 -0700 (PDT)
Subject: Drug - Enzyme Tutorial
Although I could run sucessfully speptide tutorial,while attempting the
drug-enzyme tutorial  I am getting the following error message after the
first mdrun command ( mdrun -s trp_em.tpr -o trp_em.trr -c trp_b4pr.pdb -g
em.log –e em.edr);
-
Warning: 1-4 interaction between 2100 and 2105 at distance 15.231 which is
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
---
Program mdrun_mpi, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains
 collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 19488 ]
Please report this to the mailing list (gmx-users@gromacs.org)

---

   I would be very glad to know why I get this type of error.  Thanks very
much.

   With thanks
 Sincerely Fulya


 
Food fight? Enjoy some healthy debate
in the Yahoo! Answers Food & Drink Q&A.


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--
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] Fwd: How can I do the simulation of a protein with Tyr (SO3H)

[Tsjerk Wassenaar]

Hi Fulya,

You can't just simulate everything you set your mind on. There are no
parameters for sulfite bound tyrosine in the database (just what it
says). You have to add them yourself, which I don't recommend at this
point, since it is clear you have but little experience in this field
(and parameterization is an advanced topic).

By the way, do you have some problems with the mail server?

Best,

Tsjerk

On 3/27/07, fulya caglar <[EMAIL PROTECTED]> wrote:



Note: forwarded message attached.

 
Bored stiff? Loosen up...
Download and play hundreds of games for free on Yahoo! Games.

-- Forwarded message --
From: fulya caglar <[EMAIL PROTECTED]>
To: Gromacs <[EMAIL PROTECTED]>
Date: Tue, 27 Mar 2007 04:45:43 -0700 (PDT)
Subject: How can I do the simulation of a protein with Tyr (SO3H)

Hi!
I'm trying to do a simulation of a protein with bound sulfite ion (Tyr
(SO3H)).After the first command ( pdb2gmx) I am getting the following error
message :
-
Fatal error:
Residue 'SUL' not found in residue topology database
-

I would be very glad to know why I get this type of error and what can I do
about this.  With thanks
 Sincerely Fulya


 
TV dinner still cooling?
Check out "Tonight's Picks" on Yahoo! TV.


___
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--
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] parinello-rahman coupling

[lorix]

Hi Tsjerk,

Thanks for your prompt reply.
I was asking about the average value of the property.
I understood that large fluctuations are reasonable, but I was expecting 
that the mean value
over 15 ns could be somehow as the set in the parameter file as happens 
with Berendsen pressure coupling.

I checked the archives and I did not find much about the mean value.

best regards,

lorix...


Tsjerk Wassenaar wrote:


Hi Loris,

Enjoying the nice weather here, I'll just give a gentle reiteration of
previous remarks. What you observe is caused by the fact that you only
have a very small system from which you try to extract a macroscopic
property (i.e. defined only for large systems). The large fluctuations
are normal. It would be a good idea to read some general texts about
statistical mechanics and molecular dynamics and before posting a
question to the user list, it would also be good to browse through the
archives of this list, to see if the question you're about to ask has
already been answered (and trust me, this one has been, many times).

Good luck with your simulations,

Tsjerk

On 3/27/07, lorix <[EMAIL PROTECTED]> wrote:


Dear gmx-users,

I am a new one...
coming to the point...I am simulating in parallel different
configurations and settings of a protein
around 300 residues large plus approximately 12000 water molecules.
I am simulating NPT with berendsen for P and T to equilibrate over 100
ps and then the simulation
for several ns (5-20) with nose-hoover for T and parinello-rahman for P.
But in the last step I cannot find a value for tau_p to maintained and
average of 1 bar.
Reducing the tau_p value (0.06, 0.05 and 0.01) I get many messages in
the log file like:

Grid: 11 x 10 x 9 cells
Grid: 11 x 11 x 9 cells

and then the simulation stops randomly without any messages besides the
lam-mpi ones.

does anyone have ideas?

thanks

loris...
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[gmx-users] gen_vel

[�zge]

HI EVERYBODY,
   
  I HAVE A PROBLEM WITH gen_vel.IF I MAKE AN ANALYZE WITH POSITION RESTRAINT I 
USED gen_vel=yes.AFTER FOR FULL MDP I USED gen_vel=no.AFTER THAT I USED 
gen_vel=no FOR AGAIN FULL.MDP.BUT I GOT VERY BAD RMSD GRAPHICS.ANY HELP ABOUT 
WHAT IS THE MEANING OF gen_vel=no,gen-vel=yes?
   
  THANK YOU...

 
-
Don't pick lemons.
See all the new 2007 cars at Yahoo! Autos.___
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Re: [gmx-users] parinello-rahman coupling

[Tsjerk Wassenaar]

Hi Lorix,

Sorry for that. You used the word "maintained" from which I inferred
you were referring to the fluctuations (biased by the occurrence of
the question obviously). Under normal conditions the equilibration
shouldn't take that long. How far off is the mean? Do you still
observe a trend? Still note that you're dealing with enormous, both
positive and negative, pressures, from which you try to extract an
average value. Such an average will usually not be very exact because
of the numerical inaccuracies.

Best,

Tsjerk

On 3/27/07, lorix <[EMAIL PROTECTED]> wrote:

Hi Tsjerk,

Thanks for your prompt reply.
I was asking about the average value of the property.
I understood that large fluctuations are reasonable, but I was expecting
that the mean value
over 15 ns could be somehow as the set in the parameter file as happens
with Berendsen pressure coupling.
I checked the archives and I did not find much about the mean value.

best regards,

lorix...


Tsjerk Wassenaar wrote:

> Hi Loris,
>
> Enjoying the nice weather here, I'll just give a gentle reiteration of
> previous remarks. What you observe is caused by the fact that you only
> have a very small system from which you try to extract a macroscopic
> property (i.e. defined only for large systems). The large fluctuations
> are normal. It would be a good idea to read some general texts about
> statistical mechanics and molecular dynamics and before posting a
> question to the user list, it would also be good to browse through the
> archives of this list, to see if the question you're about to ask has
> already been answered (and trust me, this one has been, many times).
>
> Good luck with your simulations,
>
> Tsjerk
>
> On 3/27/07, lorix <[EMAIL PROTECTED]> wrote:
>
>> Dear gmx-users,
>>
>> I am a new one...
>> coming to the point...I am simulating in parallel different
>> configurations and settings of a protein
>> around 300 residues large plus approximately 12000 water molecules.
>> I am simulating NPT with berendsen for P and T to equilibrate over 100
>> ps and then the simulation
>> for several ns (5-20) with nose-hoover for T and parinello-rahman for P.
>> But in the last step I cannot find a value for tau_p to maintained and
>> average of 1 bar.
>> Reducing the tau_p value (0.06, 0.05 and 0.01) I get many messages in
>> the log file like:
>>
>> Grid: 11 x 10 x 9 cells
>> Grid: 11 x 11 x 9 cells
>>
>> and then the simulation stops randomly without any messages besides the
>> lam-mpi ones.
>>
>> does anyone have ideas?
>>
>> thanks
>>
>> loris...
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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>> www interface or send it to [EMAIL PROTECTED]
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>>
>
>

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--
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] Fwd: Drug - Enzyme Tutorial

[fulya caglar]

Hi Tsjerk,
  Many thanks for your suggestions.After "grompp -f em.mdp -c trp_b4em.pdb -p 
trp.top -o trp_em.tpr  " comand there was no warning message.Then I did mdrun ( 
mdrun -s trp_em.tpr -o trp_em.trr -c trp_b4pr.pdb -g em.log -e em.edr ) and it 
was finished but
  it gave warning message(Warning: 1-4 interaction between 2100 and 2105 at 
distance 15.231 which is larger than the 1-4 table size 1.000 nm.These are 
ignored for the rest of the simulation.This usually means your system is 
exploding if not, you should increase table-extension in your mdp file)
And  after second grommp comand (grompp  -f pr.mdp -c trp_b4pr.pdb -p trp.top 
-o trp_pr.tpr)it gave that error message.
  

  File input/output error:
trp_b4pr.pdb

  
I have just checked the log file but there is no different error message.Only 
this;
   
  Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
  Variable ci has value -2147483648. It should have been within [ 0 .. 19488 ]
Please report this to the mailing list (gmx-users@gromacs.org)
   
  
--
  Thanks very much again
  Sincerely
  Fulya

Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
  Hi Fulya,

Did grompp give you any warnings? At what time did the error occur? At
the start of the simulation or later? Could you check the log file for
LINCS warnings, and try to track down the first occurrence? This would
help to be able to say some more than "your system is exploding".

Best,

Tsjerk

On 3/27/07, fulya caglar wrote:
>
>
> Note: forwarded message attached.
>
> 
> Finding fabulous fares is fun.
> Let Yahoo! FareChase search your favorite travel sites to find flight and
> hotel bargains.
>
> -- Forwarded message --
> From: fulya caglar 
> To: [EMAIL PROTECTED]
> Date: Mon, 26 Mar 2007 12:44:18 -0700 (PDT)
> Subject: Drug - Enzyme Tutorial
> Although I could run sucessfully speptide tutorial,while attempting the
> drug-enzyme tutorial I am getting the following error message after the
> first mdrun command ( mdrun -s trp_em.tpr -o trp_em.trr -c trp_b4pr.pdb -g
> em.log –e em.edr);
> -
>   
>
> ---
>
> I would be very glad to know why I get this type of error. Thanks very
> much.
>
> With thanks
> Sincerely Fulya
>
>
> 
> Food fight? Enjoy some healthy debate
> in the Yahoo! Answers Food & Drink Q&A.
>
>
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-- 
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P: +31-30-2539931
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Re: [gmx-users] gen_vel

[Tsjerk Wassenaar]

GENERATE VELOCITIES FROM A maxwell DISTRIBUTION FOR ALL ATOMS OR NOT
(keep from file or 0.0). SEE CHAPTER 7 OF THE gromacs MANUAL.

YOUR WELCOME

Tsjerk

On 3/27/07, özge kül <[EMAIL PROTECTED]> wrote:

HI EVERYBODY,

I HAVE A PROBLEM WITH gen_vel.IF I MAKE AN ANALYZE WITH POSITION RESTRAINT I
USED gen_vel=yes.AFTER FOR FULL MDP I USED gen_vel=no.AFTER THAT I USED
gen_vel=no FOR AGAIN FULL.MDP.BUT I GOT VERY BAD RMSD GRAPHICS.ANY HELP
ABOUT WHAT IS THE MEANING OF gen_vel=no,gen-vel=yes?

THANK YOU...

 
Don't pick lemons.
 See all the new 2007 cars at Yahoo! Autos.


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--
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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[gmx-users] Converting CHARMM trajectories (.trj) to GROMACS trajectories (.xtc)

[Hwankyu Lee]

Dear gmx-users,

I would like to analyze CHARMM trajectories in GROMACS, and wonder if 
there are available scripts or tools to convert CHARMM traj to GROMACS 
traj (.xtc).  I've searched the contributed software and forum 
sections, and it looks like there is a script for that, but couldn't 
find it.  If you can provide me scripts for that, it'll be appreciated.

Thanks,

best,
Hwankyu.

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Re: [gmx-users] gen_vel

[Yang Ye]

according to what you have described, it is correct. is your reference 
structure wrong for RMSD calculation?


On 3/27/2007 8:56 PM, özge kül wrote:

HI EVERYBODY,
 
I HAVE A PROBLEM WITH gen_vel.IF I MAKE AN ANALYZE WITH POSITION 
RESTRAINT I USED gen_vel=yes.AFTER FOR FULL MDP I USED 
gen_vel=no.AFTER THAT I USED gen_vel=no FOR AGAIN FULL.MDP.BUT I GOT 
VERY BAD RMSD GRAPHICS.ANY HELP ABOUT WHAT IS THE MEANING OF 
gen_vel=no,gen-vel=yes?
 
THANK YOU...



Don't pick lemons.
See all the new 2007 cars 
 
at Yahoo! Autos. 
 




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Re: [gmx-users] Topology file for D2O

[Andrés N. McCarthy]

Hi Joys Yu,

In addition to Tserks comments you might want to use a more specifically 
developed heavy water model.
Here is a reference you may find usefull:
An effective pair potential for heavy water - J. Raul Grigera 
The Journal of Chemical Physics -- May 8, 2001 -- Volume 114, Issue 18, pp. 
8064-8067.

I have created a topology file based on these parameters for a cooperation I 
did some time back. If you are interested I can email the topology & modified 
FF fiels to you.

Regards

Andrés 


El Martes, 27 de Marzo de 2007 03:29, Joys Yu escribió:
> Dear all,
>
> I would like to do simulation of bulk heavy water
> (D2O). So first thing, I need to get the topology file
> of D2O. In fact, I would like to use SPC H2O. I just
> need to change the mass of H in H2O from 1.008 to
> 2.016.
>
> I would like to use gromacs force field(#7). So I
> revised ffgms.atp. I changed the mass of water
> hydrogen from 1.008 to 2.016.
>
> When I use pdbtogmx to get the topology, it seems
> fine. I have a bulk heavy water, which has 674 D2O.
> Here is some of the running results from pdbtogmx:
>
> Now there are 674 residues with 2022 atoms
> Making bonds...
> Opening library file
> /home/gromacs-d/share/top/aminoacids.dat
> Number of bonds was 1348, now 1348
> Generating angles, dihedrals and pairs...
> There are0 dihedrals,0 impropers,  674 angles
>  0 pairs, 1348 bonds and 0 virtual
> sites
> Total mass 13501.164 a.m.u.
> Total charge 0.000 e
>
>
> The total mass for 674 D2O is correct: 674 * 20.03 =
> 13501.164
>
> Here is the topology file that I got for D2O:
>
> ;
> ;   File 'd2o.top' was generated
> ;   By user: Joys (1002)
> ;   On host: Boyang
> ;   At date: Mon Mar 26 20:15:57 2007
> ;
> ;   This is your topology file
> ;   Generated by genbox
> ;
> ; Include forcefield parameters
> #include "ffgmx.itp"
>
> ; Include water topology
> #include "spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> Generated by genbox
>
> [ molecules ]
> ; Compound#mols
> SOL   674
>
> Everything seems fine here. Then I want to do a MD
> simulation. I used grompp to get the .tpr. I could
> also run it. But in the .log file, I found the mass of
> the system is the mass of H2o ( about 12132) not
> 13501.164.
>
> I got D2O topology from pdb2gmx correctly. But it
> seems that grompp did not read in this topology.
>
> Can anybody kindly tell me where the problem is? What
> should I do to get D2O topology?
>
> Many thanks,
> Joys Yu
>
>
>
>
>
>
> ___
>_ Looking for earth-friendly autos?
> Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center.
> http://autos.yahoo.com/green_center/
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> gmx-users mailing listgmx-users@gromacs.org
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> www interface or send it to [EMAIL PROTECTED]
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-- 
--
  Dr. Andrés N. McCarthy
Instituto de Física de Líquidos y Sistemas Biológicos
(UNLP-CONICET-CIC)
Depto. Cs. Biológicas - Fac. de Cs. Exactas - Univ. Nac. de La Plata
59-789, CP (1900) La Plata, Argentina
Tel: +54-221-4254904 / +54-221-4233283
FAX: +54-221-4257317
e-mail:     [EMAIL PROTECTED]
web site:   www.iflysib.unlp.edu.ar
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Re: [gmx-users] Topology file for D2O

[David Mobley]

Hi,

I am not an expert about heavy water -- but it does seem strange to me
to think that you could get "heavy water" just by changing the mass of
the hydrogens in a conventional water model. The *only* thing this
will affect is the kinetic energy and mass of water. Presumably
changing hydrogen to deuterium *should* also affect other things, such
as perhaps slightly altering the electrostatics or dispersion
interactions, or the water molecule shape. I'm no expert -- but I bet
there's more to it than just a slight change in mass.

Maybe you might already know part of the answer to this: Why is it you
want to run with D2O instead of regular water? I'm guessing it's
because you expect some difference in behavior... Should that really
be due exclusively to a difference in mass?

David



On 3/27/07, Andrés N. McCarthy <[EMAIL PROTECTED]> wrote:

Hi Joys Yu,

In addition to Tserks comments you might want to use a more specifically
developed heavy water model.
Here is a reference you may find usefull:
An effective pair potential for heavy water - J. Raul Grigera
The Journal of Chemical Physics -- May 8, 2001 -- Volume 114, Issue 18, pp.
8064-8067.

I have created a topology file based on these parameters for a cooperation I
did some time back. If you are interested I can email the topology & modified
FF fiels to you.

Regards

Andrés


El Martes, 27 de Marzo de 2007 03:29, Joys Yu escribió:
> Dear all,
>
> I would like to do simulation of bulk heavy water
> (D2O). So first thing, I need to get the topology file
> of D2O. In fact, I would like to use SPC H2O. I just
> need to change the mass of H in H2O from 1.008 to
> 2.016.
>
> I would like to use gromacs force field(#7). So I
> revised ffgms.atp. I changed the mass of water
> hydrogen from 1.008 to 2.016.
>
> When I use pdbtogmx to get the topology, it seems
> fine. I have a bulk heavy water, which has 674 D2O.
> Here is some of the running results from pdbtogmx:
>
> Now there are 674 residues with 2022 atoms
> Making bonds...
> Opening library file
> /home/gromacs-d/share/top/aminoacids.dat
> Number of bonds was 1348, now 1348
> Generating angles, dihedrals and pairs...
> There are0 dihedrals,0 impropers,  674 angles
>  0 pairs, 1348 bonds and 0 virtual
> sites
> Total mass 13501.164 a.m.u.
> Total charge 0.000 e
>
>
> The total mass for 674 D2O is correct: 674 * 20.03 =
> 13501.164
>
> Here is the topology file that I got for D2O:
>
> ;
> ;   File 'd2o.top' was generated
> ;   By user: Joys (1002)
> ;   On host: Boyang
> ;   At date: Mon Mar 26 20:15:57 2007
> ;
> ;   This is your topology file
> ;   Generated by genbox
> ;
> ; Include forcefield parameters
> #include "ffgmx.itp"
>
> ; Include water topology
> #include "spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> Generated by genbox
>
> [ molecules ]
> ; Compound#mols
> SOL   674
>
> Everything seems fine here. Then I want to do a MD
> simulation. I used grompp to get the .tpr. I could
> also run it. But in the .log file, I found the mass of
> the system is the mass of H2o ( about 12132) not
> 13501.164.
>
> I got D2O topology from pdb2gmx correctly. But it
> seems that grompp did not read in this topology.
>
> Can anybody kindly tell me where the problem is? What
> should I do to get D2O topology?
>
> Many thanks,
> Joys Yu
>
>
>
>
>
>
> ___
>_ Looking for earth-friendly autos?
> Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center.
> http://autos.yahoo.com/green_center/
> ___
> 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

--
--
  Dr. Andrés N. McCarthy
Instituto de Física de Líquidos y Sistemas Biológicos
(UNLP-CONICET-CIC)
Depto. Cs. Biológicas - Fac. de Cs. Exactas - Univ. Nac. de La Plata
59-789, CP (1900) La Plata, Argentina
Tel: +54-221-4254904 / +54-221-4233283
FAX: +54-221-4257317
e-mail: [EMAIL PROTECTED]
web site:   www.iflysib.unlp.edu.ar
--
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Re: [gmx-users] parinello-rahman coupling

[lorix]

Hi Tsjerk,

I set the pressure in the parameter file to be 1bar and I get different
average values ranging from 0.4 to 1.7 bar. Maybe they are not significantly
different (?) but I try to simulate large conformational changes and 
according to

what I saw small difference in settings can make different trajectories.
In my simulations Berendsen barostat can keep the mean value of the 
pressure, but

according to the manual it does not yield a correct thermodynamic ensemble.

thanx

loris...



Tsjerk Wassenaar wrote:


Hi Lorix,

Sorry for that. You used the word "maintained" from which I inferred
you were referring to the fluctuations (biased by the occurrence of
the question obviously). Under normal conditions the equilibration
shouldn't take that long. How far off is the mean? Do you still
observe a trend? Still note that you're dealing with enormous, both
positive and negative, pressures, from which you try to extract an
average value. Such an average will usually not be very exact because
of the numerical inaccuracies.

Best,

Tsjerk

On 3/27/07, lorix <[EMAIL PROTECTED]> wrote:


Hi Tsjerk,

Thanks for your prompt reply.
I was asking about the average value of the property.
I understood that large fluctuations are reasonable, but I was expecting
that the mean value
over 15 ns could be somehow as the set in the parameter file as happens
with Berendsen pressure coupling.
I checked the archives and I did not find much about the mean value.

best regards,

lorix...


Tsjerk Wassenaar wrote:

> Hi Loris,
>
> Enjoying the nice weather here, I'll just give a gentle reiteration of
> previous remarks. What you observe is caused by the fact that you only
> have a very small system from which you try to extract a macroscopic
> property (i.e. defined only for large systems). The large fluctuations
> are normal. It would be a good idea to read some general texts about
> statistical mechanics and molecular dynamics and before posting a
> question to the user list, it would also be good to browse through the
> archives of this list, to see if the question you're about to ask has
> already been answered (and trust me, this one has been, many times).
>
> Good luck with your simulations,
>
> Tsjerk
>
> On 3/27/07, lorix <[EMAIL PROTECTED]> wrote:
>
>> Dear gmx-users,
>>
>> I am a new one...
>> coming to the point...I am simulating in parallel different
>> configurations and settings of a protein
>> around 300 residues large plus approximately 12000 water molecules.
>> I am simulating NPT with berendsen for P and T to equilibrate over 
100

>> ps and then the simulation
>> for several ns (5-20) with nose-hoover for T and parinello-rahman 
for P.
>> But in the last step I cannot find a value for tau_p to maintained 
and

>> average of 1 bar.
>> Reducing the tau_p value (0.06, 0.05 and 0.01) I get many messages in
>> the log file like:
>>
>> Grid: 11 x 10 x 9 cells
>> Grid: 11 x 11 x 9 cells
>>
>> and then the simulation stops randomly without any messages 
besides the

>> lam-mpi ones.
>>
>> does anyone have ideas?
>>
>> thanks
>>
>> loris...
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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>>
>
>

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Re: [gmx-users] parinello-rahman coupling

[Tsjerk Wassenaar]

Hi Loris,

You're always stuck with limitations of simulations one way or the
other. Now, berendsen barostat is disputed in some sense, but it does
a good job usually (and it is so simple). The question would be, how
far off is it from THE thermodynamic ensemble of your system (and how
far off are the others). Then you have to wonder how on earth you're
going to get THE thermodynamic ensemble with an empirical force field.
But then again, you'll probably be close enough for what you want to
see.

Now, the thing with different starting conditions giving you different
trajectories, means that you have to do multiple runs to get a proper
sample from the distribution of possible trajectories (starting from a
certain region in conformational space). You need statistics.

Hope it helps,

Tsjerk


On 3/27/07, lorix <[EMAIL PROTECTED]> wrote:

Hi Tsjerk,

I set the pressure in the parameter file to be 1bar and I get different
average values ranging from 0.4 to 1.7 bar. Maybe they are not significantly
different (?) but I try to simulate large conformational changes and
according to
what I saw small difference in settings can make different trajectories.
In my simulations Berendsen barostat can keep the mean value of the
pressure, but
according to the manual it does not yield a correct thermodynamic ensemble.

thanx

loris...



Tsjerk Wassenaar wrote:

> Hi Lorix,
>
> Sorry for that. You used the word "maintained" from which I inferred
> you were referring to the fluctuations (biased by the occurrence of
> the question obviously). Under normal conditions the equilibration
> shouldn't take that long. How far off is the mean? Do you still
> observe a trend? Still note that you're dealing with enormous, both
> positive and negative, pressures, from which you try to extract an
> average value. Such an average will usually not be very exact because
> of the numerical inaccuracies.
>
> Best,
>
> Tsjerk
>
> On 3/27/07, lorix <[EMAIL PROTECTED]> wrote:
>
>> Hi Tsjerk,
>>
>> Thanks for your prompt reply.
>> I was asking about the average value of the property.
>> I understood that large fluctuations are reasonable, but I was expecting
>> that the mean value
>> over 15 ns could be somehow as the set in the parameter file as happens
>> with Berendsen pressure coupling.
>> I checked the archives and I did not find much about the mean value.
>>
>> best regards,
>>
>> lorix...
>>
>>
>> Tsjerk Wassenaar wrote:
>>
>> > Hi Loris,
>> >
>> > Enjoying the nice weather here, I'll just give a gentle reiteration of
>> > previous remarks. What you observe is caused by the fact that you only
>> > have a very small system from which you try to extract a macroscopic
>> > property (i.e. defined only for large systems). The large fluctuations
>> > are normal. It would be a good idea to read some general texts about
>> > statistical mechanics and molecular dynamics and before posting a
>> > question to the user list, it would also be good to browse through the
>> > archives of this list, to see if the question you're about to ask has
>> > already been answered (and trust me, this one has been, many times).
>> >
>> > Good luck with your simulations,
>> >
>> > Tsjerk
>> >
>> > On 3/27/07, lorix <[EMAIL PROTECTED]> wrote:
>> >
>> >> Dear gmx-users,
>> >>
>> >> I am a new one...
>> >> coming to the point...I am simulating in parallel different
>> >> configurations and settings of a protein
>> >> around 300 residues large plus approximately 12000 water molecules.
>> >> I am simulating NPT with berendsen for P and T to equilibrate over
>> 100
>> >> ps and then the simulation
>> >> for several ns (5-20) with nose-hoover for T and parinello-rahman
>> for P.
>> >> But in the last step I cannot find a value for tau_p to maintained
>> and
>> >> average of 1 bar.
>> >> Reducing the tau_p value (0.06, 0.05 and 0.01) I get many messages in
>> >> the log file like:
>> >>
>> >> Grid: 11 x 10 x 9 cells
>> >> Grid: 11 x 11 x 9 cells
>> >>
>> >> and then the simulation stops randomly without any messages
>> besides the
>> >> lam-mpi ones.
>> >>
>> >> does anyone have ideas?
>> >>
>> >> thanks
>> >>
>> >> loris...
>> >> ___
>> >> 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
>> >>
>> >
>> >
>>
>> ___
>> 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_lis

Re: [gmx-users] gen_vel

[Mark Abraham]

? wrote:

HI EVERYBODY,
 
I HAVE A PROBLEM WITH gen_vel.IF I MAKE AN ANALYZE WITH POSITION 
RESTRAINT I USED gen_vel=yes.AFTER FOR FULL MDP I USED gen_vel=no.AFTER 
THAT I USED gen_vel=no FOR AGAIN FULL.MDP.BUT I GOT VERY BAD RMSD 
GRAPHICS.ANY HELP ABOUT WHAT IS THE MEANING OF gen_vel=no,gen-vel=yes?
 
THANK YOU...


Please do not use all capitals for posting to email newsgroups. It is 
considered to be the equivalent to shouting your question to a room full 
of people talking quietly among themselves.


Mark
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[gmx-users] tabulated nonbonded interactions and free energy calculations

[David Mobley]

All,

I'm trying to figure out how to use tabulated nonbonded interactions
in GROMACS in conjunction with free energy calculations. While the
documentation addresses both separately, I am somewhat confused about
what would happen if I try to use both simultaneously. In particular,
I'm looking at the discussion of user-defined potentials on page 126
of the 3.3 manual. If I set up a table defining f(rij), g(rij), and
h(rij) as discussed their, plus their derivatives, can I still use the
free energy code?

For example, what if I have a topology file that has full charges on
some molecule in the A state, but zero charges in the B state?
Usually, with the free energy code, the potential energy would be
V=(1-lambda)*V_A+lambda*V_B. However, if I use tabulated nonbonded
interactions, the electrostatic term is qi*qj/4pi*eps0*f(rij); I
assume this means the package will use a *particular* qi and qj (i.e.,
for the A state)?

I'm asking all this because my *goal* is to be able to do free energy
calculations using the WCA separation for LJ. I understand it's
possible to implement the WCA separation using tabulated nonbonded
interactions (at least, there's an e-mail on the list suggesting this)
but it's unclear to me whether doing so would make it impossible for
me to simultaneously do free energy calculations. I'm guessing the
answer is yes -- one can't use tabulated nonbonded interactions and
free energy simultaneously. Can anyone confirm?

Thanks,
David
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Re: [gmx-users] Converting CHARMM trajectories (.trj) to GROMACS trajectories (.xtc)

[Mark Abraham]

Hwankyu Lee wrote:

Dear gmx-users,

I would like to analyze CHARMM trajectories in GROMACS, and wonder if 
there are available scripts or tools to convert CHARMM traj to GROMACS 
traj (.xtc).  I've searched the contributed software and forum sections, 
and it looks like there is a script for that, but couldn't find it.  If 
you can provide me scripts for that, it'll be appreciated.


I'm not aware of one... if it looks like there is a script for it, why 
couldn't you find it? :-)


I think you should explore finding an intermediate format, like PDB, 
through which you can convert one to the other - you will lose 
precision, but that will not matter for analysis.


Mark
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Re: [gmx-users] Carbon Nanotube Simulations

[Tom Weingarten]

Hi,
   Actually, I believe that only one force field (ffgmx) currently has an
n2t file, at least as recently as 3.3.1. I would try running a find or
locate command to see if you even have the n2t files to begin with. I also
believe I read earlier on the mailing list that the CVS branch has some
improvements to the x2top program which may be helpful. If not you may need
to make one for your molecule.

,Tom

On 3/26/07, Mark Abraham <[EMAIL PROTECTED]> wrote:


George Abadir wrote:
> Hi,
> I am using Tubegen to generate a PDB file for carbon nanotubes. When
> I use the "x2top" command I get an error :"Library file ffG43a1.n2t not
> found in current dir nor in default directories". The same error is
> repeated with every other force field. Where can I find this file or how
> can I get around this problem? Your help is much appreciated.

I think this means you haven't set up your environment. In the gromacs
binary directory there's a file GMXRC that you need to "source" to set
up various variables to help gromacs find things.

Mark
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[gmx-users] Incorrect dihedral restraints

[Jonathan Khao]

Hi, i've solved my problem concerning dihedral restraints, hope that
it'll be usefull for those who have trouvble using it.

The constraints must have values between 0 and 360° !
Not that complicated, but it took me 2 weeks to figure that out...

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Re: [gmx-users] Deshuffling a .gro file

[toma0052]

Hi,
 Thanks for the response.  Sorry that the statement of my problem was so
cumbersome.  My problem was with the noncontinuous numbering of molecules
following deshuffling using editconf.  What I am doing, is following an md
run, performing a simple transformation of the coordinates in the resulting
*.gro file (to simulate a stretch, and then relaxation of a lipid bilayer). 
The noncontinuous numbering of the molecules following deshuffling makes this
transformation much harder.  Therefore, I was hoping to get a *.gro file
which has the correct numbering following deshuffling.  However, it appears
that deshuffling and sorting the atoms in a *.gro file is quite nontrivial,
so now I have taken to not running my simulation in parallel, or not using
the -shuffle -sort option and just dealing with the longer run times.  Thanks
for the advice.

Mike



On 27 Mar 2007, Yang Ye wrote:
> On 3/20/2007 10:03 PM, toma0052 wrote:
> > Hello,
> >  I am performing a simulation in parallel on four processors.  The
> > simulation seems to run fine, and outputs a shuffled *.gro file.  I would
> > like to change the order of atoms to what they were in the original input
> > *.gro file, but I am having some trouble.  I have seen some previous
posts
> > on this, but I am still a bit confused. 
> >
> > David van der Spoel wrote:
> >   
> > [...]
> >
> >   
> >> If your standard dsehuf.ndx for a system of N atoms starts with:
> >> [ deshuf ]
> >> 0 1 4 6 7 etc.
> >> you have to modify it to the old format:
> >> 1 N
> >> deshuf N
> >> 0 1 4 6 7 etc.
> >>
> >> You only have to change the top bit, not the actual numbers. An
> >> alternative is to modify it to be:
> >> [ deshuf ]
> >> 1 2 5 7 8 etc.
> >>
> >> That wouldn't be too hard with a script either.
> >>
> >> 
> >
> > This says that I need to alter my deshuf.ndx file a bit, and then just do
> > editconf -f shuf.gro -n deshuf.ndx -o unshuf.gro  to obtain an unchuffled
> > *.gro file.  However, my deshuf.ndx file already began counting the atoms
> > at 1, i.e.:
> >
> > [ DeShuffle ]
> >   1  2  3  4  5  6  7  8  9  10
> >   11  12  13  14  15  16  17  18  19  20
> >   21  22  23  24  25  26  27  28  29  30
> >   31  32  33  34  35  36  37  38  39  40
> >   41  42  43  44  45  46  47  48  49  50
> > ...
> >
> > So, everything already seems to be fine (other than the name in the
> > brackets, which didn't seem to matter if changed) with the deshuf.ndx
file.
> >  When I do editconf -f shuf.gro -n deshuf.ndx -o unshuf.gro  though, my
> > *.gro file does not sort properly, although some sorting does take place.

> > The atoms seem to be in the correct general order (The first series of
> > atoms are all DPPC, and the rest are all SOL) but the atom numbers are in
> > the wrong order (The order goes 1DPPC ... 44DPPC, 1257DPPC ... 1299DPPC,
> > 2513DPPC ... etc whereas it should go from 1DPPC to 128DPPC and then
begin
> > to number the SOL molecules at 129SOL).  Is this a problem with my input
> > into grompp?  I am using both -shuffle and -sort.  Is this incorrect?
> > How do I deshuffle my *.gro file to list the 128 DPPC molecules and then
> > the 3655 SOL molecules with atom numbers 1 to 17365?
> >   
> Sorry that your description was not easy to be comprehend. Perhaps this 
> is why this post was not followed.
> I would like to offer some general principles here.
> 1. deshuf.ndx is definitely not ordered so you shall see some 
> disordering in the later part of ndx file.
> 2. After deshuffling using editconf, it is normal for the resulting .gro 
> to have noncontinuous numbering for molecule. It is more important to 
> have the correct molecule type. For example, all your SOL shall be in 
> one block with no other molecules embedded.
> 
> 
> Yang Ye
> > Thank you,
> > Mike Tomasini
> >
> > ___
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> >   
> 
> 
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[gmx-users] help with g_sdf

[syma]

Hi 

Please can someone help me with g_sdf
I would like to calculate the sdfs of two different types of lipid
headgroups around another species in my system.

Specifically I have 119 lipids of one type and 116 of the other- do I need
to normalise to account for this difference? If so, any advice as to how I
would go about this?

Many thanks,

-Syma
***

Dr Syma Khalid  
Department of Biochemistry,   
University of Oxford   
South Parks Road,
Oxford
OX1 3QU
U.K.



***



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[gmx-users] Topology file for D2O

[Joys Yu]

Dear all,

Thank you so much for your suggestions. You don't know
how much you guys are helpful.

First with Tsjerk's suggestion of using gmxdump, I got
to know where the problem is. What I changed is
ffgmx.atp and spc.itp. It is useful to pdb2gmx. But
for grompp, it is not enough. I have to change the
file of ffgmxnb.itp. For some reason, grompp reads
this file and determin the mass of all atoms. So far,
I got the mass of hydrogen changed to be 2 in the
readable .tpr file. Of course, I could also see the
mass showed correctly in the log file.

Yes, Andres, I am very interested in the heavy water
poteintial. Please email me the topology and modifed
FF files. Thanks very much.

David, What you thought is very resonable. That's why
Andres said maybe I should consider more specific
heavy water model. But at this moment, I am just
trying to get some preliminary results.

Thank you all,
Joys








 

Don't get soaked.  Take a quick peek at the forecast
with the Yahoo! Search weather shortcut.
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RE: [gmx-users] help with g_sdf

[Dallas B. Warren]

> Please can someone help me with g_sdf
> I would like to calculate the sdfs of two different types of 
> lipid headgroups around another species in my system.
> 
> Specifically I have 119 lipids of one type and 116 of the 
> other- do I need to normalise to account for this difference? 
> If so, any advice as to how I would go about this?

Simply make them part of the same index group that you use to generate
the SDF to.

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] How to turn off Langevin thermostat for NVE Simulation

[WU Yanbin]

Hi,
 I would like to run NVE Simulation and so I turn off the Temperature
coupling (Nose-Hoover or Beredsen).
 Yet I guess the Langevin thermostat coupling is still on (From the manual,
in .mdp file, for Langevin Dynamics, if bd_fric is set to be zero, the
friction coefficient for each particle is calculated as mass/tau_t.)
 Does it influence my NVE simulation? Any method to turn the Langevin
Dynamics off? Thanks.
Yours
Sincerely,

WU Yanbin
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Re: [gmx-users] Deshuffling a .gro file

[Yang Ye]

toma0052 wrote:

Hi,
 Thanks for the response.  Sorry that the statement of my problem was so
cumbersome.  My problem was with the noncontinuous numbering of molecules
following deshuffling using editconf.  What I am doing, is following an md
run, performing a simple transformation of the coordinates in the resulting
*.gro file (to simulate a stretch, and then relaxation of a lipid bilayer). 
The noncontinuous numbering of the molecules following deshuffling makes this

transformation much harder.  Therefore, I was hoping to get a *.gro file
which has the correct numbering following deshuffling.  
The numbering of the solvent water doesn't have a rule, e.g. water X and 
Y could be just neighbour even X=1000 and Y=1. It only depends on 
the initial ordering imposed by the stacking algorithm of genbox. During 
the course of MD, every molecule drifts especially the solvents and ions 
so the number ordering is no longer an indicator; actually, it is always 
not an good indicator for anything. So your intention about using such 
numbering sounds not reasonable. You shall always sort your molecules 
based on their coordinates.

However, it appears
that deshuffling and sorting the atoms in a *.gro file is quite nontrivial,
so now I have taken to not running my simulation in parallel, or not using
the -shuffle -sort option and just dealing with the longer run times.  Thanks
for the advice.

Mike




On 27 Mar 2007, Yang Ye wrote:
  

On 3/20/2007 10:03 PM, toma0052 wrote:


Hello,
 I am performing a simulation in parallel on four processors.  The
simulation seems to run fine, and outputs a shuffled *.gro file.  I would
like to change the order of atoms to what they were in the original input
*.gro file, but I am having some trouble.  I have seen some previous
  

posts
  
on this, but I am still a bit confused. 


David van der Spoel wrote:
  
[...]


  
  

If your standard dsehuf.ndx for a system of N atoms starts with:
[ deshuf ]
0 1 4 6 7 etc.
you have to modify it to the old format:
1 N
deshuf N
0 1 4 6 7 etc.

You only have to change the top bit, not the actual numbers. An
alternative is to modify it to be:
[ deshuf ]
1 2 5 7 8 etc.

That wouldn't be too hard with a script either.




This says that I need to alter my deshuf.ndx file a bit, and then just do
editconf -f shuf.gro -n deshuf.ndx -o unshuf.gro  to obtain an unchuffled
*.gro file.  However, my deshuf.ndx file already began counting the atoms
at 1, i.e.:

[ DeShuffle ]
  1  2  3  4  5  6  7  8  9  10
  11  12  13  14  15  16  17  18  19  20
  21  22  23  24  25  26  27  28  29  30
  31  32  33  34  35  36  37  38  39  40
  41  42  43  44  45  46  47  48  49  50
...

So, everything already seems to be fine (other than the name in the
brackets, which didn't seem to matter if changed) with the deshuf.ndx
  

file.
  

 When I do editconf -f shuf.gro -n deshuf.ndx -o unshuf.gro  though, my
*.gro file does not sort properly, although some sorting does take place.
  


  

The atoms seem to be in the correct general order (The first series of
atoms are all DPPC, and the rest are all SOL) but the atom numbers are in
the wrong order (The order goes 1DPPC ... 44DPPC, 1257DPPC ... 1299DPPC,
2513DPPC ... etc whereas it should go from 1DPPC to 128DPPC and then
  

begin
  

to number the SOL molecules at 129SOL).  Is this a problem with my input
into grompp?  I am using both -shuffle and -sort.  Is this incorrect?
How do I deshuffle my *.gro file to list the 128 DPPC molecules and then
the 3655 SOL molecules with atom numbers 1 to 17365?
  
  
Sorry that your description was not easy to be comprehend. Perhaps this 
is why this post was not followed.

I would like to offer some general principles here.
1. deshuf.ndx is definitely not ordered so you shall see some 
disordering in the later part of ndx file.
2. After deshuffling using editconf, it is normal for the resulting .gro 
to have noncontinuous numbering for molecule. It is more important to 
have the correct molecule type. For example, all your SOL shall be in 
one block with no other molecules embedded.



Yang Ye


Thank you,
Mike Tomasini

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[gmx-users] Carbon Nanotube Simulations

[George Abadir]

Hi,
I added CNT residue in the ffgmx.rtp as follows:   

" [ CNT ]


 [ atoms ]
 C C0.00  0"
Then I used x2top to generate the topology for carbon nanotubes from the PDB file generated form 
TUBEGEN. First, if I use any format in TUBEGEN other than the PDB with periodic boundary 
conditions, I get an error "No forcefield type for atom C(1) with 1 bonds". When I use 
the PDB-PBC format, I get a warning that "all CONECT records are ignored" but there is no 
error.
Second, I don't know exactly what the next step to perform an MD simulation just for the 
CNT alone is? When I use grompp I get an error "the cut-off length is longer than 
the half the shortest box vector or longer than the smallest box diagonal element. 
Increase the box size or decrease rlist". Are there any missing steps? I would 
appreciate if anybody would inform me of the necessary steps to do such a simulation 
(actually my ultimate goal is to perform an MD simulation for a CNT-DNA and a CNT-protein 
system).
Thank you very much in advance,


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[gmx-users] Generating carbon nanotubes for GROMACS

[George Abadir]

Hi,
I am using Tubegen to generate carbon nanotubes for my simulations. 
Is there any better method to do this?

Thank you very much,
George



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Re: [gmx-users] Fwd: How can I do the simulation of a protein with Tyr (SO3H)

[fulya caglar]

Hi Tsjerk,
  Do you know how can I add parameters for sulfite bound?You are right I 
have little experience in this field but maybe one of my friends can do this.I 
would be very grateful if you can explain  parameterization briefly.
   
  And I dont think there is a problem with the mail server?Why did you ask?

Thank you very much!!!
  Sincerly
  Fulya

  
-
  From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users" 
Subject: Re: [gmx-users] Fwd: How can I do the simulation of a protein with
Tyr (SO3H)

Hi Fulya,

You can't just simulate everything you set your mind on. There are no
parameters for sulfite bound tyrosine in the database (just what it
says). You have to add them yourself, which I don't recommend at this
point, since it is clear you have but little experience in this field
(and parameterization is an advanced topic).

By the way, do you have some problems with the mail server?

Best,

Tsjerk

On 3/27/07, fulya caglar wrote:
>
>
> Note: forwarded message attached.
>
> 
> Bored stiff? Loosen up...
> Download and play hundreds of games for free on Yahoo! Games.
>
> -- Forwarded message --
> From: fulya caglar 
> To: Gromacs 
> Date: Tue, 27 Mar 2007 04:45:43 -0700 (PDT)
> Subject: How can I do the simulation of a protein with Tyr (SO3H)
>
> Hi!
> I'm trying to do a simulation of a protein with bound sulfite ion (Tyr
> (SO3H)).After the first command ( pdb2gmx) I am getting the following error
> message :
> -
> Fatal error:
> Residue 'SUL' not found in residue topology database
> -
>
> I would be very glad to know why I get this type of error and what can I do
> about this. With thanks
> Sincerely Fulya
>
>
> 
> TV dinner still cooling?
> Check out "Tonight's Picks" on Yahoo! TV.
>
>
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-- 
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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-
Don't be flakey. Get Yahoo! Mail for Mobile and 
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Re: [gmx-users] Fwd: How can I do the simulation of a protein with Tyr (SO3H)

[Mark Abraham]

fulya caglar wrote:

Hi Tsjerk,
Do you know how can I add parameters for sulfite bound?You are right 
I have little experience in this field but maybe one of my friends can 
do this.I would be very grateful if you can explain  parameterization 
briefly.


It's an involved process, which varies considerably depending on the 
force field you're trying to extend. You should start by reading the 
paper that describes the parameterization of the force field you're 
trying to extend, and then thinking hard about how you can follow a 
similar process to get parameters that are consistent.


Mark
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Re: [gmx-users] g_rdf normalisation

[Qiao Baofu]

2007/3/26, syma <[EMAIL PROTECTED]>:


Hi,

I am attempting to calculate the rdfs of the various components of my
system
wrt to DNA phosphate groups. However, I was wondering how I can normalise
so
I can compare the various rdfs? Ideally I would like to have the g(r)
normalised in the range 0-1.



In fact, there is not flag to control the normalised range. But you can take
the range, 0-1, of rdf.xvg.
The caluclated neighbour number at dr is normalised by the ideal case at dr
(average density times the volume at dr) . For the ideal condition, the
density at the short range is the same as the average density. Therefore,
..


I have read on the user list that I should get three columns in the *.xvg

output, the distance, the normalised data and the raw data, I only get two
columns.



The default rdf.xvg will give only two columns, r and g(r)


Thanks in advance for any help.


-Syma

***

Dr Syma Khalid
Department of Biochemistry,
University of Oxford
South Parks Road,
Oxford
OX1 3QU
U.K.



***


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--
Sincerely yours,
**
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**
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