Re: [gmx-users] How to do Normal Modes Analysis with Gromacs4.5.5?

[qiancheng shen]

Dear David,
 Thank you very much!!
 Your suggestion works!! After removing water and ion from my
structure, I did normal mode analysis successfully!!

  I appreciate your help.

Shen

在 2012年3月17日 下午11:45，Justin A. Lemkul 写道：

>
>
> qiancheng shen wrote:
>
>> Dear David,
>> Thank you very much.
>> /* A little modification to your first post. */
>>
>> "
>> grompp_d -f cg -o cg
>> mdrun_d -s cg/* -o*/ conf.g96  ->
>> mdrun_d -s cg /*-c*/ conf.g96  (Use -o will only output *.trr)
>>
>> grompp_d -f nm -c conf.g96 -o nm
>> mdrun_d -s nm
>> g_nmeig_d
>> "
>> And when I used "integrator = nm" in *.mdp file and run "mdrun_d -s
>> nm". Gromacs said "Constraints present with Normal Mode Analysis, this
>> combination is not supported".
>> Could give me some suggestion about that error?
>> The commands I used is listed below:
>> 1.  */pdb2gmx_d -ignh -ff /*/gromos43a1 *-f* 1OMB.pdb *-water* spce
>> *-o* conf.gro *-p* topol.top/
>> 2.  *///editconf_d -f /*/conf.gro *-o* BOX.gro *-d* 1.5/
>> 3.  */genbox_d -cp /*/BOX.gro *-cs* spc216 *-o* SOL *-p* topol.top/
>> 4.  */grompp_d -f /*/em.mdp *-c* SOL.gro *-p* topol.top *-o* em.tpr/
>> 5.  */mdrun_d -s /*/em.tpr  *-deffnm* em *-c* tx.g96 *-v*/  //Energy
>> Min
>> 6.  /*grompp_d*/ /*-f */nm.mdp /*-c*/ tx.g96 /*-o*/ nm
>> 7.  /*mdrun_d*/ /*-s*/ nm   -> A fatal error "Constraints present
>> with Normal Mode Analysis, this combination is not   supported"
>>
>>
> In adding solvent, these molecules are held rigid by the SETTLE algorithm,
> which is a type of constraint.  As the fatal error tells you, you cannot do
> this.  See below for more comments on em.mdp.
>
>  /*em.mdp*/
>>
>> define  =  -DFLEXIBLE
>> constraints =  none
>> integrator  =  steep
>> dt  =  0.002; ps !
>> nsteps  =  400
>> nstlist =  10
>> ns_type =  grid
>> rlist   =  1.0
>> coulombtype =  PME
>> rcoulomb=  1.0
>> vdwtype =  cut-off
>> rvdw=  1.4
>> optimize_fft=  yes
>> ;
>> ;Energy minimizing stuff
>> ;
>> emtol   =  1000
>> emstep  =  0.01
>>
>>
> Steepest descents EM with this large of a maximum force is not appropriate
> for running NM calculations.  You need extremely thorough EM, perhaps
> several rounds of it using either CG or L-BFGS (or both) to a maximal force
> as low as machine precision will allow.
>
> -Justin
>
>  --**-
>> /*nm.mdp*/
>>
>> constraints =  none
>> integrator  =  nm
>> dt  =  0.002; ps !
>> nsteps  =  400
>> nstlist =  10
>> ns_type =  grid
>> rlist   =  1.2
>> coulombtype =  PME-Switch
>> rcoulomb=  1.0
>> vdwtype =  Cut-off
>> rvdw=  1.4
>>
>>
>> Thank you very much.
>>
>> Shen.
>>
>> 在 2012年3月17日 下午10:46，David van der Spoel > sp...@xray.bmc.uu.se>>**写道：
>>
>>
>>On 2012-03-17 15:34, qiancheng shen wrote:
>>
>>Dear David:
>>Thank you very much!! I'm really new to Gromacs.
>>I think I should use the *.trr file(from mdrun_d, energy
>>minimization)
>>as an input file for generating *.tpr for Normal Mode Analysis.
>>
>>
>>Please read my previous email.
>>
>>
>>But what the *.mdp file looks like while using "grompp_d -f nm -c
>>conf.g96 -o nm" to make such *.tpr file?
>>
>>integrator = nm
>>
>>I appreciate your help.
>>
>>Shen
>>
>>在 2012年3月17日 下午9:47，David van der Spoel
>>mailto:sp...@xray.bmc.uu.se>
>>>**
>> >__写道：
>>
>>
>>
>>   On 2012-03-17 14:44, qiancheng shen wrote:
>>
>>   Hello Everyone，
>>   I‘m confused about Normal Mode Analysis of Gromacs. I have
>>   googled a lot
>>   but find little useful.
>>   I installed Gromacs 4.5.5 by CMake on Win7(Double
>> Precision).
>>   Gromacs manual said "It is imperative that you use the |-t|
>>   option to
>>   |grompp
>>  > Documentation/Gromacs_**Utilities/grompp
>>> Utilities/grompp
>> >
>>
>>
>>  > **Utilities/grompp
>>
>> 
>> >>>|
>>
>>   w

[gmx-users] HBonds between molecules

[Hovakim Grabski]

Dear Gromacs users,
I ran a simulation with 13 Hypericin molecules in water for 10 ns and 7 of them 
formed an aggregate.Is there any way to find out between what molecules and 
atoms Hbonds were formed?
Thanks in advance

Hovakim Grabski
Russian-Armenian(Slavonic) University
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Re: [gmx-users] HBonds between molecules

[Justin A. Lemkul]

Hovakim Grabski wrote:

Dear Gromacs users,
I ran a simulation with 13 Hypericin molecules in water for 10 ns and 7 
of them formed an aggregate.Is there any way to find out between what 
molecules and atoms Hbonds were formed?


Yes, see the various options that g_hbond provides, particularly -hbn and -hbm.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Problem Installing Gromacs

[Suhaila Haji Mohd Hussin]

Newbie here.

I'm trying to install Gromacs and I'm following the instructions at the 
following link:

http://www.gromacs.org/Downloads/Installation_Instructions

The problem is when I type

./configure --enable-float

It gives me 'No such file or directory'

I even tried

./configure --enable-float
It's still giving me the same result.

Please help.

Many thanks,
Suhaila
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Re: [gmx-users] Problem Installing Gromacs

[Justin A. Lemkul]

Suhaila Haji Mohd Hussin wrote:

Newbie here.

I'm trying to install Gromacs and I'm following the instructions at the 
following link:


http://www.gromacs.org/Downloads/Installation_Instructions

The problem is when I type

./configure --enable-float

It gives me 'No such file or directory'


I even tried

./configure --enable-float

It's still giving me the same result.



Well, that's the same command ;)

Are you in the right directory?  After unzipping the tarball, you need to enter 
the directory that is produced and execute the commands there.


-Justin

--


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


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RE: [gmx-users] Problem Installing Gromacs

[Suhaila Haji Mohd Hussin]

> Date: Sun, 18 Mar 2012 12:35:26 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Problem Installing Gromacs
> 
> 
> 
> Suhaila Haji Mohd Hussin wrote:
> > Newbie here.
> > 
> > I'm trying to install Gromacs and I'm following the instructions at the 
> > following link:
> > 
> > http://www.gromacs.org/Downloads/Installation_Instructions
> > 
> > The problem is when I type
> > 
> > ./configure --enable-float
> > 
> > It gives me 'No such file or directory'
> > 
> > 
> > I even tried
> > 
> > ./configure --enable-float
> > 
> > It's still giving me the same result.
> > 
> 
> Well, that's the same command ;)
> 
> Are you in the right directory?  After unzipping the tarball, you need to 
> enter 
> the directory that is produced and execute the commands there.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
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Oh yeah. I forgot to download and unzip it. Cheers XD

Suhaila.
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[gmx-users] electrostatics in liquid/vapor interface

[Dr. Vitaly V. Chaban]

Dear All --

I have a system of the liquid/vapor interface kind. The droplet of
liquid with a radius of about 10nm is surrounded by a volume of vacuum
of ~1000nm^3. What is the best method among those currently in
GROMACS4 to treat electrostatics in this case?


Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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[gmx-users] Problem installing Gromacs: What next?

[Suhaila Haji Mohd Hussin]

Hello.

I already installed fftw3. After unpacking it, I install via the following:

./configure
 make
 make install
But after that the instructions are not clear to me. Like, it's not telling 
where do I download Gromacs tar?
Or do I need to type some command from fftw so that Gromacs should 
automatically built?

I'm so confused. The instructions for beginners are very vague & frustrating.

Please help,
Suhaila.
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[gmx-users] FW: Problem installing Gromacs: What next?

[Suhaila Haji Mohd Hussin]

OK. I downloaded Gromacs 4.5.5. Unpacked it then type

./configure

configure: error: Cannot find fftw3f library

But I already install fftw3 properly.

What is happening?

Cheers,
Suhaila.

From: bell_beaut...@hotmail.com
To: gmx-users@gromacs.org
Subject: Problem installing Gromacs: What next?
Date: Mon, 19 Mar 2012 05:53:20 +1200







Hello.

I already installed fftw3. After unpacking it, I install via the following:

./configure
 make
 make install
But after that the instructions are not clear to me. Like, it's not telling 
where do I download Gromacs tar?
Or do I need to type some command from fftw so that Gromacs should 
automatically built?

I'm so confused. The instructions for beginners are very vague & frustrating.

Please help,
Suhaila.



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Re: [gmx-users] Problem installing Gromacs: What next?

[Justin A. Lemkul]

Suhaila Haji Mohd Hussin wrote:

Hello.

I already installed fftw3. After unpacking it, I install via the following:

./configure
 make
 make install


But after that the instructions are not clear to me. Like, it's not 
telling where do I download Gromacs tar?
Or do I need to type some command from fftw so that Gromacs should 
automatically built?




Gromacs uses fftw libraries and headers for certain functions.  You do not need 
to invoke any specific commands from fftw.


I'm so confused. The instructions for beginners are very vague & 
frustrating.




If you have specific feedback for improving the instructions, you're welcome to 
provide it.  The instructions are assembled by users and improved by users. 
We've worked very hard to make sequential instructions available.


-Justin

--


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


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Re: [gmx-users] FW: Problem installing Gromacs: What next?

[Justin A. Lemkul]

Suhaila Haji Mohd Hussin wrote:

OK. I downloaded Gromacs 4.5.5. Unpacked it then type

./configure

configure: error: Cannot find fftw3f library

But I already install fftw3 properly.

What is happening?



The commands below will install double-precision fftw, but Gromacs is single 
precision by default.  The precisions must match.  The proper commands for fftw 
in this case (as noted on 
http://www.gromacs.org/Documentation/Installation_Instructions#Details_for_building_the_FFTW_prerequisite) 
 would be:


./configure --enable-float
make
make install

-Justin


Cheers,
Suhaila.

From: bell_beaut...@hotmail.com
To: gmx-users@gromacs.org
Subject: Problem installing Gromacs: What next?
Date: Mon, 19 Mar 2012 05:53:20 +1200

Hello.

I already installed fftw3. After unpacking it, I install via the following:

./configure
 make
 make install


But after that the instructions are not clear to me. Like, it's not 
telling where do I download Gromacs tar?
Or do I need to type some command from fftw so that Gromacs should 
automatically built?


I'm so confused. The instructions for beginners are very vague & 
frustrating.


Please help,
Suhaila.




--


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


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Re: [gmx-users] FW: Problem installing Gromacs: What next?

[Justin A. Lemkul]

Please be sure to keep the discussion on the mailing list and not my personal 
email.

You may need to specify the location of the fftw installation using LDFLAGS and 
CPPFLAGS for the libraries and headers, respectively.  See example usage at:


http://www.gromacs.org/Documentation/Installation_Instructions#Using_autoconf

-Justin

Suhaila Haji Mohd Hussin wrote:


 > Date: Sun, 18 Mar 2012 14:13:29 -0400
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] FW: Problem installing Gromacs: What next?
 >
 >
 >
 > Suhaila Haji Mohd Hussin wrote:
 > > OK. I downloaded Gromacs 4.5.5. Unpacked it then type
 > >
 > > ./configure
 > >
 > > configure: error: Cannot find fftw3f library
 > >
 > > But I already install fftw3 properly.
 > >
 > > What is happening?
 > >
 >
 > The commands below will install double-precision fftw, but Gromacs is 
single
 > precision by default. The precisions must match. The proper commands 
for fftw

 > in this case (as noted on
 > 
http://www.gromacs.org/Documentation/Installation_Instructions#Details_for_building_the_FFTW_prerequisite) 


 > would be:
 >
 > ./configure --enable-float
 > make
 > make install
 >
 > -Justin
 >
 > > Cheers,
 > > Suhaila.
 > >
 > > From: bell_beaut...@hotmail.com
 > > To: gmx-users@gromacs.org
 > > Subject: Problem installing Gromacs: What next?
 > > Date: Mon, 19 Mar 2012 05:53:20 +1200
 > >
 > > Hello.
 > >
 > > I already installed fftw3. After unpacking it, I install via the 
following:

 > >
 > > ./configure
 > > make
 > > make install
 > >
 > >
 > > But after that the instructions are not clear to me. Like, it's not
 > > telling where do I download Gromacs tar?
 > > Or do I need to type some command from fftw so that Gromacs should
 > > automatically built?
 > >
 > > I'm so confused. The instructions for beginners are very vague &
 > > frustrating.
 > >
 > > Please help,
 > > Suhaila.
 > >
 > >
 >
 > --
 > 
 >
 > Justin A. Lemkul
 > Ph.D. Candidate
 > ICTAS Doctoral Scholar
 > MILES-IGERT Trainee
 > Department of Biochemistry
 > Virginia Tech
 > Blacksburg, VA
 > jalemkul[at]vt.edu | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 > 
 > --
 > gmx-users mailing list gmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to gmx-users-requ...@gromacs.org.
 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

It's still giving me the same error :(

Suhaila.



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] number of coordinates in coordinate file does not match topology

[Acoot Brett]

Dear All,
 
I am practicing the on-line tutorial 
http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/.
 
In the step "mdrun -v -deffnm 1LW9-EM-solvated" of "Energy minimization of the 
solvated system", it says "
Converged to machine precision  , but not to the requested precision Fmax < 1". 
Before this step, all the other steps run fine.
 
In the step "grompp -v -f pr.mdp -c 1LW9-EM-solvated.gro -p 1LW9.top -o 
1LW9-PR.tpr" of "Relaxation of solvent and hydrogen atom positions: Position 
restrained MD", it says "
Fatal error:  number of coordinates in coordinate file (1LW9-EM-solvated.gro, 
32748) does not match topology (1LW9.top, 0)"
 
 
I am looking forward to getting a reply from you on how to what leads to the 
error message.
 
Cheers,
 
Acoot-- 
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Re: [gmx-users] number of coordinates in coordinate file does not match topology

[Justin A. Lemkul]

Acoot Brett wrote:

Dear All,
 
I am practicing the on-line tutorial 
http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/.
 
In the step "mdrun -v -deffnm 1LW9-EM-solvated" of "Energy minimization 
of the solvated system", it says "
Converged to machine precision  , but not to the requested precision 
Fmax < 1". Before this step, all the other steps run fine.
 
In the step "grompp -v -f pr.mdp -c 1LW9-EM-solvated.gro -p 1LW9.top -o 
1LW9-PR.tpr" of "Relaxation of solvent and hydrogen atom positions: 
Position restrained MD", it says "
Fatal error:  number of coordinates in coordinate file 
(1LW9-EM-solvated.gro, 32748) does not match topology (1LW9.top, 0)"
 
 
I am looking forward to getting a reply from you on how to what leads to 
the error message.
 


http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

You need to make sure the contents of the [molecules] directive always matches 
that of the coordinate file, in terms of the number of molecules and the order 
in which they are present.


-Justin

--


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


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RE: [gmx-users] Energy minimization of crystal structure with water

[NG HUI WEN]

Hi Mark,

Thanks - I completely forgot about that!

Cheers,
Huiwen

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Mark Abraham
Sent: Sunday, March 18, 2012 2:03 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy minimization of crystal structure with water

On 18/03/2012 1:01 PM, NG HUI WEN wrote:

Hi all,



I have a seemingly simple task that turned quite tricky here.



I am trying to perform energy minimization on a crystal structure after adding 
hydrogen to the protein using pdb2gmx (OPLS).



The problem I am facing now is that after energy minimization, the protein and 
water (originally in the protein cavity) were found in completely different 
coordinate space. Using "pbc box" in VMD, I found that the water was found 
roughly at the original space but not the protein.



I have tried (all turned out futile)

1) EM with and without pbc

2) position restraint the protein backbone and water



Would someone be able to help me on this? I know I must have done something 
silly here.



This is normal. See 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark
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Fw: [gmx-users] number of coordinates in coordinate file does not match topology

[Acoot Brett]

Dear All,
 
The problem really occurs in the ion addition step.
 
In order to keep 0.1 M ion concentration, 20 Na+ and 20 C1- were added. In 
order to keep 0 charge, 8 Cl- were added.
 
From the .gro file, 48 water (72 H and 48 O) were deleted in order to add the 
38 charges, which makes there was a 96 atom reduction.
 
For the top file, we modify it in the following way, 48 SOLs were deleted, 20 
Na+ were added, and 28 Cl- added.
 
In the above manner, however, it indicated the " number of coordinates in 
coordinate file (1LW9-EM-solvated.gro, 32748) does not match topology 
(1LW9.top)".
 
Thus how do we modify the .gro file and the .top file so that the number of 
coordinated will be equal between them?
 
Cheers,
 
Acoot  


 From: Justin A. Lemkul 
To: Acoot Brett ; Discussion list for GROMACS users 
 
Sent: Monday, 19 March 2012 12:06 PM
Subject: Re: [gmx-users] number of coordinates in coordinate file does not 
match topology 
   


Acoot Brett wrote:
> Dear All,
>  I am practicing the on-line tutorial 
>http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/.
>  In the step "mdrun -v -deffnm 1LW9-EM-solvated" of "Energy minimization of 
>the solvated system", it says "
> Converged to machine precision  , but not to the requested precision Fmax < 
> 1". Before this step, all the other steps run fine.
>  In the step "grompp -v -f pr.mdp -c 1LW9-EM-solvated.gro -p 1LW9.top -o 
>1LW9-PR.tpr" of "Relaxation of solvent and hydrogen atom positions:
 Position restrained MD", it says "
> Fatal error:  number of coordinates in coordinate file (1LW9-EM-solvated.gro, 
> 32748) does not match topology (1LW9.top, 0)"
>   I am looking forward to getting a reply from you on how to what leads to 
>the error message.
>  

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

You need to make sure the contents of the [molecules] directive always matches 
that of the coordinate file, in terms of the number of molecules and the order 
in which they are present.

-Justin

-- 

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

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Re: Fw: [gmx-users] number of coordinates in coordinate file does not match topology

[Tsjerk Wassenaar]

Hi Acoot,

Read the tutorial. It's explained there... Mind that that tutorial was
written for an earlier version of Gromacs and some things have changed. The
names of ions, for instance.

Cheers,

Tsjerk

On Mar 19, 2012 6:40 AM, "Acoot Brett"  wrote:

Dear All,

The problem really occurs in the ion addition step.

In order to keep 0.1 M ion concentration, 20 Na+ and 20 C1- were added. In
order to keep 0 charge, 8 Cl- were added.

>From the .gro file, 48 water (72 H and 48 O) were deleted in order to add
the 38 charges, which makes there was a 96 atom reduction.

For the top file, we modify it in the following way, 48 SOLs were deleted,
20 Na+ were added, and 28 Cl- added.

In the above manner, however, it indicated the " number of coordinates in
coordinate file (1LW9-EM-solvated.gro, 32748) does not match topology
(1LW9.top)".

Thus how do we modify the .gro file and the .top file so that the number of
coordinated will be equal between them?

Cheers,

Acoot

  *From:* Justin A. Lemkul 
*To:* Acoot Brett ; Discussion list for GROMACS users

*Sent:* Monday, 19 March 2012 12:06 PM
*Subject:* Re: [gmx-users] number of coordinates in coordinate file does
not match topology


Acoot Brett wrote: > Dear All, >  I am practicing the on-line tutorial
http://www.nmr.chem.uu.nl...



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