[gmx-users] Re: NAMD simulation in Gromacs

[Roland Schulz]

Oguz,

in case you want to try the psfgen patch, it is now available for download
on our group website at
http://cmb.ornl.gov/resources/developments/top-patch-for-psfgen

Roland

On Thu, Sep 30, 2010 at 7:28 PM, Roland Schulz  wrote:

> Oguz,
>
> On Thu, Sep 30, 2010 at 4:52 PM, oguz gurbulak wrote:
>
>> Dear Dr. Roland Schulz,
>>
>>
>>
>> Thank you very much for your attention. I would like to have a copy of
>> patch that generates gromacs topology from psf file. And could you please
>> explain how to use this patch in detail ? Because I have no information on
>> Pär's scripts.
>>
> Do you have standard CHARMM or Amber FF? Than you don't need to convert the
> FF because it is already part of GROMACS.
>
>
>>
>> I think, In order to continue a NAMD simulation in Gromacs I should first
>> save the last coordinates (.coor file in namd ) as a pdb file and convert it
>> into gro file . But there are many ways to get a gro file
>>
> no you don't need to convert the coordinate file or get the last frame.
>
>>
>>
>> - using pdb2gmx ( but I should choose the force field in gromacs. This may
>> be a problem. ) By the way, I changed CHARMM force field and use Amber type
>> force field in NAMD.
>>
> Don't understand what you mean? Do you use CHARMM or Amber FF? If it is a
> standard molecule (e.g. protein), it will be much easier to just use pdb2gmx
> to generate the topology.
>
>
>> Could you share your ideas about this process ? What should I do ?
>>
> You would just do everything the same way as setting up a new simulation
> and use the last frame as starting structure. Make sure you use a structure
> which includes both coordinates and velocities.
>
>>   Is there a way to get a tpr file from NAMD files?
>>
> No. Not automatically. You need to get all the input files (grompp.mdp,
> topol.top, conf.gro) and then run grompp to generate your tpr.
>
> Roland
>
>>
>>
>>
>>
>> Kind regards.
>>
>>
>>
>>
>>
>> Oguz GURBULAK Ph.D. Student
>> Ege University - Faculty of Science
>> Department of Physics
>> Branch of Atomic and Molecular Physics
>>
>>
>>
>>
>>
>>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
>



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Re: [gmx-users] Another error that keeps comming up.

[Roland Schulz]

After how many steps do you get the error?

Do you get the error also with -dlb yes and
the environment variable GMX_DLB_FLOP set to 1 or 2?

Roland

On Tue, Sep 28, 2010 at 12:54 PM, TJ Mustard  wrote:

>  Found that if I set the setting of "-dlb no" when running the mdrun it
> would not fail. How could dynamic load balancing do this?
>
>
>
> TJ Mustard
>
>
>
> On September 28, 2010 at 3:21 AM TJ Mustard 
> wrote:
>
>  Hey all,
>
>
>
> Here is another error that I keep getting. I am trying to "speed up" my md
> runs with -heavyh and longer time steps. I don't get LINCS errors but I do
> get this...
>
>
>
>
>
>
>
> Back Off! I just backed up prlog.log to ./#prlog.log.1#
> Getting Loaded...
> Reading file monomer_pr.tpr, VERSION 4.5.1 (single precision)
> Starting 2 threads
> Loaded with Money
>
> Making 1D domain decomposition 2 x 1 x 1
>
> Back Off! I just backed up pr.edr to ./#pr.edr.1#
> starting mdrun 'Protein in water'
> 25000 steps,100.0 ps.
> step 900, will finish Mon Sep 27 18:19:07 2010imb F 18%
> NOTE: Turning on dynamic load balancing
>
> step 1600, will finish Mon Sep 27 18:18:42 2010vol 0.92  imb F  1%
> A list of missing interactions:
> LJC Pairs NB of278 missing  1
>   exclusions of   6966 missing  1
>
> ---
> Program g4.5.1-mdrun, VERSION 4.5.1
> Source code file: domdec_top.c, line: 173
>
> Software inconsistency error:
> Some interactions seem to be assigned multiple times
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
>
>
>
>
> Some settings:
>
>
>
> define   = -DPOSRES
>
> dt   = 0.004
> nsteps   = 25000
>
>
>
>
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype  = PME  ; = Cutoff
> rcoulomb-switch  = 0; = 0
> rcoulomb = 0.9  ; = 1
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r= 1; = 1
> epsilon_rf   = 1; = 1
> ; Method for doing Van der Waals
> vdw-type = Cut-off  ; = Cut-off
> ; cut-off lengths
> rvdw-switch  = 0; = 0
> rvdw = 1; = 1
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = No   ; = No
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension  = 1; = 1
> ; Seperate tables between energy group pairs
> energygrp_table  =  ; =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing   = 0.12 ; = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx   = 0; = 0
> fourier_ny   = 0; = 0
> fourier_nz   = 0; = 0
> ; EWALD/PME/PPPM parameters
> pme_order= 6; = 4
> ewald_rtol   = 1e-05; = 1e-05
> ewald_geometry   = 3d   ; = 3d
> epsilon_surface  = 0; = 0
> optimize_fft = yes  ; = no
>
>
>
>
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> tcoupl   = v-rescale; = No
> nsttcouple   = -1   ; = -1
> nh-chain-length  = 10   ; = 10
> ; Groups to couple separately
> tc-grps  = RNA SOL  ; =
> ; Time constant (ps) and reference temperature (K)
> tau-t= 0.1 0.1  ; =
> ref-t= 300 300  ; =
> ; Pressure coupling
> Pcoupl   = Parrinello-Rahman; = No
> Pcoupltype   = Isotropic
> nstpcouple   = -1   ; = -1
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau-p= 1; = 1
> compressibility  = 4.5e-5   ; =
> ref-p= 1.0  ; =
> ; Scaling of reference coordinates, No, All or COM
> refcoord_scaling = No   ; = No
> ; Random seed for Andersen thermostat
> andersen_seed= 815131   ; = 815131
>
>
>
>
>
> gen-vel  = yes  ; = no
> gen-temp = 300  ; = 300
> gen-seed = 173529   ; = 173529
>
>
>
>
>
> constraints  = all-bonds
>
>
>
> Any help would be appreciated. It also seems to be intermittent as I have
> 21 identical runs (with different lambda values) and some work and some
> don't. It also changes every time I run them.
>
> Thank you,
>
> TJ Mustard
> Email: musta...@onid.orst.edu
>
>
>
> TJ Mustard
> Email: musta...@onid.orst.edu
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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[gmx-users] Re: NAMD simulation in Gromacs

[Roland Schulz]

Oguz,

On Thu, Sep 30, 2010 at 4:52 PM, oguz gurbulak wrote:

> Dear Dr. Roland Schulz,
>
>
>
> Thank you very much for your attention. I would like to have a copy of
> patch that generates gromacs topology from psf file. And could you please
> explain how to use this patch in detail ? Because I have no information on
> Pär's scripts.
>
Do you have standard CHARMM or Amber FF? Than you don't need to convert the
FF because it is already part of GROMACS.


>
> I think, In order to continue a NAMD simulation in Gromacs I should first
> save the last coordinates (.coor file in namd ) as a pdb file and convert it
> into gro file . But there are many ways to get a gro file
>
no you don't need to convert the coordinate file or get the last frame.

>
>
> - using pdb2gmx ( but I should choose the force field in gromacs. This may
> be a problem. ) By the way, I changed CHARMM force field and use Amber type
> force field in NAMD.
>
Don't understand what you mean? Do you use CHARMM or Amber FF? If it is a
standard molecule (e.g. protein), it will be much easier to just use pdb2gmx
to generate the topology.


> Could you share your ideas about this process ? What should I do ?
>
You would just do everything the same way as setting up a new simulation and
use the last frame as starting structure. Make sure you use a structure
which includes both coordinates and velocities.

>   Is there a way to get a tpr file from NAMD files?
>
No. Not automatically. You need to get all the input files (grompp.mdp,
topol.top, conf.gro) and then run grompp to generate your tpr.

Roland

>
>
>
>
> Kind regards.
>
>
>
>
>
> Oguz GURBULAK Ph.D. Student
> Ege University - Faculty of Science
> Department of Physics
> Branch of Atomic and Molecular Physics
>
>
>
>
>
>


-- 
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865-241-1537, ORNL PO BOX 2008 MS6309
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RE: [gmx-users] grompp Input/Output Error

[Dallas Warren]

You don't have writing permissions for the directory in which you are
running the script.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Peter Nash
Sent: Friday, 1 October 2010 5:36 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] grompp Input/Output Error

 

Hey, 

I'm a new GROMACS user using 4.5.1... I'm working through whatever
tutorials I can find to learn the program.  I'm having major problems
using grompp... No matter which tutorial I'm working through, when I run
the program to create a .trp file, I get an input/out error message. 

I'm going to use the offical Water demo as an example.  I have the
conf.gro , spc216.pdb, topol.top, and grompp.mdp files in the default
directory.  I run grompp using the following command line from within
the directory with the necessary input files:

/home/[usr]/bin/gromacs/bin/grompp -v -f grompp.mdp -c conf.gro -p
topol.top -o topol_full.tpr 

I've also tried running it without the -v tag... Just to experiment.
When I enter the above command, I get the following output in the
terminal: 




Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Ignoring obsolete mdp entry 'domain-decomposition'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Ignoring obsolete mdp entry 'dihre-tau'
Ignoring obsolete mdp entry 'nstdihreout'
Ignoring obsolete mdp entry 'nstcheckpoint'
Sorry couldn't backup mdpout.mdp to ./#mdout.mdp.1#


Program grompp, VERSION 4.5.1
Source code file: futil.c, line: 459

File input/output error:
mdout.mdp

For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors




I'm not sure why the program is having an issue here since I'm following
the manual exactly. I also get a similar error whenever I try to run
grompp using any other .mdp file as well... No idea what the program is
telling me, either. 

If anyone could give me input on this error, I'd greatly appreciate it.
Thank you! 



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[gmx-users] g_principal outputs

[Payman Pirzadeh]

Hello,

When we calculate the principal axes of protein, for each axis file, there
are 4 columns. The first one is the time (ps), but there are no descriptions
in the files about the rest. A little explanation will be very helpful.

Regards,

 

Payman

 

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Re: [gmx-users] NAMD simulation in Gromacs

[Francesco Oteri]

 Fro the majority of the analisys implemented in gromacs, you don't 
need the tpr, a pdb and the xtc are ok.
If you use the latest gromacs version (4.5.1) you need only the pdb 
because gromacs is able to read each format vmd is able to read.

To enable this feature, you have:
1.Compiling gromacs with the flags "-L/usr/lib -ldl"
2.At runtime setting the VMD_PLUGIN_PATH to the sub-directory molfile of VMD

If you do this, you can do:
trjconv -f trajectpry.dcd -s file.pdb 

and the same with each tools

Regarding conversion,  I think editconf is the bestsolution





Il 30/09/2010 22:57, oguz gurbulak ha scritto:


Dear All,

I think, In order to continue a NAMD simulation in Gromacs I should 
first save the last coordinates (.coor file in namd ) as a pdb file 
and convert it into gro file . But there are many ways to get a gro file


- using pdb2gmx ( but I should choose the force field in gromacs. This 
may be a problem. ) By the way, I changed CHARMM force field and use 
Amber type force field in NAMD.


-using VMD ( but I’m not sure if it works )

-using editconf in gromacs ( if you have the structure in pdb format, 
you can convert it into a .gro file with editconf. Also, the size of 
the box should be specified (in gromacs the length for the vectors a, 
b and c is in nm, not angstrom)


|editconf -f file.pdb -o file.gro -box a b c -angles 90 90 90|

Could you share your ideas about this process ? What should I do ?

Then I should convert the psf file into gromacs top file.

If I get a gro and top file correctly, I can continue NAMD simulation 
in Gromacs. Is it true ?


I examined the gromacs tutorials. And I think I must have a tpr and a 
xtc file to use gromacs analysis tools. I can get a xtc file from NAMD 
dcd file but how can I create a tpr file ? Is there a way to get a tpr 
file from NAMD files?


Kind regards.

--- On *Thu, 9/30/10, Roland Schulz //* wrote:


From: Roland Schulz 
Subject: Re: [gmx-users] NAMD simulation in Gromacs
To: "Discussion list for GROMACS users" 
Date: Thursday, September 30, 2010, 10:13 AM



On Thu, Sep 30, 2010 at 7:55 AM, Mark Abraham
http://us.mc363.mail.yahoo.com/mc/compose?to=mark.abra...@anu.edu.au>>
wrote:



- Original Message -
From: oguz gurbulak http://us.mc363.mail.yahoo.com/mc/compose?to=gurbulako...@yahoo.com>>
Date: Thursday, September 30, 2010 21:38
Subject: [gmx-users] NAMD simulation in Gromacs
To: gmx-users@gromacs.org


> Dear All,

> I performed a 50 ns md simulation using NAMD and want to
continue this simulation for 10 ns in Gromacs. Is it possible
to continue a NAMD simulation in Gromacs ? If so, could you
please give me the information about this process ?


Not really. You would need to generate a .top in the normal
way, and this process cannot use any topology information that
NAMD was using. You could start the GROMACS simulation from
the endpoint of the NAMD simulation, but it would not be
continuous in any sense.


We have a patch to psfgen to generate gromacs topology. We plan to
put this on our website. While it hasn't be uploaded yet, please
write me in case you would like to have a copy. It does convert
the parameter files. We use Pär's scripts to do that part.

Secondly can I convert NAMD output files into gromacs output
files and use gromacs analysis tools ? Could you please also
give me the information about this issue ?

If you have VMD installed then GROMACS is supposed to be able
to link to its libraries to enable GROMACS tools to read any
file format that VMD can read, which will include all NAMD
formats. I'm unaware that anybody has written any
documentation about this, however. That's probably the path of
least resistance.


Yes as long as VMD is installed (and GROMACS is compiled with
DLOPEN support - which is default) all the GROMACS tools
automatically can read most VMD supported format. The exception is
any format which doesn't record the number of atoms (as e.g. Amber).

Roland

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Re: [gmx-users] NAMD simulation in Gromacs

[oguz gurbulak]

Dear All, 
 
I think, In order to continue a NAMD simulation in Gromacs I should first save 
the last coordinates (.coor file in namd ) as a pdb file and convert it into 
gro file . But there are many ways to get a gro file 
 
- using pdb2gmx ( but I should choose the force field in gromacs. This may be a 
problem. ) By the way, I changed CHARMM force field and use Amber type force 
field in NAMD.
 
-using VMD ( but I’m not sure if it works )
 
-using editconf in gromacs ( if you have the structure in pdb format, you can 
convert it into a .gro file with editconf. Also, the size of the box should be 
specified (in gromacs the length for the vectors a, b and c is in nm, not 
angstrom)
 editconf -f file.pdb -o file.gro -box a b c -angles 90 90 90
 
Could you share your ideas about this process ? What should I do ?
 
Then I should convert the psf file into gromacs top file. 
 
If I get a gro and top file correctly, I can continue NAMD simulation in 
Gromacs. Is it true ?
 
I examined the gromacs tutorials. And I think I must have a tpr and a xtc file 
to use gromacs analysis tools. I can get a xtc file from NAMD dcd file but how 
can I create a tpr file ?  Is there a way to get a tpr file from NAMD files? 
 
  
Kind regards.

--- On Thu, 9/30/10, Roland Schulz  wrote:


From: Roland Schulz 
Subject: Re: [gmx-users] NAMD simulation in Gromacs
To: "Discussion list for GROMACS users" 
Date: Thursday, September 30, 2010, 10:13 AM





On Thu, Sep 30, 2010 at 7:55 AM, Mark Abraham  wrote:




- Original Message -
From: oguz gurbulak 
Date: Thursday, September 30, 2010 21:38
Subject: [gmx-users] NAMD simulation in Gromacs
To: gmx-users@gromacs.org







> Dear All,
 
> I performed a 50 ns md simulation using NAMD and want to continue this 
> simulation for 10 ns in Gromacs. Is it possible to continue a NAMD simulation 
> in Gromacs ? If so, could you please give me the information about this 
> process ? 



Not really. You would need to generate a .top in the normal way, and this 
process cannot use any topology information that NAMD was using. You could 
start the GROMACS simulation from the endpoint of the NAMD simulation, but it 
would not be continuous in any sense.



We have a patch to psfgen to generate gromacs topology. We plan to put this on 
our website. While it hasn't be uploaded yet, please write me in case you would 
like to have a copy. It does convert the parameter files. We use Pär's scripts 
to do that part.
 







Secondly can I convert NAMD output files into gromacs output files and use 
gromacs analysis tools ? Could you please also give me the information about 
this issue ?
 
If you have VMD installed then GROMACS is supposed to be able to link to its 
libraries to enable GROMACS tools to read any file format that VMD can read, 
which will include all NAMD formats. I'm unaware that anybody has written any 
documentation about this, however. That's probably the path of least resistance.


Yes as long as VMD is installed (and GROMACS is compiled with DLOPEN support - 
which is default) all the GROMACS tools automatically can read most VMD 
supported format. The exception is any format which doesn't record the number 
of atoms (as e.g. Amber).


Roland
 
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Re: [gmx-users] grompp Input/Output Error

[Justin A. Lemkul]

Peter Nash wrote:

Hey,

I'm a new GROMACS user using 4.5.1... I'm working through whatever 
tutorials I can find to learn the program.  I'm having major problems 
using grompp... No matter which tutorial I'm working through, when I run 
the program to create a .trp file, I get an input/out error message.


I'm going to use the offical Water demo as an example.  I have the 
conf.gro , spc216.pdb, topol.top, and grompp.mdp files in the default 
directory.  I run grompp using the following command line from within 
the directory with the necessary input files:


/home/[usr]/bin/gromacs/bin/grompp -v -f grompp.mdp -c conf.gro -p 
topol.top -o topol_full.tpr


I've also tried running it without the -v tag... Just to experiment.  
When I enter the above command, I get the following output in the terminal:





Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘cpp’
Ignoring obsolete mdp entry ‘domain-decomposition’
Replacing old mdp entry ‘unconstrained-start’ by ‘continuation’
Ignoring obsolete mdp entry ‘dihre-tau’
Ignoring obsolete mdp entry ‘nstdihreout’
Ignoring obsolete mdp entry ‘nstcheckpoint’
Sorry couldn’t backup mdpout.mdp to ./#mdout.mdp.1#


Program grompp, VERSION 4.5.1
Source code file: futil.c, line: 459

File input/output error:
mdout.mdp

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors




I'm not sure why the program is having an issue here since I'm following 
the manual exactly. I also get a similar error whenever I try to run 
grompp using any other .mdp file as well... No idea what the program is 
telling me, either.


If anyone could give me input on this error, I'd greatly appreciate it.  
Thank you!





Looks like you don't have write permissions in the directory where you're 
running grompp.


-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] grompp Input/Output Error

[Peter Nash]

Hey,

I'm a new GROMACS user using 4.5.1... I'm working through whatever tutorials
I can find to learn the program.  I'm having major problems using grompp...
No matter which tutorial I'm working through, when I run the program to
create a .trp file, I get an input/out error message.

I'm going to use the offical Water demo as an example.  I have the conf.gro
, spc216.pdb, topol.top, and grompp.mdp files in the default directory.  I
run grompp using the following command line from within the directory with
the necessary input files:

/home/[usr]/bin/gromacs/bin/grompp -v -f grompp.mdp -c conf.gro -p topol.top
-o topol_full.tpr

I've also tried running it without the -v tag... Just to experiment.  When I
enter the above command, I get the following output in the terminal:




Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘cpp’
Ignoring obsolete mdp entry ‘domain-decomposition’
Replacing old mdp entry ‘unconstrained-start’ by ‘continuation’
Ignoring obsolete mdp entry ‘dihre-tau’
Ignoring obsolete mdp entry ‘nstdihreout’
Ignoring obsolete mdp entry ‘nstcheckpoint’
Sorry couldn’t backup mdpout.mdp to ./#mdout.mdp.1#


Program grompp, VERSION 4.5.1
Source code file: futil.c, line: 459

File input/output error:
mdout.mdp

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors




I'm not sure why the program is having an issue here since I'm following the
manual exactly. I also get a similar error whenever I try to run grompp
using any other .mdp file as well... No idea what the program is telling me,
either.

If anyone could give me input on this error, I'd greatly appreciate it.
Thank you!
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Re: [gmx-users] viscosity calculation_2

[David van der Spoel]

On 2010-09-30 19.36, Payman Pirzadeh wrote:

It does not explain for all files or all columns. For example, in the
evisco.xvg, the following lines are written, but there are 5 columns (one of
which is time). What are the rest? And the unit of the column (written
below) is not clear to me.
@title "Shear viscosity using Einstein relation"
@xaxis  label "Time (ps)"
@yaxis  label "(kg m\S-1\N s\S-1\N)"

Same column are in the eviscoi.xvg (below).
@title "Shear viscosity integral"
@xaxis  label "Time (ps)"
@yaxis  label "(kg m\S-1\N s\S-1\N ps)"

I do not exactly know the relation between the two files and how I should
use them. Also, the enecorr.xvg looks like to be a correlation function. But
its unit is not clear and I do not know how to use it.
I will be appreciated if you could clarify them.
Regards,


I recommend that you read the paper by Hess (JCP 2002) about viscosity.


Payman

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Dallas Warren
Sent: September 29, 2010 7:11 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] viscosity calculation_2

Sorry, haven't looked at these files before so this might not be the
case, but doesn't the top of the .xvg file explain what each column is?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.



--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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RE: [gmx-users] viscosity calculation_2

[Payman Pirzadeh]

It does not explain for all files or all columns. For example, in the
evisco.xvg, the following lines are written, but there are 5 columns (one of
which is time). What are the rest? And the unit of the column (written
below) is not clear to me. 
@title "Shear viscosity using Einstein relation"
@xaxis  label "Time (ps)"
@yaxis  label "(kg m\S-1\N s\S-1\N)"

Same column are in the eviscoi.xvg (below). 
@title "Shear viscosity integral"
@xaxis  label "Time (ps)"
@yaxis  label "(kg m\S-1\N s\S-1\N ps)"

I do not exactly know the relation between the two files and how I should
use them. Also, the enecorr.xvg looks like to be a correlation function. But
its unit is not clear and I do not know how to use it.
I will be appreciated if you could clarify them.
Regards,

Payman

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Dallas Warren
Sent: September 29, 2010 7:11 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] viscosity calculation_2

Sorry, haven't looked at these files before so this might not be the
case, but doesn't the top of the .xvg file explain what each column is?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] gromacs (4.5) installation problem

[Justin A. Lemkul]

Moeed wrote:

Dear experts,

I have installed newest version of gromacs (4.5) on our cluster. When I
issue the command below to test installation I get an error about atom type
CU+2. I am not using such atom type at all! Could you please help me what
wrong is. Thanks.

My system contains only C and H atoms!. Force field: OPLSAA


grompp -f *.mdp -c *.gro -p *.top -o out >& output.grompp_md

NOTE 1 [file md-NVT-revised.mdp]:
 nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
 nstcomm to nstcalcenergy

Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations

---
Program grompp, VERSION 4.5
Source code file: toppush.c, line: 1166

Fatal error:
Atomtype CU2+ not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors






This is probably a bug that has already been fixed, but is only available in the 
git repository.  The fix is to change the capitalization of both CU2+ and ZN2+ 
in oplsaa.ff/ions.itp.  They should be Cu2+ and Zn2+, respectively.  Otherwise, 
don't #include "ions.itp" in your topology if you don't need it.


-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] g_hbond segmentation fault

[Justin A. Lemkul]

Yao Yao wrote:



Hi Gmxers,

Sorry, Eric and David,

I cannot transfer my trr file to report a bug because of its huge size.
It is just a regular protein with 70 Angstrom cubic TIP5P water box
in Charmm27 force field. That's all of the system.



Then simplify the problem.  Do you get the same result when processing a single 
.gro or .pdb file?  What about a shorter .trr file, containing only a few 
frames?  If the same problem persists, then you can file a bug report with files 
that are significantly smaller.



But anyway, i included the mdp file in the attachment.



This doesn't indicate any obvious problem.

-Justin


Hopefully someone can help me.

Many thanks,

Yao 





--- On Wed, 9/29/10, Erik Marklund > wrote:

 > From: Erik Marklund >
 > Subject: Re: [gmx-users] g_hbond segmentation fault
 > To: "Discussion list for GROMACS users" >
 > Date: Wednesday, September 29, 2010, 7:55 AM
 >
 >
 >   
 >
 > 
 >   
 >   
 > Hi,

 >
 > 
 >

 > Could you file a bugzilla and attach the trr and tpr
 > files please?
 > If you do I'll try to sort it out today or at least
 > this week.
 >
 > 
 >

 > Erik
 >
 > 
 >

 > Yao Yao skrev 2010-09-29 08.22:
 > 
 >   
 > 
 >   
 > 
 >   
 >
 >   
 >   
 >
 >   
 >   I tried without -dt or -e, still the same

 > problem exists
 >   in either case.
 >   
 >
 >   
 >   Thanks,
 >   
 >
 >   
 >   Yao

 >
 > 
 >

 > --- On Wed, 9/29/10, David van der Spoel
 > >
 > wrote:
 >
 > 
 >

 >   From: David van der Spoel >
 >
 >   Subject: Re: [gmx-users] g_hbond
 > segmentation fault
 >
 >   To: "Discussion list for GROMACS
 > users"
 >   >
 >
 >   Date: Wednesday, September 29, 2010, 6:11
 > AM
 >
 >   
 >

 >   On
 > 2010-09-29 08.02, Yao Yao
 > wrote:
 >
 > > Hi Gmxers,
 >
 > >
 >
 > > I used the command line,
 >
 > >
 >
 > > g_hbond -f tst.trr -s tst.tpr -ac
 > test -e 500
 > -dt 1
 >
 > >
 >
 > > and I got the message like,
 >
 > >
 >
 > try without the -dt 1
 >
 > 
 >

 > >
 > --
 >
 > > Found 1048 different hydrogen
 > bonds in
 > trajectory
 >
 > > Found 2292 different atom-pairs
 > within hydrogen
 > bonding distance
 >
 > > Merging hbonds with Acceptor and
 > Donor swapped
 >
 > > 2/10915 *Segmentation fault*
 >
 > >
 > __
 >
 > >
 >
 > > Anyone knows what could be the
 > reason for this
 > Segmentation Fault ?
 >
 > >
 >
 > > A couple of Q's I am also
 > curious,
 >
 > >
 >
 > > why do we need to swap Acceptors
 > and Acceptors
 > when merging hbonds?
 >
 > >
 >
 > > Does gromacs suggest that the
 > number of
 > different hydrogen bonds in
 >
 > > trajectory
 >
 > > should be the same as that of
 > different
 > atom-pairs within hydrogen
 >
 > > bonding distance?
 >
 > >
 >
 > > Thanks,
 >
 > >
 >
 > > Yao
 >
 > >
 >
 > >
 >
 > >
 >
 > 
 >
 > 
 >

 > --
 >
 > David van der Spoel, Ph.D., Professor
 > of Biology
 >
 > Dept. of Cell & Molec. Biol.,
 > Uppsala
 >  

Re: [gmx-users] Usage of new features in 4.5.1

[Roland Schulz]

On Thu, Sep 30, 2010 at 12:31 PM, Francesco Oteri  wrote:

>  Problem solved,
> I've recompiled gromacs with option adding "-L/usr/lib -ldl" and after
> setting the VMD_PLUGIN_PATH environment variable
> gromacs works.
>

Glad that it works. But odd that you had to recompile. configure/cmake
should have automatically figured out that it requires "-ldl". Could you
send me your config.log (if you use configure) or your  CMakeCache.txt (if
you use cmake) of the gromacs versin without "-L/usr/lib -ldl"? Then I can
check why it didn't work automatically.

Roland

>
>
>
> On 30/09/2010 16:03, Roland Schulz wrote:
>
> Hi,
>
>  Do you get any other messages before that last message? It might tell you
> that you have to set the VMD_PLUGIN_PATH.
>
>  GROMACS has to be compiled with dlopen support for this to work. Did you
> compile with cmake or configure? Could you please look into the config.h and
> see whether GMX_DLOPEN is set?
>
>  Roland
>
> On Thu, Sep 30, 2010 at 9:30 AM, Francesco Oteri <
> francesco.ot...@gmail.com> wrote:
>
>> Dear all,
>> I would like to know how to analyze dcd trajectory in gromacs.
>> I successfully installed gromacs, but if I use
>>
>>
>> trjconv -f neck.dcd -s ../neck_model.pdb  -o next.xtc
>>
>> I obtain the following error:
>>
>>
>> Fatal error:
>> Not supported in read_first_frame: neck.dcd
>>
>>
>>
>> Any suggestion?
>>
>> --
>> gmx-users mailing listgmx-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
>>
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>



-- 
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865-241-1537, ORNL PO BOX 2008 MS6309
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Re: Re: [gmx-users] Free Energy Calculation

[Петр Попов]

>> Hello, dear users!
>>
>> I want to study different components in total free energy.
>> Could you tell me in what gromacs program and in what place exactly force
and energy are calculated?

>I think your question is too general. I don't know whether you've already
done a calculation, are planning one, or want to look at source code. Please
ask a more specific question.
>
>Mark

I've already run md and I've got a pmf. Bun I want to split this pmf into
several, each of which corresponds to different components of total force or
energy. So I want to look at source code and try to change them or is
another way to do this?

Petr.
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[gmx-users] gromacs (4.5) installation problem

[Moeed]

Dear experts,

I have installed newest version of gromacs (4.5) on our cluster. When I
issue the command below to test installation I get an error about atom type
CU+2. I am not using such atom type at all! Could you please help me what
wrong is. Thanks.

My system contains only C and H atoms!. Force field: OPLSAA


grompp -f *.mdp -c *.gro -p *.top -o out >& output.grompp_md

NOTE 1 [file md-NVT-revised.mdp]:
 nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
 nstcomm to nstcalcenergy

Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations

---
Program grompp, VERSION 4.5
Source code file: toppush.c, line: 1166

Fatal error:
Atomtype CU2+ not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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Re: [gmx-users] Usage of new features in 4.5.1

[Francesco Oteri]

Problem solved,
I've recompiled gromacs with option adding "-L/usr/lib -ldl" and after 
setting the VMD_PLUGIN_PATH environment variable

gromacs works.



On 30/09/2010 16:03, Roland Schulz wrote:

Hi,

Do you get any other messages before that last message? It might tell 
you that you have to set the VMD_PLUGIN_PATH.


GROMACS has to be compiled with dlopen support for this to work. Did 
you compile with cmake or configure? Could you please look into the 
config.h and see whether GMX_DLOPEN is set?


Roland

On Thu, Sep 30, 2010 at 9:30 AM, Francesco Oteri 
mailto:francesco.ot...@gmail.com>> wrote:


Dear all,
I would like to know how to analyze dcd trajectory in gromacs.
I successfully installed gromacs, but if I use


trjconv -f neck.dcd -s ../neck_model.pdb  -o next.xtc

I obtain the following error:


Fatal error:
Not supported in read_first_frame: neck.dcd



Any suggestion?

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--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 
865-241-1537, ORNL PO BOX 2008 MS6309


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[gmx-users] g_hbond segmentation fault

[Yao Yao]

Hi Gmxers,

Sorry, Eric and David, 

I cannot transfer my trr file to report a bug because of its huge size.
It is just a regular protein with 70 Angstrom cubic TIP5P water box in Charmm27 
force field. That's all of the system.

But anyway, i included the mdp file in the attachment.

Hopefully someone can help me.

Many thanks,

Yao  




--- On Wed, 9/29/10, Erik Marklund  wrote:

> From: Erik Marklund 
> Subject: Re: [gmx-users] g_hbond segmentation fault
> To: "Discussion list for GROMACS users" 
> Date: Wednesday, September 29, 2010, 7:55 AM
> 
> 
>   
> 
>     
>   
>   
>     Hi,
> 
>     
> 
>     Could you file a bugzilla and attach the trr and tpr
> files please?
>     If you do I'll try to sort it out today or at least
> this week.
> 
>     
> 
>     Erik
> 
>     
> 
>     Yao Yao skrev 2010-09-29 08.22:
>     
>       
>         
>           
>             
>               
> 
>               
>               
> 
>               
>               I tried without -dt or -e, still the same
> problem exists
>               in either case.
>               
> 
>               
>               Thanks,
>               
> 
>               
>               Yao
> 
>                 
> 
>                 --- On Wed, 9/29/10, David van der Spoel
> 
>                 wrote:
> 
>                 
> 
>                   From: David van der Spoel 
> 
>                   Subject: Re: [gmx-users] g_hbond
> segmentation fault
> 
>                   To: "Discussion list for GROMACS
> users"
>                   
> 
>                   Date: Wednesday, September 29, 2010, 6:11
> AM
> 
>                   
> 
>                   On
> 2010-09-29 08.02, Yao Yao
>                     wrote:
> 
>                     > Hi Gmxers,
> 
>                     >
> 
>                     > I used the command line,
> 
>                     >
> 
>                     > g_hbond -f tst.trr -s tst.tpr -ac
> test -e 500
>                     -dt 1
> 
>                     >
> 
>                     > and I got the message like,
> 
>                     >
> 
>                     try without the -dt 1
> 
>                     
> 
>                     >
> --
> 
>                     > Found 1048 different hydrogen
> bonds in
>                     trajectory
> 
>                     > Found 2292 different atom-pairs
> within hydrogen
>                     bonding distance
> 
>                     > Merging hbonds with Acceptor and
> Donor swapped
> 
>                     > 2/10915 *Segmentation fault*
> 
>                     >
> __
> 
>                     >
> 
>                     > Anyone knows what could be the
> reason for this
>                     Segmentation Fault ?
> 
>                     >
> 
>                     > A couple of Q's I am also
> curious,
> 
>                     >
> 
>                     > why do we need to swap Acceptors
> and Acceptors
>                     when merging hbonds?
> 
>                     >
> 
>                     > Does gromacs suggest that the
> number of
>                     different hydrogen bonds in
> 
>                     > trajectory
> 
>                     > should be the same as that of
> different
>                     atom-pairs within hydrogen
> 
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Re: [gmx-users] RE: Error in mdrun

[Justin A. Lemkul]

Nimesh Jain wrote:

Hi,

I keep getting the following error when I do mdrun:

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.

I moved the particles sufficiently apart so that there are no overlaps. 
I still get this error. Can someone tell me what else can I do?


Please let me know if you need any other info.



An .mdp file, a description of your system, and a list of commands that shows 
how you built it would be required to get any useful advice.  Otherwise, the 
standard advice is (as always) found here:


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Troubleshooting tips are listed there.

-Justin


Thanks,
Nimesh



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] NAMD simulation in Gromacs

[Roland Schulz]

On Thu, Sep 30, 2010 at 7:55 AM, Mark Abraham wrote:

>
>
> - Original Message -
> From: oguz gurbulak 
> Date: Thursday, September 30, 2010 21:38
> Subject: [gmx-users] NAMD simulation in Gromacs
> To: gmx-users@gromacs.org
>
>  > Dear All,
>
>
>
> > I performed a 50 ns md simulation using NAMD and want to continue this
> simulation for 10 ns in Gromacs. Is it possible to continue a NAMD
> simulation in Gromacs ? If so, could you please give me the information
> about this process ?
>
>
> Not really. You would need to generate a .top in the normal way, and this
> process cannot use any topology information that NAMD was using. You could
> start the GROMACS simulation from the endpoint of the NAMD simulation, but
> it would not be continuous in any sense.
>

We have a patch to psfgen to generate gromacs topology. We plan to put this
on our website. While it hasn't be uploaded yet, please write me in case you
would like to have a copy. It does convert the parameter files. We use Pär's
scripts to do that part.


>  Secondly can I convert NAMD output files into gromacs output files and
> use gromacs analysis tools ? Could you please also give me the information
> about this issue ?
>
>
>
> If you have VMD installed then GROMACS is supposed to be able to link to
> its libraries to enable GROMACS tools to read any file format that VMD can
> read, which will include all NAMD formats. I'm unaware that anybody has
> written any documentation about this, however. That's probably the path of
> least resistance.
>

Yes as long as VMD is installed (and GROMACS is compiled with DLOPEN support
- which is default) all the GROMACS tools automatically can read most VMD
supported format. The exception is any format which doesn't record the
number of atoms (as e.g. Amber).

Roland
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[gmx-users] RE: Error in mdrun

[Nimesh Jain]

Hi,

I keep getting the following error when I do mdrun:

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.

I moved the particles sufficiently apart so that there are no overlaps. I
still get this error. Can someone tell me what else can I do?

Please let me know if you need any other info.

Thanks,
Nimesh
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Re: [gmx-users] NAMD simulation in Gromacs

[André Farias de Moura]

I have never tried it myself, but Wordom should be able to convert between
dcd and xtc file formats, take a look at
http://www.biochem-caflisch.unizh.ch/wordom/Home

I hope it helps.

best regards

Andre

On Thu, Sep 30, 2010 at 8:55 AM, Mark Abraham wrote:

>
>
> - Original Message -
> From: oguz gurbulak 
> Date: Thursday, September 30, 2010 21:38
> Subject: [gmx-users] NAMD simulation in Gromacs
> To: gmx-users@gromacs.org
>
> > Dear All,
>
>
>
> > I performed a 50 ns md simulation using NAMD and want to continue this
> simulation for 10 ns in Gromacs. Is it possible to continue a NAMD
> simulation in Gromacs ? If so, could you please give me the information
> about this process ?
>
>
> Not really. You would need to generate a .top in the normal way, and this
> process cannot use any topology information that NAMD was using. You could
> start the GROMACS simulation from the endpoint of the NAMD simulation, but
> it would not be continuous in any sense.
>
>
>
> Secondly can I convert NAMD output files into gromacs output files and use
> gromacs analysis tools ? Could you please also give me the information about
> this issue ?
>
>
>
> If you have VMD installed then GROMACS is supposed to be able to link to
> its libraries to enable GROMACS tools to read any file format that VMD can
> read, which will include all NAMD formats. I'm unaware that anybody has
> written any documentation about this, however. That's probably the path of
> least resistance.
>
>
> Mark
>
> --
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Re: [gmx-users] Usage of new features in 4.5.1

[Roland Schulz]

Hi,

Do you get any other messages before that last message? It might tell you
that you have to set the VMD_PLUGIN_PATH.

GROMACS has to be compiled with dlopen support for this to work. Did you
compile with cmake or configure? Could you please look into the config.h and
see whether GMX_DLOPEN is set?

Roland

On Thu, Sep 30, 2010 at 9:30 AM, Francesco Oteri
wrote:

>  Dear all,
> I would like to know how to analyze dcd trajectory in gromacs.
> I successfully installed gromacs, but if I use
>
>
> trjconv -f neck.dcd -s ../neck_model.pdb  -o next.xtc
>
> I obtain the following error:
>
>
> Fatal error:
> Not supported in read_first_frame: neck.dcd
>
>
>
> Any suggestion?
>
> --
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[gmx-users] Usage of new features in 4.5.1

[Francesco Oteri]

Dear all,
I would like to know how to analyze dcd trajectory in gromacs.
I successfully installed gromacs, but if I use


trjconv -f neck.dcd -s ../neck_model.pdb  -o next.xtc

I obtain the following error:


Fatal error:
Not supported in read_first_frame: neck.dcd



Any suggestion?
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Re: [gmx-users] Free Energy Calculation

[Mark Abraham]

- Original Message -
From: Петр Попов 
Date: Thursday, September 30, 2010 22:39
Subject: [gmx-users] Free Energy Calculation
To: gmx-users@gromacs.org

> Hello, dear users!
> 
> I want to study different components in total free energy.
> Could you tell me in what gromacs program and in what place exactly force and 
> energy are calculated?

I think your question is too general. I don't know whether you've already done 
a calculation, are planning one, or want to look at source code. Please ask a 
more specific question.

Mark

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[gmx-users] Free Energy Calculation

[Петр Попов]

Hello, dear users!

I want to study different components in total free energy.
Could you tell me in what gromacs program and in what place exactly force
and energy are calculated?

With best regards!
Popov Petr
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[gmx-users] RE : gmx-users Digest, Vol 77 , Issue 201

[ABEL Stephane 175950]

OK Mark and Justin, thank you for the pointer
 
I will take a look about it
 
A bientot
 
Stephane
 
--
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CEA Saclay DSV/IBITEC-S/SB2SM
91191 Saclay, FRANCE
website: http://www.st-abel.com
--



De: gmx-users-boun...@gromacs.org de la part de gmx-users-requ...@gromacs.org
Date: jeu. 30/09/2010 13:56
À: gmx-users@gromacs.org
Objet : gmx-users Digest, Vol 77, Issue 201



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Today's Topics:

   1. Re: Re: Error : There is no domain decomposition for 
  (Mark Abraham)
   2. Re: NAMD simulation in Gromacs (Mark Abraham)


--

Message: 1
Date: Thu, 30 Sep 2010 21:48:05 +1000
From: Mark Abraham 
Subject: Re: [gmx-users] Re: Error : There is no domain decomposition
for 
To: Discussion list for GROMACS users 
Message-ID: 
Content-Type: text/plain; charset="us-ascii"



- Original Message -
From: ABEL Stephane 175950 
Date: Thursday, September 30, 2010 21:43
Subject: [gmx-users] Re: Error : There is no domain decomposition for 
To: gmx-users@gromacs.org

> Mark,
> 
> These long range parameters have been used by Bjelkmar et
> al.  in their recent paper [1]for simulations of CHARMM ff
> in GROMACS. So I use it !
> 
> [1] Bjelkmar, P., P. Larsson, et al. (2010). "Implementation of
> the CHARMM Force Field in GROMACS: Analysis of Protein Stability
> Effects from Correction Maps, Virtual Interaction Sites, and
> Water Models." J. Chem. Theory Comput. 6(2): 459-466.

I'm not questioning any .mdp file settings. However the combination of topology 
and initial coordinates contains some kind of bonded interaction between atoms 
that are much further apart than you would normally suppose. You should explore 
what is going on there.

Mark

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Message: 2
Date: Thu, 30 Sep 2010 21:55:04 +1000
From: Mark Abraham 
Subject: Re: [gmx-users] NAMD simulation in Gromacs
To: Discussion list for GROMACS users 
Message-ID: 
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- Original Message -
From: oguz gurbulak 
Date: Thursday, September 30, 2010 21:38
Subject: [gmx-users] NAMD simulation in Gromacs
To: gmx-users@gromacs.org

---
|   > Dear All,
  
  > I performed a 50 ns md simulation using NAMD and want to continue this 
simulation for 10 ns in Gromacs. Is it possible to continue a NAMD simulation 
in Gromacs ? If so, could you please give me the information about this process 
?



Not really. You would need to generate a .top in the normal way, and this 
process cannot use any topology information that NAMD was using. You could 
start the GROMACS simulation from the endpoint of the NAMD simulation, but it 
would not be continuous in any sense.

  
  Secondly can I convert NAMD output files into gromacs output files and use 
gromacs analysis tools ? Could you please also give me the information about 
this issue ?
  
If you have VMD installed then GROMACS is supposed to be able to link to its 
libraries to enable GROMACS tools to read any file format that VMD can read, 
which will include all NAMD formats. I'm unaware that anybody has written any 
documentation about this, however. That's probably the path of least resistance.


Mark

 |
---

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End of gmx-users Digest, Vol 77, Issue 201
**


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[gmx-users] Re: gromacs

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing the message to the list; please continue any 
future discussion there.


See comments below.

Miroslawa aleksandrowa wrote:

Dear Justin, My name is Miroslava Nedyalkova from Sofia University, Bulgaria.
I am usuing GROMACS since 6 months. I think that is really great program ,but
I have some problems :( I want to ask you for help, my problems are force
field. Till now I was make calculations with methane sphere with Na and Ca2+
ions with different concentrations of ions, I do this investigation with goal
to study overcharging procession on the methane sphere surface . But now the
problem :) I want to study process with overcharging with 3+ ions, like Fe.
To this moment with Na and Ca 2+ ions I used G4a13 ans SPC model for water.
My question is what do you thing for  using OPLS-AA for 3+ ions? How can I
convert the parameters of Na and Ca from the opls to the standard gromacs
force-field ? Please help me if you can :) Mira



Dealing with transition metals is a complicated question.  See here:

http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

I have no idea whether or not suitable parameters exist within OPLS-AA for any 
of these 3+ species.


Also realize that the task of "converting parameters" for Na+ and Ca2+ is not 
one you should undertake.  All Gromacs force fields, as far as I know, contain 
parameters for these two ions.  Thus you should not try to port any parameters 
from one force field to another, for reasons explained on the Parameterization 
page linked above.  Force fields should not be mixed or manipulated.  Further 
(just FYI), there is no such thing as a "standard Gromacs force field."  Please 
see the manual for the reasons why this statement is incorrect.


If you started your project with a Gromos96 force field, and are now realizing 
that OPLS-AA may be the better choice, you should start over, appreciating now 
that force field choice is something that should be researched in-depth before 
starting a project, not mid-stream.


-Justin


--


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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] NAMD simulation in Gromacs

[Mark Abraham]

- Original Message -
From: oguz gurbulak 
Date: Thursday, September 30, 2010 21:38
Subject: [gmx-users] NAMD simulation in Gromacs
To: gmx-users@gromacs.org

---
|   > Dear All,
   
  > I performed a 50 ns md simulation using NAMD and want to continue this 
simulation for 10 ns in Gromacs. Is it possible to continue a NAMD simulation 
in Gromacs ? If so, could you please give me the information about this process 
? 



Not really. You would need to generate a .top in the normal way, and this 
process cannot use any topology information that NAMD was using. You could 
start the GROMACS simulation from the endpoint of the NAMD simulation, but it 
would not be continuous in any sense.

   
  Secondly can I convert NAMD output files into gromacs output files and use 
gromacs analysis tools ? Could you please also give me the information about 
this issue ?
   
If you have VMD installed then GROMACS is supposed to be able to link to its 
libraries to enable GROMACS tools to read any file format that VMD can read, 
which will include all NAMD formats. I'm unaware that anybody has written any 
documentation about this, however. That's probably the path of least resistance.


Mark

 |
---

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Re: [gmx-users] Re: Error : There is no domain decomposition for ....

[Mark Abraham]

- Original Message -
From: ABEL Stephane 175950 
Date: Thursday, September 30, 2010 21:43
Subject: [gmx-users] Re: Error : There is no domain decomposition for 
To: gmx-users@gromacs.org

> Mark, 
>  
> These long range parameters have been used by Bjelkmar et 
> al.  in their recent paper [1]for simulations of CHARMM ff 
> in GROMACS. So I use it ! 
>  
> [1] Bjelkmar, P., P. Larsson, et al. (2010). "Implementation of 
> the CHARMM Force Field in GROMACS: Analysis of Protein Stability 
> Effects from Correction Maps, Virtual Interaction Sites, and 
> Water Models." J. Chem. Theory Comput. 6(2): 459-466.

I'm not questioning any .mdp file settings. However the combination of topology 
and initial coordinates contains some kind of bonded interaction between atoms 
that are much further apart than you would normally suppose. You should explore 
what is going on there.

Mark

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[gmx-users] Re: Error : There is no domain decomposition for ....

[ABEL Stephane 175950]

g 
> hMRP1_K-TM17_bDM_h2o_Cl_md.log
>
> -- error
>
> Initializing Domain Decomposition on 4 nodes
>
> Dynamic load balancing: auto
>
> Will sort the charge groups at every domain (re)decomposition
>
> Initial maximum inter charge-group distances:
>
> two-body bonded interactions: 6.729 nm, LJ-14, atoms 11100 11107
>
> multi-body bonded interactions: 6.729 nm, U-B, atoms 11100 11106
>
> Minimum cell size due to bonded interactions: 7.402 nm
>
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm
>
> Estimated maximum distance required for P-LINCS: 0.819 nm
>
> Using 0 separate PME nodes
>
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>
> Optimizing the DD grid for 4 cells with a minimum initial size of 9.252 nm
>
> The maximum allowed number of cells is: X 0 Y 0 Z 0
>
> ---
>
> Program mdrun_mpi, VERSION 4.5.1
>
> Source code file: domdec.c, line: 6428
>
> Fatal error:
>
> There is no domain decomposition for 4 nodes that is compatible with the 
> given box and a minimum cell size of 9.25216 nm
>
> Change the number of nodes or mdrun option -rdd or -dds
>
> Look in the log file for details on the domain decomposition
>
> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors 
> <http://www.gromacs.org/Documentation/Errors> 
>
> ---
>
> "Player Sleeps With the Fishes" (Ein Bekanntes Spiel Von ID Software)
>
> I have also checked the mimized structure at different minimization step, and 
> I saw no problems.
>
> I don't know what is problem here. Could you help me ?
>

http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm
 
<http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm>
 

-Justin

> Thank you in advance for your advices and comments.
>
> Stephane
>

--


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 
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> 




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Message: 2
Date: Thu, 30 Sep 2010 21:27:11 +1000
From: Mark Abraham 
Subject: Re: [gmx-users] Error : There is no domain decomposition for
To: Discussion list for GROMACS users 
Message-ID: 
Content-Type: text/plain; charset="us-ascii"



- Original Message -
From: ABEL Stephane 175950 
Date: Thursday, September 30, 2010 21:21
Subject: [gmx-users] Error : There is no domain decomposition for
To: gmx-users@gromacs.org

> Yeah Justin, I have already read the comments related to the
> link before to post in the mailing list. But I don't know how to
> correct this ?
> 
> Increase/decrease the number of node or CPU ?

No, you should address the underlying issue. You have a very long-range 
interaction. What is it, and why?

> Initial maximum inter charge-group distances:
>
> two-body bonded interactions: 6.729 nm, LJ-14, atoms 11100 11107
>
> multi-body bonded interactions: 6.729 nm, U-B, atoms 11100 11106
>
> Minimum cell size due to bonded interactions: 7.402 nm

Mark


> 
> Thank you again for your help
> 
> Stephane 
>
> ABEL Stephane 175950 wrote:
> > Dear All,
> >
> > I am trying to do a MD of a system containing TIP3P water, a
> peptide, some glycolipids molecule and ions in a cubic box. The
> forcefield used is CHARMM and are taken from previous MD. The
> bonded and nonbonded parameters was converted in GROMACS
> manually because some parameters are not in present in current
> GMX (v 4.5.1) distribution.
> >
> > I have minimized successfully the system. see below
> >
> >  em.mdp ---
> >
> > title = bDM+KTM17 in water
> >
> > ; Preprocessor - specify a full path if necessary.
> >
> > cpp = cpp
> >
> > include = -I../top
> >
> > d

[gmx-users] NAMD simulation in Gromacs

[oguz gurbulak]

Dear All,

 

I performed a 50 ns md simulation
using NAMD and want to continue this simulation for 10 ns in Gromacs. Is it
possible to continue a NAMD simulation in Gromacs ? If so, could you please
give me the information about this process ? 

 

Secondly can I convert NAMD
output files into gromacs output files and use gromacs analysis tools ? Could
you please also give me the information about this issue ?

 

Thank you very much for your attention.

 

Kind regards.

 




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Re: [gmx-users] Error : There is no domain decomposition for

[Justin A. Lemkul]

ABEL Stephane 175950 wrote:
Yeah Justin, I have already read the comments related to the link before to post in the mailing list. But I don't know how to correct this ? 
 
Increase/decrease the number of node or CPU ? 
 


If you can't meet a minimum cell size with 4 processors, then you certainly 
won't be able to meet this requirement by trying to further subdivide the 
system.  It seems to me like something is going wrong here:


two-body bonded interactions: 6.729 nm, LJ-14, atoms 11100 11107

multi-body bonded interactions: 6.729 nm, U-B, atoms 11100 11106

It looks like these species are incredibly far apart, almost as if the starting 
geometry is incorrect.  Normally these values should be on the order of 10 times 
lower.  Did you do all of your parameter conversions correctly (i.e, Angstrom -> 
nm)?


-Justin


Thank you again for your help
 
Stephane  


ABEL Stephane 175950 wrote:

Dear All,

I am trying to do a MD of a system containing TIP3P water, a peptide, some 
glycolipids molecule and ions in a cubic box. The forcefield used is CHARMM and 
are taken from previous MD. The bonded and nonbonded parameters was converted 
in GROMACS manually because some parameters are not in present in current GMX 
(v 4.5.1) distribution.

I have minimized successfully the system. see below

 em.mdp ---

title = bDM+KTM17 in water

; Preprocessor - specify a full path if necessary.

cpp = cpp

include = -I../top

define = -DFLEXIBLE

integrator = steep

nstcgsteep = 5000

emstep = 0.01

emtol = 500.0

;dt = 0.002

pbc = xyz

nsteps = 5000

nstlist = 5

ns_type = grid

rlist = 1.2

coulombtype = PME

rcoulomb = 1.2

rvdw = 1.2

fourierspacing = 0.12

pme_order = 4

ewald_rtol = 1e-05

optimize_fft = yes

---

 Final results of energy minimization process

Energies (kJ/mol)

Bond Angle U-B Proper Dih. Improper Dih.

3.58212e+04 1.88051e+04 6.00353e+03 3.58404e+04 7.30187e+00

CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR)

-1.39601e+02 1.11718e+04 1.76772e+05 1.66576e+05 -1.30112e+06

Coul. recip. Potential Pressure (bar)

-1.17090e+05 -9.67347e+05 0.0e+00

Steepest Descents converged to Fmax < 500 in 107 steps

Potential Energy = -9.67347283476003e+05

Maximum force = 4.75153618041724e+02 on atom 313

Norm of force = 9.37591893853129e+00

But when i try to equilibrate this system in NVT ensemble for 100 ps with the 
md.mdp below

 nvt.mdp ---

title = KTM17-bDM MD

;define = -DPOSRES ; position restrain the protein

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 5 ; 2 * 5 = 100 ps

dt = 0.002 ; 2 fs

; Output control

nstxout = 100 ; save coordinates every 0.2 ps

nstvout = 100 ; save velocities every 0.2 ps

nstenergy = 100 ; save energies every 0.2 ps

nstlog = 100 ; update log file every 0.2 ps

; Bond parameters

continuation = no ; first dynamics run

constraint_algorithm = lincs ; holonomic constraints

constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained

lincs_iter = 1 ; accuracy of LINCS

lincs_order = 4 ; also related to accuracy

; Neighborsearching

vdw-type = cut-off

ns_type = grid ; search neighboring grid cels

nstlist = 5 ; 10 fs

rlist = 1.2 ; short-range neighborlist cutoff (in nm)

rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)

rvdw = 1.2 ; short-range van der Waals cutoff (in nm)

; Electrostatics

coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics

pme_order = 4 ; cubic interpolation

fourierspacing = 0.12 ; grid spacing for FFT

; Temperature coupling is on

tcoupl = V-rescale ; modified Berendsen thermostat

tc-grps = System ; one coupling groups - more accurate

tau_t = 0.1 ; time constant, in ps

ref_t = 300 ; reference temperature, one for each group, in K

; Pressure coupling is off

pcoupl = no ; no pressure coupling in NVT

; Periodic boundary conditions

pbc = xyz ; 3-D PBC

; Dispersion correction

DispCorr = EnerPres ; account for cut-off vdW scheme

; Velocity generation

gen_vel = yes ; assign velocities from Maxwell distribution

gen_temp = 300 ; temperature for Maxwell distribution

gen_seed = -1 ; generate a random seed

-

I obtain the following error with mdrun_mpi command

/usr/pbs/bin/mpiexec mdrun_mpi -s hMRP1_K-TM17_md.tpr -o hMRP1_K-TM17_md.trr -c 
hMRP1_K-TM17_md.gro -e hMRP1_K-TM17_bDM_h2o_Cl_md.edr -g 
hMRP1_K-TM17_bDM_h2o_Cl_md.log

-- error

Initializing Domain Decomposition on 4 nodes

Dynamic load balancing: auto

Will sort the charge groups at every domain (re)decomposition

Initial maximum inter charge-group distances:

two-body bonded interactions: 6.729 nm, LJ-14, atoms 11100 11107

multi-body bonded interactions: 6.729 nm, U-B, atoms 11100 11106

Minimum cell size due to bonded interactions: 7.402 nm

Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm

Estimated maximum distance required for P-LINCS: 0.819 nm

Using 0 separate PME nodes

Scaling the initial minimum size

Re: [gmx-users] Error : There is no domain decomposition for

[Mark Abraham]

- Original Message -
From: ABEL Stephane 175950 
Date: Thursday, September 30, 2010 21:21
Subject: [gmx-users] Error : There is no domain decomposition for
To: gmx-users@gromacs.org

> Yeah Justin, I have already read the comments related to the 
> link before to post in the mailing list. But I don't know how to 
> correct this ? 
>  
> Increase/decrease the number of node or CPU ? 

No, you should address the underlying issue. You have a very long-range 
interaction. What is it, and why?

> Initial maximum inter charge-group distances:
>
> two-body bonded interactions: 6.729 nm, LJ-14, atoms 11100 11107
>
> multi-body bonded interactions: 6.729 nm, U-B, atoms 11100 11106
>
> Minimum cell size due to bonded interactions: 7.402 nm

Mark


>  
> Thank you again for your help
>  
> Stephane  
> 
> ABEL Stephane 175950 wrote:
> > Dear All,
> >
> > I am trying to do a MD of a system containing TIP3P water, a 
> peptide, some glycolipids molecule and ions in a cubic box. The 
> forcefield used is CHARMM and are taken from previous MD. The 
> bonded and nonbonded parameters was converted in GROMACS 
> manually because some parameters are not in present in current 
> GMX (v 4.5.1) distribution.
> >
> > I have minimized successfully the system. see below
> >
> >  em.mdp ---
> >
> > title = bDM+KTM17 in water
> >
> > ; Preprocessor - specify a full path if necessary.
> >
> > cpp = cpp
> >
> > include = -I../top
> >
> > define = -DFLEXIBLE
> >
> > integrator = steep
> >
> > nstcgsteep = 5000
> >
> > emstep = 0.01
> >
> > emtol = 500.0
> >
> > ;dt = 0.002
> >
> > pbc = xyz
> >
> > nsteps = 5000
> >
> > nstlist = 5
> >
> > ns_type = grid
> >
> > rlist = 1.2
> >
> > coulombtype = PME
> >
> > rcoulomb = 1.2
> >
> > rvdw = 1.2
> >
> > fourierspacing = 0.12
> >
> > pme_order = 4
> >
> > ewald_rtol = 1e-05
> >
> > optimize_fft = yes
> >
> > ---
> >
> >  Final results of energy minimization process
> >
> > Energies (kJ/mol)
> >
> > Bond Angle U-B Proper Dih. Improper Dih.
> >
> > 3.58212e+04 1.88051e+04 6.00353e+03 3.58404e+04 7.30187e+00
> >
> > CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR)
> >
> > -1.39601e+02 1.11718e+04 1.76772e+05 1.66576e+05 -1.30112e+06
> >
> > Coul. recip. Potential Pressure (bar)
> >
> > -1.17090e+05 -9.67347e+05 0.0e+00
> >
> > Steepest Descents converged to Fmax < 500 in 107 steps
> >
> > Potential Energy = -9.67347283476003e+05
> >
> > Maximum force = 4.75153618041724e+02 on atom 313
> >
> > Norm of force = 9.37591893853129e+00
> >
> > But when i try to equilibrate this system in NVT ensemble for 
> 100 ps with the md.mdp below
> >
> >  nvt.mdp ---
> >
> > title = KTM17-bDM MD
> >
> > ;define = -DPOSRES ; position restrain the protein
> >
> > ; Run parameters
> >
> > integrator = md ; leap-frog integrator
> >
> > nsteps = 5 ; 2 * 5 = 100 ps
> >
> > dt = 0.002 ; 2 fs
> >
> > ; Output control
> >
> > nstxout = 100 ; save coordinates every 0.2 ps
> >
> > nstvout = 100 ; save velocities every 0.2 ps
> >
> > nstenergy = 100 ; save energies every 0.2 ps
> >
> > nstlog = 100 ; update log file every 0.2 ps
> >
> > ; Bond parameters
> >
> > continuation = no ; first dynamics run
> >
> > constraint_algorithm = lincs ; holonomic constraints
> >
> > constraints = all-bonds ; all bonds (even heavy atom-H bonds) 
> constrained>
> > lincs_iter = 1 ; accuracy of LINCS
> >
> > lincs_order = 4 ; also related to accuracy
> >
> > ; Neighborsearching
> >
> > vdw-type = cut-off
> >
> > ns_type = grid ; search neighboring grid cels
> >
> > nstlist = 5 ; 10 fs
> >
> > rlist = 1.2 ; short-range neighborlist cutoff (in nm)
> >
> > rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
> >
> > rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
> >
> > ; Electrostatics
> >
> > coulombtype = PME ; Particle Mesh Ewald for long-range 
> electrostatics>
> > pme_order = 4 ; cubic interpolation
> >
> > fourierspacing = 0.12 ; grid spacing for FFT
> >
> > ; Temperature coupling is on
> >
> > tcoupl = V-rescale ; modified Berendsen thermostat
> >
> > tc-grps = System ; one coupling groups - more accurate
> >
> > tau_t = 0.1 ; time constant, in ps
> >
> > ref_t = 300 ; reference temperature, one for each group, in K
> >
> > ; Pressure coupling is off
> >
> > pcoupl = no ; no pressure coupling in NVT
> >
> > ; Periodic boundary conditions
> >
> > pbc = xyz ; 3-D PBC
> >
> > ; Dispersion correction
> >
> > DispCorr = EnerPres ; account for cut-off vdW scheme
> >
> > ; Velocity generation
> >
> > gen_vel = yes ; assign velocities from Maxwell distribution
> >
> > gen_temp = 300 ; temperature for Maxwell distribution
> >
> > gen_seed = -1 ; generate a random seed
> >
> > -
> >
> > I obtain the following error with mdrun_mpi command
> >
> > /usr/pbs/bin/mpiexec mdrun_mpi -s hMRP1_K-TM17_md.tpr -o 
> hMRP1_K-TM17_md.trr -c hMRP1_K-TM17_md.gro -e hMRP1_K-
> TM17_bDM_h2o_Cl_md.edr -g hMRP1_K-TM17_bDM_h2o_Cl_md.log
> >
> > -- error
> >
>

[gmx-users] Error : There is no domain decomposition for

[ABEL Stephane 175950]

Yeah Justin, I have already read the comments related to the link before to 
post in the mailing list. But I don't know how to correct this ? 
 
Increase/decrease the number of node or CPU ? 
 
Thank you again for your help
 
Stephane  

ABEL Stephane 175950 wrote:
> Dear All,
>
> I am trying to do a MD of a system containing TIP3P water, a peptide, some 
> glycolipids molecule and ions in a cubic box. The forcefield used is CHARMM 
> and are taken from previous MD. The bonded and nonbonded parameters was 
> converted in GROMACS manually because some parameters are not in present in 
> current GMX (v 4.5.1) distribution.
>
> I have minimized successfully the system. see below
>
>  em.mdp ---
>
> title = bDM+KTM17 in water
>
> ; Preprocessor - specify a full path if necessary.
>
> cpp = cpp
>
> include = -I../top
>
> define = -DFLEXIBLE
>
> integrator = steep
>
> nstcgsteep = 5000
>
> emstep = 0.01
>
> emtol = 500.0
>
> ;dt = 0.002
>
> pbc = xyz
>
> nsteps = 5000
>
> nstlist = 5
>
> ns_type = grid
>
> rlist = 1.2
>
> coulombtype = PME
>
> rcoulomb = 1.2
>
> rvdw = 1.2
>
> fourierspacing = 0.12
>
> pme_order = 4
>
> ewald_rtol = 1e-05
>
> optimize_fft = yes
>
> ---
>
>  Final results of energy minimization process
>
> Energies (kJ/mol)
>
> Bond Angle U-B Proper Dih. Improper Dih.
>
> 3.58212e+04 1.88051e+04 6.00353e+03 3.58404e+04 7.30187e+00
>
> CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR)
>
> -1.39601e+02 1.11718e+04 1.76772e+05 1.66576e+05 -1.30112e+06
>
> Coul. recip. Potential Pressure (bar)
>
> -1.17090e+05 -9.67347e+05 0.0e+00
>
> Steepest Descents converged to Fmax < 500 in 107 steps
>
> Potential Energy = -9.67347283476003e+05
>
> Maximum force = 4.75153618041724e+02 on atom 313
>
> Norm of force = 9.37591893853129e+00
>
> But when i try to equilibrate this system in NVT ensemble for 100 ps with the 
> md.mdp below
>
>  nvt.mdp ---
>
> title = KTM17-bDM MD
>
> ;define = -DPOSRES ; position restrain the protein
>
> ; Run parameters
>
> integrator = md ; leap-frog integrator
>
> nsteps = 5 ; 2 * 5 = 100 ps
>
> dt = 0.002 ; 2 fs
>
> ; Output control
>
> nstxout = 100 ; save coordinates every 0.2 ps
>
> nstvout = 100 ; save velocities every 0.2 ps
>
> nstenergy = 100 ; save energies every 0.2 ps
>
> nstlog = 100 ; update log file every 0.2 ps
>
> ; Bond parameters
>
> continuation = no ; first dynamics run
>
> constraint_algorithm = lincs ; holonomic constraints
>
> constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
>
> lincs_iter = 1 ; accuracy of LINCS
>
> lincs_order = 4 ; also related to accuracy
>
> ; Neighborsearching
>
> vdw-type = cut-off
>
> ns_type = grid ; search neighboring grid cels
>
> nstlist = 5 ; 10 fs
>
> rlist = 1.2 ; short-range neighborlist cutoff (in nm)
>
> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
>
> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
>
> ; Electrostatics
>
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
>
> pme_order = 4 ; cubic interpolation
>
> fourierspacing = 0.12 ; grid spacing for FFT
>
> ; Temperature coupling is on
>
> tcoupl = V-rescale ; modified Berendsen thermostat
>
> tc-grps = System ; one coupling groups - more accurate
>
> tau_t = 0.1 ; time constant, in ps
>
> ref_t = 300 ; reference temperature, one for each group, in K
>
> ; Pressure coupling is off
>
> pcoupl = no ; no pressure coupling in NVT
>
> ; Periodic boundary conditions
>
> pbc = xyz ; 3-D PBC
>
> ; Dispersion correction
>
> DispCorr = EnerPres ; account for cut-off vdW scheme
>
> ; Velocity generation
>
> gen_vel = yes ; assign velocities from Maxwell distribution
>
> gen_temp = 300 ; temperature for Maxwell distribution
>
> gen_seed = -1 ; generate a random seed
>
> -
>
> I obtain the following error with mdrun_mpi command
>
> /usr/pbs/bin/mpiexec mdrun_mpi -s hMRP1_K-TM17_md.tpr -o hMRP1_K-TM17_md.trr 
> -c hMRP1_K-TM17_md.gro -e hMRP1_K-TM17_bDM_h2o_Cl_md.edr -g 
> hMRP1_K-TM17_bDM_h2o_Cl_md.log
>
> -- error
>
> Initializing Domain Decomposition on 4 nodes
>
> Dynamic load balancing: auto
>
> Will sort the charge groups at every domain (re)decomposition
>
> Initial maximum inter charge-group distances:
>
> two-body bonded interactions: 6.729 nm, LJ-14, atoms 11100 11107
>
> multi-body bonded interactions: 6.729 nm, U-B, atoms 11100 11106
>
> Minimum cell size due to bonded interactions: 7.402 nm
>
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm
>
> Estimated maximum distance required for P-LINCS: 0.819 nm
>
> Using 0 separate PME nodes
>
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>
> Optimizing the DD grid for 4 cells with a minimum initial size of 9.252 nm
>
> The maximum allowed number of cells is: X 0 Y 0 Z 0
>
> ---
>
> Program mdrun_mpi, VERSION 4.5.1
>
> Source code file: domdec.c, line: 6428
>
> Fatal error:
>
> The

Re: [gmx-users] distance restrained D simulations

[Mark Abraham]

- Original Message -
From: jayant james 
Date: Thursday, September 30, 2010 9:36
Subject: [gmx-users] distance restrained D simulations
To: Discussion list for GROMACS users 

> > Hi!
> I am trying to perform distance restrained MD simulations of a protein with 
> Gromacs4.0.5.
> I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am 
> incorporating simular to NOE distance restraints in NMR.

The details of how you tried to do this are important. See 
http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm
 and consider section 5.4 of the manual. There might be a solution that does 
not have this issue.

Mark

>  When I use one processor for the simulations its all fine, but, when I use 
> multiple processors I get a bunch of errors
> lets me start with the "NOTE" found below. Well do not want to increase the 
> cut-off distance but want the program to use multiple processors. How can I 
> overcome this problem?
> I would appreciate your input
> Thanks
> JJ
> 
> NOTE: atoms involved in distance restraints should be within the longest 
> cut-off distance, if this is not the case mdrun generates a fatal error, in 
> that case use particle decomposition (mdrun option -pd) > > > WARNING: Can 
> not write distance restraint data to energy file with domain decomposition > 
> Loaded with Money> > > 
> --- > Program mdrun_mpi, 
> VERSION 4.0.5> Source code file: ../../../src/mdlib/domdec.c, line: 5873 > > 
> Fatal error:> There is no domain decomposition for 4 nodes that is compatible 
> with the given box and a minimum cell size of 8.89355 nm > Change the number 
> of nodes or mdrun option -rdd or -dds> Look in the log file for details on 
> the domain decomposition > 
> ---> > "What Kind Of Guru 
> are You, Anyway ?" (F. Zappa) > > Error on node 0, will try to stop all the 
> nodes> Halting parallel program mdrun_mpi on CPU 0 out of 4 > > gcq#21: "What 
> Kind Of Guru are You, Anyway ?" (F. Zappa)> > 
> -- > 
> mpirun has exited due to process rank 2 with PID 28700 on> node 
> compute-3-73.local exiting without calling "finalize". This may > have caused 
> other processes in the application to be> terminated by signals sent by 
> mpirun (as reported here). > 
> -> 
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with 
> errorcode -1.> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI 
> processes. > You may or may not see output from other processes, depending 
> on> exactly when Open MPI kills them. > 
> --> 
> 
> 
> 
> 
> 
> 
> 
> -- 
> Jayasundar Jayant James
> 
 > www.chick.com/reading/tracts/0096/0096_01.asp) 
> 
 > -- 
> gmx-users mailing listgmx-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!
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Re: [gmx-users] Water molecule starting at atom x can not be settled - minimization step

[Justin A. Lemkul]

Trang wrote:

Dear gmx-users,
I do a minimization run with this mdp:
-
constraints =  none
;define  =  -DFLEX_SPC
integrator  = cg
;nstcgsteep = 300
emtol   =  100.0
emstep  =  0.005
dt  =  0.001; ps !
nsteps  =  20  ; total 200 ps.
nstcomm =  100
nstxout =  1
nstvout =  0
nstfout =  0
nstlog  =  1
nstenergy   =  1000
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
coulombtype =  PME ; Reaction-Field
fourierspacing  =  0.12
pme_order   =  4
optimize_fft=  yes
;epsilon_r   =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc-grps =  Protein  SOL
tau_t   =  0.010.01
ref_t   =  310 310
; Energy monitoring
energygrps  =  Protein SOL
; Isotropic pressure coupling is now on
Pcoupl  = berendsen
Pcoupltype  = isotropic
tau_p   =  0.25
compressibility =  5.4e-5
ref_p   =  1.0
; Generate velocites is off at 300 K.
gen_vel =  no
;gen_temp=  300.0
;gen_seed=  749261

---
and get the error, output like this:

Polak-Ribiere Conjugate Gradients:
   Tolerance (Fmax)   =  1.0e+02
   Number of steps=   20
   F-max =  4.69437e+04 on atom 2513
   F-Norm=  1.05294e+03


step -1: Water molecule starting at atom 43372 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

...

Fatal error:
1 particles communicated to PME node 4 are more than 2/3 times the 
cut-off out of the domain decomposition cell of their charge group in 
dimension y.

This usually means that your system is not well equilibrated.
--

I did a successful run with another equivalent system (same protein 
sequence, same number of atoms), even with a LARGER TIMESTEP, 0.002 ps
I found a lot of people encounter the same error, but in production run 
step. And in those cases, they're advised to minimize/equilibrate the 
system more thoroughly. What can I do to resolve this problem in 
MINIMIZATION step?




You likely have some unresolvable atomic clash(es) in your system that can't be 
energy-minimized.  Check your structure around the location of the problematic 
water molecule to see if anything is overlapping.


-Justin


Many thanks
Trang



--


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] Error : There is no domain decomposition for 4 nodes that compatible with the given box

[Justin A. Lemkul]

ABEL Stephane 175950 wrote:

Dear All,

I am trying to do a MD of a system containing TIP3P water, a peptide, some 
glycolipids molecule and ions in a cubic box. The forcefield used is CHARMM and 
are taken from previous MD. The bonded and nonbonded parameters was converted 
in GROMACS manually because some parameters are not in present in current GMX 
(v 4.5.1) distribution.

I have minimized successfully the system. see below 


 em.mdp ---

title = bDM+KTM17 in water

; Preprocessor - specify a full path if necessary.

cpp = cpp

include = -I../top

define = -DFLEXIBLE

integrator = steep

nstcgsteep = 5000

emstep = 0.01

emtol = 500.0

;dt = 0.002

pbc = xyz

nsteps = 5000

nstlist = 5

ns_type = grid

rlist = 1.2

coulombtype = PME

rcoulomb = 1.2

rvdw = 1.2

fourierspacing = 0.12

pme_order = 4

ewald_rtol = 1e-05

optimize_fft = yes

---

 Final results of energy minimization process

Energies (kJ/mol)

Bond Angle U-B Proper Dih. Improper Dih.

3.58212e+04 1.88051e+04 6.00353e+03 3.58404e+04 7.30187e+00

CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR)

-1.39601e+02 1.11718e+04 1.76772e+05 1.66576e+05 -1.30112e+06

Coul. recip. Potential Pressure (bar)

-1.17090e+05 -9.67347e+05 0.0e+00

Steepest Descents converged to Fmax < 500 in 107 steps

Potential Energy = -9.67347283476003e+05

Maximum force = 4.75153618041724e+02 on atom 313

Norm of force = 9.37591893853129e+00

But when i try to equilibrate this system in NVT ensemble for 100 ps with the md.mdp below 


 nvt.mdp ---

title = KTM17-bDM MD

;define = -DPOSRES ; position restrain the protein

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 5 ; 2 * 5 = 100 ps

dt = 0.002 ; 2 fs

; Output control

nstxout = 100 ; save coordinates every 0.2 ps

nstvout = 100 ; save velocities every 0.2 ps

nstenergy = 100 ; save energies every 0.2 ps

nstlog = 100 ; update log file every 0.2 ps

; Bond parameters

continuation = no ; first dynamics run

constraint_algorithm = lincs ; holonomic constraints

constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained

lincs_iter = 1 ; accuracy of LINCS

lincs_order = 4 ; also related to accuracy

; Neighborsearching

vdw-type = cut-off

ns_type = grid ; search neighboring grid cels

nstlist = 5 ; 10 fs

rlist = 1.2 ; short-range neighborlist cutoff (in nm)

rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)

rvdw = 1.2 ; short-range van der Waals cutoff (in nm)

; Electrostatics

coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics

pme_order = 4 ; cubic interpolation

fourierspacing = 0.12 ; grid spacing for FFT

; Temperature coupling is on

tcoupl = V-rescale ; modified Berendsen thermostat

tc-grps = System ; one coupling groups - more accurate

tau_t = 0.1 ; time constant, in ps

ref_t = 300 ; reference temperature, one for each group, in K

; Pressure coupling is off

pcoupl = no ; no pressure coupling in NVT

; Periodic boundary conditions

pbc = xyz ; 3-D PBC

; Dispersion correction

DispCorr = EnerPres ; account for cut-off vdW scheme

; Velocity generation

gen_vel = yes ; assign velocities from Maxwell distribution

gen_temp = 300 ; temperature for Maxwell distribution

gen_seed = -1 ; generate a random seed

-

I obtain the following error with mdrun_mpi command

/usr/pbs/bin/mpiexec mdrun_mpi -s hMRP1_K-TM17_md.tpr -o hMRP1_K-TM17_md.trr -c 
hMRP1_K-TM17_md.gro -e hMRP1_K-TM17_bDM_h2o_Cl_md.edr -g 
hMRP1_K-TM17_bDM_h2o_Cl_md.log

-- error 


Initializing Domain Decomposition on 4 nodes

Dynamic load balancing: auto

Will sort the charge groups at every domain (re)decomposition

Initial maximum inter charge-group distances:

two-body bonded interactions: 6.729 nm, LJ-14, atoms 11100 11107

multi-body bonded interactions: 6.729 nm, U-B, atoms 11100 11106

Minimum cell size due to bonded interactions: 7.402 nm

Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm

Estimated maximum distance required for P-LINCS: 0.819 nm

Using 0 separate PME nodes

Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25

Optimizing the DD grid for 4 cells with a minimum initial size of 9.252 nm

The maximum allowed number of cells is: X 0 Y 0 Z 0

---

Program mdrun_mpi, VERSION 4.5.1

Source code file: domdec.c, line: 6428

Fatal error:

There is no domain decomposition for 4 nodes that is compatible with the given 
box and a minimum cell size of 9.25216 nm

Change the number of nodes or mdrun option -rdd or -dds

Look in the log file for details on the domain decomposition

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

---

"Player Sleeps With the Fishes" (Ein Bekanntes Spiel Von ID Software)

I have also checked the mimized structure at different minim

[gmx-users] Error : There is no domain decomposition for 4 nodes that compatible with the given box

[ABEL Stephane 175950]

Dear All,

I am trying to do a MD of a system containing TIP3P water, a peptide, some 
glycolipids molecule and ions in a cubic box. The forcefield used is CHARMM and 
are taken from previous MD. The bonded and nonbonded parameters was converted 
in GROMACS manually because some parameters are not in present in current GMX 
(v 4.5.1) distribution.

I have minimized successfully the system. see below 

 em.mdp ---

title = bDM+KTM17 in water

; Preprocessor - specify a full path if necessary.

cpp = cpp

include = -I../top

define = -DFLEXIBLE

integrator = steep

nstcgsteep = 5000

emstep = 0.01

emtol = 500.0

;dt = 0.002

pbc = xyz

nsteps = 5000

nstlist = 5

ns_type = grid

rlist = 1.2

coulombtype = PME

rcoulomb = 1.2

rvdw = 1.2

fourierspacing = 0.12

pme_order = 4

ewald_rtol = 1e-05

optimize_fft = yes

---

 Final results of energy minimization process

Energies (kJ/mol)

Bond Angle U-B Proper Dih. Improper Dih.

3.58212e+04 1.88051e+04 6.00353e+03 3.58404e+04 7.30187e+00

CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR)

-1.39601e+02 1.11718e+04 1.76772e+05 1.66576e+05 -1.30112e+06

Coul. recip. Potential Pressure (bar)

-1.17090e+05 -9.67347e+05 0.0e+00

Steepest Descents converged to Fmax < 500 in 107 steps

Potential Energy = -9.67347283476003e+05

Maximum force = 4.75153618041724e+02 on atom 313

Norm of force = 9.37591893853129e+00

But when i try to equilibrate this system in NVT ensemble for 100 ps with the 
md.mdp below 

 nvt.mdp ---

title = KTM17-bDM MD

;define = -DPOSRES ; position restrain the protein

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 5 ; 2 * 5 = 100 ps

dt = 0.002 ; 2 fs

; Output control

nstxout = 100 ; save coordinates every 0.2 ps

nstvout = 100 ; save velocities every 0.2 ps

nstenergy = 100 ; save energies every 0.2 ps

nstlog = 100 ; update log file every 0.2 ps

; Bond parameters

continuation = no ; first dynamics run

constraint_algorithm = lincs ; holonomic constraints

constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained

lincs_iter = 1 ; accuracy of LINCS

lincs_order = 4 ; also related to accuracy

; Neighborsearching

vdw-type = cut-off

ns_type = grid ; search neighboring grid cels

nstlist = 5 ; 10 fs

rlist = 1.2 ; short-range neighborlist cutoff (in nm)

rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)

rvdw = 1.2 ; short-range van der Waals cutoff (in nm)

; Electrostatics

coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics

pme_order = 4 ; cubic interpolation

fourierspacing = 0.12 ; grid spacing for FFT

; Temperature coupling is on

tcoupl = V-rescale ; modified Berendsen thermostat

tc-grps = System ; one coupling groups - more accurate

tau_t = 0.1 ; time constant, in ps

ref_t = 300 ; reference temperature, one for each group, in K

; Pressure coupling is off

pcoupl = no ; no pressure coupling in NVT

; Periodic boundary conditions

pbc = xyz ; 3-D PBC

; Dispersion correction

DispCorr = EnerPres ; account for cut-off vdW scheme

; Velocity generation

gen_vel = yes ; assign velocities from Maxwell distribution

gen_temp = 300 ; temperature for Maxwell distribution

gen_seed = -1 ; generate a random seed

-

I obtain the following error with mdrun_mpi command

/usr/pbs/bin/mpiexec mdrun_mpi -s hMRP1_K-TM17_md.tpr -o hMRP1_K-TM17_md.trr -c 
hMRP1_K-TM17_md.gro -e hMRP1_K-TM17_bDM_h2o_Cl_md.edr -g 
hMRP1_K-TM17_bDM_h2o_Cl_md.log

-- error 

Initializing Domain Decomposition on 4 nodes

Dynamic load balancing: auto

Will sort the charge groups at every domain (re)decomposition

Initial maximum inter charge-group distances:

two-body bonded interactions: 6.729 nm, LJ-14, atoms 11100 11107

multi-body bonded interactions: 6.729 nm, U-B, atoms 11100 11106

Minimum cell size due to bonded interactions: 7.402 nm

Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm

Estimated maximum distance required for P-LINCS: 0.819 nm

Using 0 separate PME nodes

Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25

Optimizing the DD grid for 4 cells with a minimum initial size of 9.252 nm

The maximum allowed number of cells is: X 0 Y 0 Z 0

---

Program mdrun_mpi, VERSION 4.5.1

Source code file: domdec.c, line: 6428

Fatal error:

There is no domain decomposition for 4 nodes that is compatible with the given 
box and a minimum cell size of 9.25216 nm

Change the number of nodes or mdrun option -rdd or -dds

Look in the log file for details on the domain decomposition

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

---

"Player Sleeps With the Fishes" (Ein Bekanntes Spiel Von ID Software)

I have also checked the mimized structure at different minimization step, and I 
saw no proble