[gmx-users] Periodic Boundary Conditions g_mindist -pi

[ifat shub]

Hi,



I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see
if the complex is seeing its next periodic image, so I used the g_mindist
command with the -pi option. My command line was:

g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi

The output (see below) was stable until ~344ps when there is a  jump in the
max internal distance (third column) from ~6nm to ~22nm. After the jump the
numbers are reduced back to ~6nm and remained stable until the run is
completed at 1ns.

Does anyone know how to explain this jump? Is this a real problem or just a
visualization artifact? Is there a way to avoid such jumps?



Here is the mdp file I used:

--run.mdp--

integrator  = md

nsteps  = 100

dt  = 0.001

coulombtype = pme

vdw-type= cut-off

tcoupl  = Berendsen

tc-grps = protein non-protein

tau-t   = 0.1 0.1

ref-t   = 310 310

nstxout = 100

nstvout = 0

nstxtcout   = 100

nstenergy   = 100

comm_mode = Linear ; Angular

comm_grps= Protein

xtc_grps   = Protein

energygrps = Protein

--



Thanks,

Ifat



The output:

343.7   10.813 5.924   16.445 16.445 16.445

343.8   10.809 5.949   16.445 16.445 16.445

343.9   10.804 5.959   16.445 16.445 16.445

344  10.808 5.974   16.445 16.445 16.445

344.1   0.18 21.982 16.445 16.445 16.445

344.2   10.778 5.977   16.445 16.445 16.445

344.3   10.768 5.996   16.445 16.445 16.445

344.4   10.764 6.016   16.445 16.445 16.445

344.5   10.722 6.029   16.445 16.445 16.445

344.6   10.774 6.01 16.445 16.445 16.445

344.7   0.174   21.984 16.445 16.445 16.445

344.8   0.176   21.98   16.445 16.445 16.445

344.9   0.17 22.002 16.445 16.445 16.445

345  0.173   21.981 16.445 16.445 16.445

345.1   0.191   21.954 16.445 16.445 16.445

345.2   0.183   21.958 16.445 16.445 16.445

345.3   0.181   22.012 16.445 16.445 16.445

345.4   0.17 22.054 16.445 16.445 16.445

345.5   0.168   22.054 16.445 16.445 16.445

345.6   0.189   22.039 16.445 16.445 16.445

345.7   0.171   22.007 16.445 16.445 16.445

345.8   0.186   22.031 16.445 16.445 16.445

345.9   0.171   22.077 16.445 16.445 16.445

346  0.187   21.99   16.445 16.445 16.445

346.1   0.173   21.984 16.445 16.445 16.445

346.2   0.181   22.02   16.445 16.445 16.445

346.3   10.82   5.984   16.445 16.445 16.445

346.4   10.81   6.002   16.445 16.445 16.445

346.5   10.819 6.008   16.445 16.445 16.445

346.6   10.813 5.996   16.445 16.445 16.445

346.7   10.781 6.006   16.445 16.445 16.445

346.8   10.793 6.026   16.445 16.445 16.445

346.9   10.745 5.985   16.445 16.445 16.445

347  10.762 5.999   16.445 16.445 16.445

347.1   10.781 5.984   16.445 16.445 16.445

347.2   10.784 6.002   16.445 16.445 16.445
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Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi

[Tsjerk Wassenaar]

Hi Ifat,

I guess this is a jump over the periodic boundaries. You should remove
jumps from the trajectory (-pbc nojump) before running g_mindist -pi.

Cheers,

Tsjerk

On Wed, Feb 16, 2011 at 10:19 AM, ifat shub  wrote:
> Hi,
>
>
>
> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see
> if the complex is seeing its next periodic image, so I used the g_mindist
> command with the -pi option. My command line was:
>
> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>
> The output (see below) was stable until ~344ps when there is a  jump in the
> max internal distance (third column) from ~6nm to ~22nm. After the jump the
> numbers are reduced back to ~6nm and remained stable until the run is
> completed at 1ns.
>
> Does anyone know how to explain this jump? Is this a real problem or just a
> visualization artifact? Is there a way to avoid such jumps?
>
>
>
> Here is the mdp file I used:
>
> --run.mdp--
>
> integrator  = md
>
> nsteps  = 100
>
> dt  = 0.001
>
> coulombtype = pme
>
> vdw-type    = cut-off
>
> tcoupl  = Berendsen
>
> tc-grps = protein non-protein
>
> tau-t   = 0.1 0.1
>
> ref-t   = 310 310
>
> nstxout = 100
>
> nstvout = 0
>
> nstxtcout   = 100
>
> nstenergy       = 100
>
> comm_mode     = Linear ; Angular
>
> comm_grps    = Protein
>
> xtc_grps   = Protein
>
> energygrps = Protein
>
> --
>
>
>
> Thanks,
>
> Ifat
>
>
>
> The output:
>
> 343.7   10.813 5.924   16.445 16.445 16.445
>
> 343.8   10.809 5.949   16.445 16.445 16.445
>
> 343.9   10.804 5.959   16.445 16.445 16.445
>
> 344  10.808 5.974   16.445 16.445 16.445
>
> 344.1   0.18 21.982 16.445 16.445 16.445
>
> 344.2   10.778 5.977   16.445 16.445 16.445
>
> 344.3   10.768 5.996   16.445 16.445 16.445
>
> 344.4   10.764 6.016   16.445 16.445 16.445
>
> 344.5   10.722 6.029   16.445 16.445 16.445
>
> 344.6   10.774 6.01 16.445 16.445 16.445
>
> 344.7   0.174   21.984 16.445 16.445 16.445
>
> 344.8   0.176   21.98   16.445 16.445 16.445
>
> 344.9   0.17 22.002 16.445 16.445 16.445
>
> 345  0.173   21.981 16.445 16.445 16.445
>
> 345.1   0.191   21.954 16.445 16.445 16.445
>
> 345.2   0.183   21.958 16.445 16.445 16.445
>
> 345.3   0.181   22.012 16.445 16.445 16.445
>
> 345.4   0.17 22.054 16.445 16.445 16.445
>
> 345.5   0.168   22.054 16.445 16.445 16.445
>
> 345.6   0.189   22.039 16.445 16.445 16.445
>
> 345.7   0.171   22.007 16.445 16.445 16.445
>
> 345.8   0.186   22.031 16.445 16.445 16.445
>
> 345.9   0.171   22.077 16.445 16.445 16.445
>
> 346  0.187   21.99   16.445 16.445 16.445
>
> 346.1   0.173   21.984 16.445 16.445 16.445
>
> 346.2   0.181   22.02   16.445 16.445 16.445
>
> 346.3   10.82   5.984   16.445 16.445 16.445
>
> 346.4   10.81   6.002   16.445 16.445 16.445
>
> 346.5   10.819 6.008   16.445 16.445 16.445
>
> 346.6   10.813 5.996   16.445 16.445 16.445
>
> 346.7   10.781 6.006   16.445 16.445 16.445
>
> 346.8   10.793 6.026   16.445 16.445 16.445
>
> 346.9   10.745 5.985   16.445 16.445 16.445
>
> 347  10.762 5.999   16.445 16.445 16.445
>
> 347.1   10.781 5.984   16.445 16.445 16.445
>
> 347.2   10.784 6.002   16.445 16.445 16.445
>
>
>
>
>
> --
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] g_rmsf reference structure?

[Tsjerk Wassenaar]

Hi,

The reference is used for fitting. The RMSF is calculated with respect
to the average (fitted) structure, unless you explicitly specify that
deviations from the reference should be used.

Cheers,

Tsjerk

On Wed, Feb 16, 2011 at 7:08 AM, Mark Abraham  wrote:
> On 16/02/2011 3:44 PM, kulleperuma.kulleper...@utoronto.ca wrote:
>>
>> Dear all,
>>
>> I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms
>> with reference to the average structure between 5-10 ns of a total of 10 ns
>> simulation as below;
>> g_rmsf  ?f md.xtc  ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg
>>
>> My understanding of the RMSF is as follows;
>>
>>  RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2)
>>
>> where T is the time over which one wants to average, and Xi is the
>> reference position of particle i, which is the time-averaged position of the
>> same particle i.
>> What I am confused is whether g_rmsf takes the reference structure from
>> the structure file (-s), which in my case, the md.tpr and NOT the time
>> averaged position over the specified time?
>
> It does take the reference structure from -s. Whether you actually want the
> RMSF from the non-physical time-averaged structure is up to you. IIRC you
> might be able to get such an average from g_cluster.
>
> Mark
> --
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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[gmx-users] Re: gromacs QM/MM compilation with gaussian

[Txema Mercero]

Hi there!

We are trying to compile gromacs with Gaussian 03 rev D.02 (we also
have g09). We followed the instructions in
http://wwwuser.gwdg.de/~ggroenh/roadmap.pdf despite that they do no
fit exactly  with the g03 rev d03 version,for instance, FrcNCN is no
in l710 but in utilam.F

Despite of that, we compiled gromacs and  apparently everything was
fine, but we get a segmentation fault when we run gromacs. We have the
following questions

1.- Is it possible to get a more detailed/or specific instructions?
2.- I think that three variables GAUSS_EXE, GAUSS_DIR and DEVEL_DIR
should be defined. Where should GAUSS_EXE and GAUSS_DIR point exactly?

Thanks for your attention, any help will be appreciated.

Regards,

Txema Mercero
IZO/SGI
UPV/EHU
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[gmx-users] Re: Periodic Boundary Conditions g_mindist -pi

[ifat shub]

Hi Tsjerk,
Thank you for your reply.
I am aware of the trajconv option but I wanted to know if there is a way to
avoid these kind of jumps over the periodic boundaries during the mdrun and
not post process?
Thanks,
Ifat

 message: 4
> Date: Wed, 16 Feb 2011 11:19:14 +0200
> From: ifat shub 
> Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi
> To: gmx-users@gromacs.org
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
>
>
> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see
> if the complex is seeing its next periodic image, so I used the g_mindist
> command with the -pi option. My command line was:
>
> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>
> The output (see below) was stable until ~344ps when there is a  jump in the
> max internal distance (third column) from ~6nm to ~22nm. After the jump the
> numbers are reduced back to ~6nm and remained stable until the run is
> completed at 1ns.
>
> Does anyone know how to explain this jump? Is this a real problem or just a
> visualization artifact? Is there a way to avoid such jumps?
>
>
>
> Here is the mdp file I used:
>
> --run.mdp--
>
> integrator  = md
>
> nsteps  = 100
>
> dt  = 0.001
>
> coulombtype = pme
>
> vdw-type= cut-off
>
> tcoupl  = Berendsen
>
> tc-grps = protein non-protein
>
> tau-t   = 0.1 0.1
>
> ref-t   = 310 310
>
> nstxout = 100
>
> nstvout = 0
>
> nstxtcout   = 100
>
> nstenergy   = 100
>
> comm_mode = Linear ; Angular
>
> comm_grps= Protein
>
> xtc_grps   = Protein
>
> energygrps = Protein
>
> --
>
>
>
> Thanks,
>
> Ifat
>
>
>
> The output:
>
> 343.7   10.813 5.924   16.445 16.445 16.445
>
> 343.8   10.809 5.949   16.445 16.445 16.445
>
> 343.9   10.804 5.959   16.445 16.445 16.445
>
> 344  10.808 5.974   16.445 16.445 16.445
>
> 344.1   0.18 21.982 16.445 16.445 16.445
>
> 344.2   10.778 5.977   16.445 16.445 16.445
>
> 344.3   10.768 5.996   16.445 16.445 16.445
>
> 344.4   10.764 6.016   16.445 16.445 16.445
>
> 344.5   10.722 6.029   16.445 16.445 16.445
>
> 344.6   10.774 6.01 16.445 16.445 16.445
>
> 344.7   0.174   21.984 16.445 16.445 16.445
>
> 344.8   0.176   21.98   16.445 16.445 16.445
>
> 344.9   0.17 22.002 16.445 16.445 16.445
>
> 345  0.173   21.981 16.445 16.445 16.445
>
> 345.1   0.191   21.954 16.445 16.445 16.445
>
> 345.2   0.183   21.958 16.445 16.445 16.445
>
> 345.3   0.181   22.012 16.445 16.445 16.445
>
> 345.4   0.17 22.054 16.445 16.445 16.445
>
> 345.5   0.168   22.054 16.445 16.445 16.445
>
> 345.6   0.189   22.039 16.445 16.445 16.445
>
> 345.7   0.171   22.007 16.445 16.445 16.445
>
> 345.8   0.186   22.031 16.445 16.445 16.445
>
> 345.9   0.171   22.077 16.445 16.445 16.445
>
> 346  0.187   21.99   16.445 16.445 16.445
>
> 346.1   0.173   21.984 16.445 16.445 16.445
>
> 346.2   0.181   22.02   16.445 16.445 16.445
>
> 346.3   10.82   5.984   16.445 16.445 16.445
>
> 346.4   10.81   6.002   16.445 16.445 16.445
>
> 346.5   10.819 6.008   16.445 16.445 16.445
>
> 346.6   10.813 5.996   16.445 16.445 16.445
>
> 346.7   10.781 6.006   16.445 16.445 16.445
>
> 346.8   10.793 6.026   16.445 16.445 16.445
>
> 346.9   10.745 5.985   16.445 16.445 16.445
>
> 347  10.762 5.999   16.445 16.445 16.445
>
> 347.1   10.781 5.984   16.445 16.445 16.445
>
> 347.2   10.784 6.002   16.445 16.445 16.445
> -- next part --
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> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html
>
> --
>
> Message: 5
> Date: Wed, 16 Feb 2011 10:43:56 +0100
> From: Tsjerk Wassenaar 
> Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi
> To: Discussion list for GROMACS users 
> Message-ID:
>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Ifat,
>
> I guess this is a jump over the periodic boundaries. You should remove
> jumps from the trajectory (-pbc nojump) before running g_mindist -pi.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Feb 16, 2011 at 10:19 AM, ifat shub  wrote:
> > Hi,
> >
> >
> >
> > I am running a simulation on the complex 1aik.pdb in 310K. I wanted to
> see
> > if the complex is seeing its next periodic image, so I used the g_mindist
&

Re: [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi

[Mark Abraham]

On 16/02/2011 10:30 PM, ifat shub wrote:


Hi Tsjerk,
Thank you for your reply.
I am aware of the trajconv option but I wanted to know if there is a 
way to avoid these kind of jumps over the periodic boundaries during 
the mdrun and not post process?


No. mdrun does not know in advance what your visualization requirements 
are, and frankly there are better things to do with expensive compute 
cluster time. Post-processing a small number of frames elsewhere is much 
better use of resources.


Mark



message: 4
Date: Wed, 16 Feb 2011 11:19:14 +0200
From: ifat shub mailto:shubi...@gmail.com>>
Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID:
mailto:sgjftmrf-0nvmzzogfs%2bxhyxv5u6ggfnhr...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"

Hi,



I am running a simulation on the complex 1aik.pdb in 310K. I
wanted to see
if the complex is seeing its next periodic image, so I used the
g_mindist
command with the -pi option. My command line was:

g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi

The output (see below) was stable until ~344ps when there is a
 jump in the
max internal distance (third column) from ~6nm to ~22nm. After the
jump the
numbers are reduced back to ~6nm and remained stable until the run is
completed at 1ns.

Does anyone know how to explain this jump? Is this a real problem
or just a
visualization artifact? Is there a way to avoid such jumps?



Here is the mdp file I used:

--run.mdp--

integrator  = md

nsteps  = 100

dt  = 0.001

coulombtype = pme

vdw-type= cut-off

tcoupl  = Berendsen

tc-grps = protein non-protein

tau-t   = 0.1 0.1

ref-t   = 310 310

nstxout = 100

nstvout = 0

nstxtcout   = 100

nstenergy   = 100

comm_mode = Linear ; Angular

comm_grps= Protein

xtc_grps   = Protein

energygrps = Protein

--



Thanks,

Ifat



The output:

343.7   10.813 5.924   16.445 16.445 16.445

343.8   10.809 5.949   16.445 16.445 16.445

343.9   10.804 5.959   16.445 16.445 16.445

344  10.808 5.974   16.445 16.445 16.445

344.1   0.18 21.982 16.445 16.445 16.445

344.2   10.778 5.977   16.445 16.445 16.445

344.3   10.768 5.996   16.445 16.445 16.445

344.4   10.764 6.016   16.445 16.445 16.445

344.5   10.722 6.029   16.445 16.445 16.445

344.6   10.774 6.01 16.445 16.445 16.445

344.7   0.174   21.984 16.445 16.445 16.445

344.8   0.176   21.98   16.445 16.445 16.445

344.9   0.17 22.002 16.445 16.445 16.445

345  0.173   21.981 16.445 16.445 16.445

345.1   0.191   21.954 16.445 16.445 16.445

345.2   0.183   21.958 16.445 16.445 16.445

345.3   0.181   22.012 16.445 16.445 16.445

345.4   0.17 22.054 16.445 16.445 16.445

345.5   0.168   22.054 16.445 16.445 16.445

345.6   0.189   22.039 16.445 16.445 16.445

345.7   0.171   22.007 16.445 16.445 16.445

345.8   0.186   22.031 16.445 16.445 16.445

345.9   0.171   22.077 16.445 16.445 16.445

346  0.187   21.99   16.445 16.445 16.445

346.1   0.173   21.984 16.445 16.445 16.445

346.2   0.181   22.02   16.445 16.445 16.445

346.3   10.82   5.984   16.445 16.445 16.445

346.4   10.81   6.002   16.445 16.445 16.445

346.5   10.819 6.008   16.445 16.445 16.445

346.6   10.813 5.996   16.445 16.445 16.445

346.7   10.781 6.006   16.445 16.445 16.445

346.8   10.793 6.026   16.445 16.445 16.445

346.9   10.745 5.985   16.445 16.445 16.445

347  10.762 5.999   16.445 16.445 16.445

347.1   10.781 5.984   16.445 16.445 16.445

347.2   10.784 6.002   16.445 16.445 16.445
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Message: 5
Date: Wed, 16 Feb 2011 10:43:56 +0100
From: Tsjerk Wassenaar mailto:tsje...@gmail.com>>
Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID:
mailto:abxfur%2badkenmxem...@mail.gmail.com>>
Content-Type: text/plain; charset=ISO-8859-1

Hi Ifat,

I guess this is a jump over the periodic boundaries. You should remove
jumps from the trajectory (-pbc nojump) before running g_mindist -pi.

Cheers,

Tsjerk

On Wed, Feb 16, 2011 at 10:19 AM, ifat shub mailto:shubi...@gmail.com>> wrote:
> Hi,
>
>
>
  

[gmx-users] initial structures for md simulations

[oguz gurbulak]

Dear All, 

  

I want to generate some initial crystalline structures of
my target molecules for md simulations. Are there any free softwares to do this?

 

And are there any complete sources that give the
theoretical structures of organic molecules ( like hydrocarbons ) determined by
the experiments  and give the x-ray, neutron scattering, NMR, IR or Raman
results of organic molecules apart from the articles ? Could you please share
your  thoughts about this issue ? 

  

Thank you very much for your attention. 

  

Kind regards. 




  -- 
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Re: [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi

[Tsjerk Wassenaar]

On Wed, Feb 16, 2011 at 1:00 PM, Mark Abraham  wrote:
> On 16/02/2011 10:30 PM, ifat shub wrote:
>
> Hi Tsjerk,
> Thank you for your reply.
> I am aware of the trajconv option but I wanted to know if there is a way to
> avoid these kind of jumps over the periodic boundaries during the mdrun and
> not post process?
>
> No. mdrun does not know in advance what your visualization requirements are,
> and frankly there are better things to do with expensive compute cluster
> time. Post-processing a small number of frames elsewhere is much better use
> of resources.
>

Or:

No. mdrun takes the internal representation that is most efficient,
and there are better things to do with expensive compute cluster time
than writing out a trajectory without jumps, which might not even be
what you want in the end. :)

Tsjerk

> Mark
>
>
>> message: 4
>> Date: Wed, 16 Feb 2011 11:19:14 +0200
>> From: ifat shub 
>> Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi
>> To: gmx-users@gromacs.org
>> Message-ID:
>>        
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi,
>>
>>
>>
>> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see
>> if the complex is seeing its next periodic image, so I used the g_mindist
>> command with the -pi option. My command line was:
>>
>> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>>
>> The output (see below) was stable until ~344ps when there is a  jump in
>> the
>> max internal distance (third column) from ~6nm to ~22nm. After the jump
>> the
>> numbers are reduced back to ~6nm and remained stable until the run is
>> completed at 1ns.
>>
>> Does anyone know how to explain this jump? Is this a real problem or just
>> a
>> visualization artifact? Is there a way to avoid such jumps?
>>
>>
>>
>> Here is the mdp file I used:
>>
>> --run.mdp--
>>
>> integrator      = md
>>
>> nsteps          = 100
>>
>> dt              = 0.001
>>
>> coulombtype     = pme
>>
>> vdw-type        = cut-off
>>
>> tcoupl          = Berendsen
>>
>> tc-grps         = protein non-protein
>>
>> tau-t           = 0.1 0.1
>>
>> ref-t           = 310 310
>>
>> nstxout         = 100
>>
>> nstvout         = 0
>>
>> nstxtcout       = 100
>>
>> nstenergy           = 100
>>
>> comm_mode     = Linear ; Angular
>>
>> comm_grps        = Protein
>>
>> xtc_grps               = Protein
>>
>> energygrps         = Protein
>>
>> --
>>
>>
>>
>> Thanks,
>>
>> Ifat
>>
>>
>>
>> The output:
>>
>> 343.7   10.813 5.924   16.445 16.445 16.445
>>
>> 343.8   10.809 5.949   16.445 16.445 16.445
>>
>> 343.9   10.804 5.959   16.445 16.445 16.445
>>
>> 344      10.808 5.974   16.445 16.445 16.445
>>
>> 344.1   0.18     21.982 16.445 16.445 16.445
>>
>> 344.2   10.778 5.977   16.445 16.445 16.445
>>
>> 344.3   10.768 5.996   16.445 16.445 16.445
>>
>> 344.4   10.764 6.016   16.445 16.445 16.445
>>
>> 344.5   10.722 6.029   16.445 16.445 16.445
>>
>> 344.6   10.774 6.01     16.445 16.445 16.445
>>
>> 344.7   0.174   21.984 16.445 16.445 16.445
>>
>> 344.8   0.176   21.98   16.445 16.445 16.445
>>
>> 344.9   0.17     22.002 16.445 16.445 16.445
>>
>> 345      0.173   21.981 16.445 16.445 16.445
>>
>> 345.1   0.191   21.954 16.445 16.445 16.445
>>
>> 345.2   0.183   21.958 16.445 16.445 16.445
>>
>> 345.3   0.181   22.012 16.445 16.445 16.445
>>
>> 345.4   0.17     22.054 16.445 16.445 16.445
>>
>> 345.5   0.168   22.054 16.445 16.445 16.445
>>
>> 345.6   0.189   22.039 16.445 16.445 16.445
>>
>> 345.7   0.171   22.007 16.445 16.445 16.445
>>
>> 345.8   0.186   22.031 16.445 16.445 16.445
>>
>> 345.9   0.171   22.077 16.445 16.445 16.445
>>
>> 346      0.187   21.99   16.445 16.445 16.445
>>
>> 346.1   0.173   21.984 16.445 16.445 16.445
>>
>> 346.2   0.181   22.02   16.445 16.445 16.445
>>
>> 346.3   10.82   5.984   16.445 16.445 16.445
>>
>> 346.4   10.81   6.002   16.445 16.445 16.445
>>
>> 346.5   10.819 6.008   16.445 16.445 16.445
>>
>> 346.6   10.813 5.996   16.445 16.445 16.445
>>
>> 346.7   10.781 6.006   16.445 16.445 16.445
>>
>> 346.8   10.793 6.026   

Re: [gmx-users] initial structures for md simulations

[Mark Abraham]

On 16/02/2011 11:24 PM, oguz gurbulak wrote:


/Dear All/,

I want to generate some initial crystalline structures of my 
targetmolecules for md simulations. /Are there any free softwares/ to 
do this?




Some sources for obtaining initial coordinates can be found here 
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File. I 
doubt there is going to be software to generate "crystalline" structures 
(whatever you mean by that). You could get a structure and replicate it 
with (e.g. genconf).


And are there any complete sources that give the theoretical 
structures of organic molecules ( like hydrocarbons ) determined by 
the experiments  and give the x-ray, neutron scattering, NMR, IR or 
Raman results of organic molecules apart from the articles ? Could you 
please share your  thoughts about this issue ?




Theoretical structures you compute according to some model. Experimental 
data tends to live in original literature and lots of specialist 
databases. Which do you actually want? Google is your friend either way.


Mark
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[gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

[Gerrit Groenhof]

.174   21.984 16.445 16.445 16.445
>> 
>> 344.8   0.176   21.98   16.445 16.445 16.445
>> 
>> 344.9   0.17 22.002 16.445 16.445 16.445
>> 
>> 345  0.173   21.981 16.445 16.445 16.445
>> 
>> 345.1   0.191   21.954 16.445 16.445 16.445
>> 
>> 345.2   0.183   21.958 16.445 16.445 16.445
>> 
>> 345.3   0.181   22.012 16.445 16.445 16.445
>> 
>> 345.4   0.17 22.054 16.445 16.445 16.445
>> 
>> 345.5   0.168   22.054 16.445 16.445 16.445
>> 
>> 345.6   0.189   22.039 16.445 16.445 16.445
>> 
>> 345.7   0.171   22.007 16.445 16.445 16.445
>> 
>> 345.8   0.186   22.031 16.445 16.445 16.445
>> 
>> 345.9   0.171   22.077 16.445 16.445 16.445
>> 
>> 346  0.187   21.99   16.445 16.445 16.445
>> 
>> 346.1   0.173   21.984 16.445 16.445 16.445
>> 
>> 346.2   0.181   22.02   16.445 16.445 16.445
>> 
>> 346.3   10.82   5.984   16.445 16.445 16.445
>> 
>> 346.4   10.81   6.002   16.445 16.445 16.445
>> 
>> 346.5   10.819 6.008   16.445 16.445 16.445
>> 
>> 346.6   10.813 5.996   16.445 16.445 16.445
>> 
>> 346.7   10.781 6.006   16.445 16.445 16.445
>> 
>> 346.8   10.793 6.026   16.445 16.445 16.445
>> 
>> 346.9   10.745 5.985   16.445 16.445 16.445
>> 
>> 347  10.762 5.999   16.445 16.445 16.445
>> 
>> 347.1   10.781 5.984   16.445 16.445 16.445
>> 
>> 347.2   10.784 6.002   16.445 16.445 16.445
>> -- next part --
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html
>> 
>> --
>> 
>> Message: 5
>> Date: Wed, 16 Feb 2011 10:43:56 +0100
>> From: Tsjerk Wassenaar 
>> Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi
>> To: Discussion list for GROMACS users 
>> Message-ID:
>>   
>> Content-Type: text/plain; charset=ISO-8859-1
>> 
>> Hi Ifat,
>> 
>> I guess this is a jump over the periodic boundaries. You should remove
>> jumps from the trajectory (-pbc nojump) before running g_mindist -pi.
>> 
>> Cheers,
>> 
>> Tsjerk
>> 
>> On Wed, Feb 16, 2011 at 10:19 AM, ifat shub  wrote:
>>> Hi,
>>> 
>>> 
>>> 
>>> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to
>> see
>>> if the complex is seeing its next periodic image, so I used the g_mindist
>>> command with the -pi option. My command line was:
>>> 
>>> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>>> 
>>> The output (see below) was stable until ~344ps when there is a  jump in
>> the
>>> max internal distance (third column) from ~6nm to ~22nm. After the jump
>> the
>>> numbers are reduced back to ~6nm and remained stable until the run is
>>> completed at 1ns.
>>> 
>>> Does anyone know how to explain this jump? Is this a real problem or just
>> a
>>> visualization artifact? Is there a way to avoid such jumps?
>>> 
>>> 
>>> 
>>> Here is the mdp file I used:
>>> 
>>> --run.mdp--
>>> 
>>> integrator  = md
>>> 
>>> nsteps  = 100
>>> 
>>> dt  = 0.001
>>> 
>>> coulombtype = pme
>>> 
>>> vdw-type= cut-off
>>> 
>>> tcoupl  = Berendsen
>>> 
>>> tc-grps = protein non-protein
>>> 
>>> tau-t   = 0.1 0.1
>>> 
>>> ref-t   = 310 310
>>> 
>>> nstxout = 100
>>> 
>>> nstvout = 0
>>> 
>>> nstxtcout   = 100
>>> 
>>> nstenergy   = 100
>>> 
>>> comm_mode = Linear ; Angular
>>> 
>>> comm_grps= Protein
>>> 
>>> xtc_grps   = Protein
>>> 
>>> energygrps = Protein
>>> 
>>> --
>>> 
>>> 
>>> 
>>> Thanks,
>>> 
>>> Ifat
>>> 
>>> 
>>> 
>>> The output:
>>> 
>>> 343.7   10.813 5.924   16.445 16.445 16.445
>>> 
>>> 343.8   10.809 5.949   16.445 16.445 16.445
>>> 
>>> 343.9   10.804 5.959   16.445 16.445 16.445
>>> 
>>> 344  10.808 5.974   16.445 16.445 16.445
>>> 
>>> 344.1   0.18

Re: [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

[Txema Mercero]

;>
>>> 345      0.173   21.981 16.445 16.445 16.445
>>>
>>> 345.1   0.191   21.954 16.445 16.445 16.445
>>>
>>> 345.2   0.183   21.958 16.445 16.445 16.445
>>>
>>> 345.3   0.181   22.012 16.445 16.445 16.445
>>>
>>> 345.4   0.17     22.054 16.445 16.445 16.445
>>>
>>> 345.5   0.168   22.054 16.445 16.445 16.445
>>>
>>> 345.6   0.189   22.039 16.445 16.445 16.445
>>>
>>> 345.7   0.171   22.007 16.445 16.445 16.445
>>>
>>> 345.8   0.186   22.031 16.445 16.445 16.445
>>>
>>> 345.9   0.171   22.077 16.445 16.445 16.445
>>>
>>> 346      0.187   21.99   16.445 16.445 16.445
>>>
>>> 346.1   0.173   21.984 16.445 16.445 16.445
>>>
>>> 346.2   0.181   22.02   16.445 16.445 16.445
>>>
>>> 346.3   10.82   5.984   16.445 16.445 16.445
>>>
>>> 346.4   10.81   6.002   16.445 16.445 16.445
>>>
>>> 346.5   10.819 6.008   16.445 16.445 16.445
>>>
>>> 346.6   10.813 5.996   16.445 16.445 16.445
>>>
>>> 346.7   10.781 6.006   16.445 16.445 16.445
>>>
>>> 346.8   10.793 6.026   16.445 16.445 16.445
>>>
>>> 346.9   10.745 5.985   16.445 16.445 16.445
>>>
>>> 347      10.762 5.999   16.445 16.445 16.445
>>>
>>> 347.1   10.781 5.984   16.445 16.445 16.445
>>>
>>> 347.2   10.784 6.002   16.445 16.445 16.445
>>> -- next part --
>>> An HTML attachment was scrubbed...
>>> URL:
>>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html
>>>
>>> --
>>>
>>> Message: 5
>>> Date: Wed, 16 Feb 2011 10:43:56 +0100
>>> From: Tsjerk Wassenaar 
>>> Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi
>>> To: Discussion list for GROMACS users 
>>> Message-ID:
>>>       
>>> Content-Type: text/plain; charset=ISO-8859-1
>>>
>>> Hi Ifat,
>>>
>>> I guess this is a jump over the periodic boundaries. You should remove
>>> jumps from the trajectory (-pbc nojump) before running g_mindist -pi.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Wed, Feb 16, 2011 at 10:19 AM, ifat shub  wrote:
>>>> Hi,
>>>>
>>>>
>>>>
>>>> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to
>>> see
>>>> if the complex is seeing its next periodic image, so I used the g_mindist
>>>> command with the -pi option. My command line was:
>>>>
>>>> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>>>>
>>>> The output (see below) was stable until ~344ps when there is a  jump in
>>> the
>>>> max internal distance (third column) from ~6nm to ~22nm. After the jump
>>> the
>>>> numbers are reduced back to ~6nm and remained stable until the run is
>>>> completed at 1ns.
>>>>
>>>> Does anyone know how to explain this jump? Is this a real problem or just
>>> a
>>>> visualization artifact? Is there a way to avoid such jumps?
>>>>
>>>>
>>>>
>>>> Here is the mdp file I used:
>>>>
>>>> --run.mdp--
>>>>
>>>> integrator      = md
>>>>
>>>> nsteps          = 100
>>>>
>>>> dt              = 0.001
>>>>
>>>> coulombtype     = pme
>>>>
>>>> vdw-type        = cut-off
>>>>
>>>> tcoupl          = Berendsen
>>>>
>>>> tc-grps         = protein non-protein
>>>>
>>>> tau-t           = 0.1 0.1
>>>>
>>>> ref-t           = 310 310
>>>>
>>>> nstxout         = 100
>>>>
>>>> nstvout         = 0
>>>>
>>>> nstxtcout       = 100
>>>>
>>>> nstenergy           = 100
>>>>
>>>> comm_mode     = Linear ; Angular
>>>>
>>>> comm_grps        = Protein
>>>>
>>>> xtc_grps               = Protein
>>>>
>>>> energygrps         = Protein
>>>>
>>>> --
>>>>
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Ifat
>>>>
>>>>
>>>>
>>>

Re: [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

[Gerrit Groenhof]

 = 310 310
>>>> 
>>>> nstxout = 100
>>>> 
>>>> nstvout = 0
>>>> 
>>>> nstxtcout   = 100
>>>> 
>>>> nstenergy   = 100
>>>> 
>>>> comm_mode = Linear ; Angular
>>>> 
>>>> comm_grps= Protein
>>>> 
>>>> xtc_grps   = Protein
>>>> 
>>>> energygrps = Protein
>>>> 
>>>> --
>>>> 
>>>> 
>>>> 
>>>> Thanks,
>>>> 
>>>> Ifat
>>>> 
>>>> 
>>>> 
>>>> The output:
>>>> 
>>>> 343.7   10.813 5.924   16.445 16.445 16.445
>>>> 
>>>> 343.8   10.809 5.949   16.445 16.445 16.445
>>>> 
>>>> 343.9   10.804 5.959   16.445 16.445 16.445
>>>> 
>>>> 344  10.808 5.974   16.445 16.445 16.445
>>>> 
>>>> 344.1   0.18 21.982 16.445 16.445 16.445
>>>> 
>>>> 344.2   10.778 5.977   16.445 16.445 16.445
>>>> 
>>>> 344.3   10.768 5.996   16.445 16.445 16.445
>>>> 
>>>> 344.4   10.764 6.016   16.445 16.445 16.445
>>>> 
>>>> 344.5   10.722 6.029   16.445 16.445 16.445
>>>> 
>>>> 344.6   10.774 6.01 16.445 16.445 16.445
>>>> 
>>>> 344.7   0.174   21.984 16.445 16.445 16.445
>>>> 
>>>> 344.8   0.176   21.98   16.445 16.445 16.445
>>>> 
>>>> 344.9   0.17 22.002 16.445 16.445 16.445
>>>> 
>>>> 345  0.173   21.981 16.445 16.445 16.445
>>>> 
>>>> 345.1   0.191   21.954 16.445 16.445 16.445
>>>> 
>>>> 345.2   0.183   21.958 16.445 16.445 16.445
>>>> 
>>>> 345.3   0.181   22.012 16.445 16.445 16.445
>>>> 
>>>> 345.4   0.17 22.054 16.445 16.445 16.445
>>>> 
>>>> 345.5   0.168   22.054 16.445 16.445 16.445
>>>> 
>>>> 345.6   0.189   22.039 16.445 16.445 16.445
>>>> 
>>>> 345.7   0.171   22.007 16.445 16.445 16.445
>>>> 
>>>> 345.8   0.186   22.031 16.445 16.445 16.445
>>>> 
>>>> 345.9   0.171   22.077 16.445 16.445 16.445
>>>> 
>>>> 346  0.187   21.99   16.445 16.445 16.445
>>>> 
>>>> 346.1   0.173   21.984 16.445 16.445 16.445
>>>> 
>>>> 346.2   0.181   22.02   16.445 16.445 16.445
>>>> 
>>>> 346.3   10.82   5.984   16.445 16.445 16.445
>>>> 
>>>> 346.4   10.81   6.002   16.445 16.445 16.445
>>>> 
>>>> 346.5   10.819 6.008   16.445 16.445 16.445
>>>> 
>>>> 346.6   10.813 5.996   16.445 16.445 16.445
>>>> 
>>>> 346.7   10.781 6.006   16.445 16.445 16.445
>>>> 
>>>> 346.8   10.793 6.026   16.445 16.445 16.445
>>>> 
>>>> 346.9   10.745 5.985   16.445 16.445 16.445
>>>> 
>>>> 347  10.762 5.999   16.445 16.445 16.445
>>>> 
>>>> 347.1   10.781 5.984   16.445 16.445 16.445
>>>> 
>>>> 347.2   10.784 6.002   16.445 16.445 16.445
>>>> -- next part --
>>>> An HTML attachment was scrubbed...
>>>> URL:
>>>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html
>>>> 
>>>> --
>>>> 
>>>> Message: 5
>>>> Date: Wed, 16 Feb 2011 10:43:56 +0100
>>>> From: Tsjerk Wassenaar 
>>>> Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi
>>>> To: Discussion list for GROMACS users 
>>>> Message-ID:
>>>>   
>>>> Content-Type: text/plain; charset=ISO-8859-1
>>>> 
>>>> Hi Ifat,
>>>> 
>>>> I guess this is a jump over the periodic boundaries. You should remove
>>>> jumps from the trajectory (-pbc nojump) before running g_mindist -pi.
>>>> 
>>>> Cheers,
>>>> 
>>>> Tsjerk
>>>> 
>>>> On Wed, Feb 16, 2011 at 10:19 AM, ifat shub  wrote:
>>>>> Hi,
>>>>> 
>>>>> 
>>>>> 
>>>>> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to
>>>> see
>>>>> if the complex is seeing its next periodi

[gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

[Xiaohu Li]

4 16.445 16.445 16.445

346.2   0.181   22.02   16.445 16.445 16.445

346.3   10.82   5.984   16.445 16.445 16.445

346.4   10.81   6.002   16.445 16.445 16.445

346.5   10.819 6.008   16.445 16.445 16.445

346.6   10.813 5.996   16.445 16.445 16.445

346.7   10.781 6.006   16.445 16.445 16.445

346.8   10.793 6.026   16.445 16.445 16.445

346.9   10.745 5.985   16.445 16.445 16.445

347  10.762 5.999   16.445 16.445 16.445

347.1   10.781 5.984   16.445 16.445 16.445

347.2   10.784 6.002   16.445 16.445 16.445
-- next part --
An HTML attachment was scrubbed...
URL:
http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html

--

Message: 5
Date: Wed, 16 Feb 2011 10:43:56 +0100
From: Tsjerk Wassenaar 
Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi
To: Discussion list for GROMACS users 
Message-ID:
  
Content-Type: text/plain; charset=ISO-8859-1

Hi Ifat,

I guess this is a jump over the periodic boundaries. You should remove
jumps from the trajectory (-pbc nojump) before running g_mindist -pi.

Cheers,

Tsjerk

On Wed, Feb 16, 2011 at 10:19 AM, ifat shub  wrote:


Hi,



I am running a simulation on the complex 1aik.pdb in 310K. I wanted to
  

see


if the complex is seeing its next periodic image, so I used the g_mindist
command with the -pi option. My command line was:

g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi

The output (see below) was stable until ~344ps when there is a  jump in
  

the


max internal distance (third column) from ~6nm to ~22nm. After the jump
  

the


numbers are reduced back to ~6nm and remained stable until the run is
completed at 1ns.

Does anyone know how to explain this jump? Is this a real problem or just
  

a


visualization artifact? Is there a way to avoid such jumps?



Here is the mdp file I used:

--run.mdp--

integrator  = md

nsteps  = 100

dt  = 0.001

coulombtype = pme

vdw-type= cut-off

tcoupl  = Berendsen

tc-grps = protein non-protein

tau-t   = 0.1 0.1

ref-t   = 310 310

nstxout = 100

nstvout = 0

nstxtcout   = 100

nstenergy   = 100

comm_mode = Linear ; Angular

comm_grps= Protein

xtc_grps   = Protein

energygrps = Protein

--



Thanks,

Ifat



The output:

343.7   10.813 5.924   16.445 16.445 16.445

343.8   10.809 5.949   16.445 16.445 16.445

343.9   10.804 5.959   16.445 16.445 16.445

344  10.808 5.974   16.445 16.445 16.445

344.1   0.18 21.982 16.445 16.445 16.445

344.2   10.778 5.977   16.445 16.445 16.445

344.3   10.768 5.996   16.445 16.445 16.445

344.4   10.764 6.016   16.445 16.445 16.445

344.5   10.722 6.029   16.445 16.445 16.445

344.6   10.774 6.01 16.445 16.445 16.445

344.7   0.174   21.984 16.445 16.445 16.445

344.8   0.176   21.98   16.445 16.445 16.445

344.9   0.17 22.002 16.445 16.445 16.445

345  0.173   21.981 16.445 16.445 16.445

345.1   0.191   21.954 16.445 16.445 16.445

345.2   0.183   21.958 16.445 16.445 16.445

345.3   0.181   22.012 16.445 16.445 16.445

345.4   0.17 22.054 16.445 16.445 16.445

345.5   0.168   22.054 16.445 16.445 16.445

345.6   0.189   22.039 16.445 16.445 16.445

345.7   0.171   22.007 16.445 16.445 16.445

345.8   0.186   22.031 16.445 16.445 16.445

345.9   0.171   22.077 16.445 16.445 16.445

346  0.187   21.99   16.445 16.445 16.445

346.1   0.173   21.984 16.445 16.445 16.445

346.2   0.181   22.02   16.445 16.445 16.445

346.3   10.82   5.984   16.445 16.445 16.445

346.4   10.81   6.002   16.445 16.445 16.445

346.5   10.819 6.008   16.445 16.445 16.445

346.6   10.813 5.996   16.445 16.445 16.445

346.7   10.781 6.006   16.445 16.445 16.445

346.8   10.793 6.026   16.445 16.445 16.445

346.9   10.745 5.985   16.445 16.445 16.445

347  10.762 5.999   16.445 16.445 16.445

347.1   10.781 5.984   16.445 16.445 16.445

347.2   10.784 6.002   16.445 16.445 16.445





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* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
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[gmx-users] Re: Re: g_rmsf reference structure? (Tsjerk Wassenaar)

[kulleperuma . kulleperuma]

Thank you very much for the clarification!



Message: 1
Date: Wed, 16 Feb 2011 10:46:18 +0100
From: Tsjerk Wassenaar 
Subject: Re: [gmx-users] g_rmsf reference structure?
To: Discussion list for GROMACS users 
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1

Hi,

The reference is used for fitting. The RMSF is calculated with respect
to the average (fitted) structure, unless you explicitly specify that
deviations from the reference should be used.

Cheers,

Tsjerk

On Wed, Feb 16, 2011 at 7:08 AM, Mark Abraham   
 wrote:

On 16/02/2011 3:44 PM, kulleperuma.kulleper...@utoronto.ca wrote:


Dear all,

I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms
with reference to the average structure between 5-10 ns of a total of 10 ns
simulation as below;
g_rmsf  ?f md.xtc  ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg

My understanding of the RMSF is as follows;

 RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2)

where T is the time over which one wants to average, and Xi is the
reference position of particle i, which is the time-averaged   
position of the

same particle i.
What I am confused is whether g_rmsf takes the reference structure from
the structure file (-s), which in my case, the md.tpr and NOT the time
averaged position over the specified time?


It does take the reference structure from -s. Whether you actually want the
RMSF from the non-physical time-averaged structure is up to you. IIRC you
might be able to get such an average from g_cluster.

Mark
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Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands


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[gmx-users] Protein-membrane system

[Aldo Segura]

Dear
gmx-users,



I
completed a MD (10 ns) of my protein-membrane system. When I perform a visual 
inspection
(VMD) of md_0_1.gro file
I
observed a few water molecules within the
bilayer. In previous steps (e.g. equilibration) this was not observed. Could be
expected such behavior?



Best regards,




== =
Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: asegu...@ipn.mx; aldoseg...@gmail.com
== ===


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Re: [gmx-users] Protein-membrane system

[Justin A. Lemkul]

Aldo Segura wrote:

Dear gmx-users,

I completed a MD (10 ns) of my protein-membrane system. When I perform a 
visual inspection (VMD) of md_0_1.gro file I observed a few water 
molecules within the bilayer. In previous steps (e.g. equilibration) 
this was not observed. Could be expected such behavior?


Membrane protein systems take a long time (tens of ns or maybe more) to 
equilibrate, so some water may drift in and out during the initial few ns as 
voids in the lipids open and close.  Nothing to worry about, unless for some 
reason they persist out past the expected equilibration time.


-Justin



Best regards,


*//*

*/== =
Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: asegu...@ipn.mx ; aldoseg...@gmail.com 


== ===/*


 



--


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 and 4.5.2 version

[Zuzana Benkova]

Dear Justin, maybe following information helps you. When I evaluated the number of hydrogen bonds between two different groups, particularly, water and frozen atoms of the siloxane surface I got the same results with both version of GROMACS, 4.0.3 and 4.5.2.GreetingsZuzanaOn 02/15/11, Zuzana Benkova   wrote:Hello Justin, I was using cubic boxes. GreetingsZuzanaOn 02/15/11, Erik Marklund   wrote:Justin A. Lemkul skrev 2011-02-09 23.03:>>>Zuzana Benkova wrote:>>Dear GROMACS users,I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average  number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and  per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond.>>However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2.>>I would appreciate any help. Thank you in advance.Try pulling the latest stable development version.  This issue was reported in 4.5.1:>>http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html>>but not fixed until after 4.5.3 was released:>>http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html>>-Justin>>>Greetings>>Zuzana>>>Are people who are reporting this error using a triclinic boxes or cuboid boxes. That information may help my bugfixing.-- ---Erik Marklund, PhD studentDept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596,    75124 Uppsala, Swedenphone:    +46 18 471 4537    fax: +46 18 511 755er...@xray.bmc.uu.se    http://folding.bmc.uu.se/-- gmx-users mailing list    gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease 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

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[gmx-users] Re: angle constrain, constrained PF6 anion

[Vitaly Chaban]

Hello,

I got your files. However, the error is completely another than you
mention and it occurs directly at the first time-step of the
simulation.


Inner product between old and new vector <= 0.0!
constraint #1 atoms 1377 and 1381
Wrote pdb files with previous and current coordinates
step 0Inner product between old and new vector <= 0.0!
constraint #1 atoms 2177 and 2181
Wrote pdb files with previous and current coordinates
Inner product between old and new vector <= 0.0!
constraint #1 atoms 2 and 6
Wrote pdb files with previous and current coordinates
Segmentation fault


There are a number of strange things in your configuration with the
unhealthy defined constraints in topology as probably the most severe
one. If you have constraints, why do you define bonds force constants
at the same time?

Good luck with your study,
Vitaly




On Wed, Feb 16, 2011 at 1:58 PM,   wrote:
>
> Hi Vitaly,
>
> Thanks for your answer. I was busy with other stuff these last two weeks,
> that's why I have time to reply only now.
>
> So the system is the BMIM PF6 ionic liquid.
> We chose two potentials to describe the system, and both treat the anion as
> rigid. We cannot use LINCS because it shouldn't be used if one constrains
> not only bonds but angles too, so we have to use SHAKE.
>
> But with SHAKE I encountered some strange things as I wrote in my first
> thread. In the attachement I am sending you all the files needed for the
> simulation, maybe you'll find the problem.
>
> I haven"t mentioned but we try to constrain the angles by adding fictious
> bonds. Maybe there is something wrong with this...
>
> Thank you in advance for your help.
>
> All the best,
> Gyorgy
>
>
> Quoting Vitaly Chaban :
>
>> Hey  Gyorgy,
>>
>> Your current topology file(s) is(are) also important to analyze the
>> situation and fix the problem.
>>
>> Pass my kind regards to Julia...
>>
>> 
>> Dr. Vitaly V. Chaban, Ph.D.
>> Department of Chemistry
>> University of Rochester
>> Rochester, New York 14627-0216
>> The United States of America
>> =
>>
>>
>>> The mdp file is attached.
>>> Best,
>>> Gyorgy
>>>
>>> Quoting "Justin A. Lemkul" :
>>>


 gyorgy.han...@fc.up.pt wrote:
>
> Dear all,
>
> I am setting up a simulation of ionic liquids with the PF6 anion.
> According to the potential, the anion should be kept rigid, wich
> obviously means that bond lengths and angles have to be
> constrained. LINCS doesn't work with angle constraints (i.e.
> constraing a triangle), so we decided to use SHAKE. However, SHAKE
> seems to work a bit strangely: I know SHAKE mustn't be used with
> domain decomposition, but even if I set the corresponding variable
> to NO in the mdp file, the simulation crashes on 8 procs and gives
> the following error message:
>
> Fatal error:
> 1 particles communicated to PME node 7 are more than a cell length
> out of the domain decomposition cell of their charge group.
>
> If I try to run mdrun with -pd (to 'really' switch off domain
> decomposition), the simulation doesn't chrash but gives nonsense
> (the energy seems to increase constantly).
>
> I am not an expert user so maybe I do something wrong but, anyway,
> does anyone have an idea how to constrain this anion with Gromacs?
> I checked mailing list archive but couldn't find any answer
> corresponding to my question.
>

 Without seeing a complete .mdp file, it's not possible to fully
 diagnose this problem.  The combination of SHAKE + particle
 decomposition should be stable, but there are a whole host of different
 things that can go wrong.

 -Justin

> Thanks in advance.
>
> Gyorgy
>
>

 --
 

 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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>>>
>>>
>>> -- next part --
>>> title                    = BMIM PF6 bulk simulation
>>> cpp                      = /usr/bin/cpp
>>>
>>> ; RUN CONTROL PARAMETERS  ;l_bfgs
>>> integrator               = md;steep
>>> ; Start time and timestep in ps
>>> tinit                    = 0
>

Re: [gmx-users] g_hbond and 4.5.2 version

[Erik Marklund]

Hi,

That suggets it's related to the new merge-on-the-fly-code and not the 
pbc handling.


And it's me, not Justin, who's fixing and probably creating the bugs. :-)

Cheers,

Erik

Zuzana Benkova skrev 2011-02-16 19.58:

Dear Justin,

maybe following information helps you. When I evaluated the number of 
hydrogen bonds between two different groups, particularly, water and 
frozen atoms of the siloxane surface I got the same results with both 
version of GROMACS, 4.0.3 and 4.5.2.


Greetings
Zuzana

On 02/15/11, *Zuzana Benkova *  wrote:

Hello Justin,

I was using cubic boxes.

Greetings
Zuzana

On 02/15/11, *Erik Marklund *  wrote:

Justin A. Lemkul skrev 2011-02-09 23.03:
>
>
>Zuzana Benkova wrote:
>>Dear GROMACS users,
>>
>>I have used g_hbond of version 4.5.2 to analyze number of hydrogen 
bonds in water. I got the average  number per time frame and number 
of water oxygen atoms equal to 0.839. When I used g_hbond of version 
4.0.7 I got 1.677, which is twice the former value. TIP3P model 
predicts over 3 hydrogen bonds per one water molecule. I am a bit 
puzzled. If I multiply the digit from version 4.0.7. by 2 I get the 
expected number. That is why I supposed that the number of 1.677 
means per one water oxygen and  per one water molecule means 2x1.677 
since two water molecules participate at one hydrogen bond.
>>However, I do not know yet if my interpretation is correct and how 
to interpret the number obtained by version 4.5.2.

>>I would appreciate any help. Thank you in advance.
>>
>
>Try pulling the latest stable development version.  This issue was 
reported in 4.5.1:

>
>http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html
>
>but not fixed until after 4.5.3 was released:
>
>http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html
>
>-Justin
>
>>Greetings
>>Zuzana
>>
>
Are people who are reporting this error using a triclinic boxes or 
cuboid boxes. That information may help my bugfixing.


--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/

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---
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] mpirun error?

[Justin Kat]

Dear Gromacs,

My colleague has attempted to issue this command:


mpirun -np 8 (or 7) mdrun_mpi .. (etc)


According to him, he gets the following error message:


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.
--


---
Program mdrun_mpi, VERSION 4.0.7
Source code file: domdec.c, line: 5888

Fatal error:
There is no domain decomposition for 7 nodes that is compatible with the
given box and a minimum cell size of 0.955625 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS
settings


However, when he uses say, -np 6, he seems to get no error. Any insight on
why this might be happening?

Also, when he saves the output to a file, sometimes he sees the following:


NOTE: Turning on dynamic load balancing


Is this another flag that might be causing the crash? What does that line
mean?

Thanks!
Justin
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Re: [gmx-users] mpirun error?

[Justin A. Lemkul]

Justin Kat wrote:

Dear Gromacs,

My colleague has attempted to issue this command:


mpirun -np 8 (or 7) mdrun_mpi .. (etc)


According to him, he gets the following error message:


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.

--


--- 
Program mdrun_mpi, VERSION 4.0.7

Source code file: domdec.c, line: 5888

Fatal error:
There is no domain decomposition for 7 nodes that is compatible with the 
given box and a minimum cell size of 0.955625 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS 
settings



However, when he uses say, -np 6, he seems to get no error. Any insight 
on why this might be happening?




When any error comes up, the first port of call should be the Gromacs site, 
followed by a mailing list search.  In this case, the website works quite nicely:


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


Also, when he saves the output to a file, sometimes he sees the following:


NOTE: Turning on dynamic load balancing


Is this another flag that might be causing the crash? What does that 
line mean?


See the manual and/or Gromacs 4 paper for an explanation of dynamic load 
balancing.  This is a normal message.


-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] Protein-membrane system

[Itamar Kass]

Dear Aldo,

It is totally OK to see water molecules within the bilayer, both in 
simulations and real life. If I am not totally wrong, 3000 water 
molecule per lipids per second are being transferred across the bilayer 
without any protein involvement.


If your system is stable, the lipids density profile seems OK as well as 
its the thickness, you are fine.


Cheers,
Itamar.

On 17/02/11 5:48 AM, Justin A. Lemkul wrote:


Aldo Segura wrote:

Dear gmx-users,

I completed a MD (10 ns) of my protein-membrane system. When I 
perform a visual inspection (VMD) of md_0_1.gro file I observed a few 
water molecules within the bilayer. In previous steps (e.g. 
equilibration) this was not observed. Could be expected such behavior?


Membrane protein systems take a long time (tens of ns or maybe more) 
to equilibrate, so some water may drift in and out during the initial 
few ns as voids in the lipids open and close.  Nothing to worry about, 
unless for some reason they persist out past the expected 
equilibration time.


-Justin



Best regards,


*//*

*/== =
Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: asegu...@ipn.mx ; 
aldoseg...@gmail.com 

== ===/*








--


"In theory, there is no difference between theory and practice. But, in practice, 
there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu


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[gmx-users] zero atoms for FE P

[Moeed]

Hello,

I tried to follow the FE tutorials and get my own system working but it
seems I am missing something coz I get a blank dgdl file. log file is
saying:


There are 0 atoms and 0 charges for free energy perturbation
Removing pbc first time

What I do is running EM (lambda 0) on a solvated system which is already
equilibrated (and density is obtained by NPT) followed by a MD NVT since
density has to be fixed. My guess is I am making mistake in combining itp
file of hexane into  polymer (solute).

EM

grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr >&
output.grompp_em

mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g  em-l0.log -e em-l0.edr -v
>& output.mdrun_em

MD

grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n
PE-HEX.ndx>& output.grompp_md

mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr -x
md-l0.xtc -dgdl md-l0.dgdl -v >& output.mdrun_md


PE60-0c-itp.top  is:
==
; Include forcefield parameters
#include "ffoplsaa.itp"

#include "Hexane-0c.itp"

[ moleculetype ]
; Namenrexcl
Polymer 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
 1   opls_135  1   EthB C1  1  0 12.011   ; qtot
0
 2   opls_140  1   EthBH11  1  0  1.008   ; qtot
0
 3   opls_140  1   EthBH12  1  0  1.008   ; qtot
0
 4   opls_140  1   EthBH13  1  0  1.008   ; qtot
0
 5   opls_136  1   EthB C2  2  0 12.011   ; qtot
0

.
.
; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Polymer

[ molecules ]
; Compound#mols
Polymer 4
Hexane  480
===

Please help me what wrong is...

Thanks
moeed
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Re: [gmx-users] zero atoms for FE P

[Justin A. Lemkul]

Moeed wrote:

Hello,

I tried to follow the FE tutorials and get my own system working but it 
seems I am missing something coz I get a blank dgdl file. log file is 
saying:



There are 0 atoms and 0 charges for free energy perturbation 
Removing pbc first time


What I do is running EM (lambda 0) on a solvated system which is already 
equilibrated (and density is obtained by NPT) followed by a MD NVT since 
density has to be fixed. My guess is I am making mistake in combining 
itp file of hexane into  polymer (solute).


EM

grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr >& 
output.grompp_em


mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g  em-l0.log -e em-l0.edr 
-v >& output.mdrun_em


MD

grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n 
PE-HEX.ndx>& output.grompp_md


mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr 
-x md-l0.xtc -dgdl md-l0.dgdl -v >& output.mdrun_md




PE60-0c-itp.top  is:
==
; Include forcefield parameters
#include "ffoplsaa.itp"

#include "Hexane-0c.itp"

[ moleculetype ]
; Namenrexcl
Polymer 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  
typeBchargeB  massB
 1   opls_135  1   EthB C1  1  0 12.011   ; 
qtot 0
 2   opls_140  1   EthBH11  1  0  1.008   ; 
qtot 0
 3   opls_140  1   EthBH12  1  0  1.008   ; 
qtot 0
 4   opls_140  1   EthBH13  1  0  1.008   ; 
qtot 0
 5   opls_136  1   EthB C2  2  0 12.011   ; 
qtot 0


.
.
; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Polymer

[ molecules ]
; Compound#mols
Polymer 4
Hexane  480   
===


Please help me what wrong is...



Probably the most important piece of information is your .mdp file, but you 
didn't post it, so please do.


-Justin


Thanks
moeed



--


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] Protein-membrane system

[Jianguo Li]

Hi,

"3000 water molecule per lipids per second" corresponds to 0.000384 water 
molecules transferred across the membrane per nano second (assume the system 
contains 128 lipids). It seems water translocation should not be observed in a 
simulation of 10 ns, but I am not sure. And I only find one reference 
paper(Biophysical Journal, Volume 96, 2009, pg4493–4501) about the water 
translocation across the membrane, in which a asymmetric membrane is used.  


I also have similar observations for my protein-membrane system. I observed 
10~15 times water translocation arosss the membrane during 100 ns simulation 
when my protein adsorbed on the membrane. I am wondering these water 
translocation is normal in all-atom simulations or they are due to the 
protein-induced membrane deformation?

Any comment is highly appreciated, thank you!

best regards,
Jianguo






From: Itamar Kass 
To: Discussion list for GROMACS users 
Sent: Thursday, 17 February 2011 07:20:19
Subject: Re: [gmx-users] Protein-membrane system

Dear Aldo,

It is totally OK to see water molecules within the bilayer, both in simulations 
and real life. If I am not totally wrong, 3000 water molecule per lipids per 
second are being transferred across the bilayer without any protein involvement.

If your system is stable, the lipids density profile seems OK as well as its 
the 
thickness, you are fine.

Cheers,
Itamar.

On 17/02/11 5:48 AM, Justin A. Lemkul wrote:
> 
> Aldo Segura wrote:
>> Dear gmx-users,
>> 
>> I completed a MD (10 ns) of my protein-membrane system. When I perform a 
>> visual 
>>inspection (VMD) of md_0_1.gro file I observed a few water molecules within 
>>the 
>>bilayer. In previous steps (e.g. equilibration) this was not observed. Could 
>>be 
>>expected such behavior?
> 
> Membrane protein systems take a long time (tens of ns or maybe more) to 
>equilibrate, so some water may drift in and out during the initial few ns as 
>voids in the lipids open and close.  Nothing to worry about, unless for some 
>reason they persist out past the expected equilibration time.
> 
> -Justin
> 
>> 
>> Best regards,
>> 
>> 
>> *//*
>> 
>> */== =
>> Aldo Segura-Cabrera
>> Laboratorio de Bioinformática
>> Centro de Biotecnología Genómica
>> Instituto Politécnico Nacional
>> Blvd. Del Maestro esquina Elías Piña, 88710
>> Reynosa, Tamaulipas, México.
>> (899)9243627 ext. 87747
>> e-mail: asegu...@ipn.mx ; aldoseg...@gmail.com 
>>
>> == ===/*
>> 
>> 
>> 
>> 
> 

-- 

"In theory, there is no difference between theory and practice. But, in 
practice, there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu


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[gmx-users] RE: simulation of a metal binding sites

[bharat gupta]

Hi,

I have incorporated some metal binding sites(zinc ion) in my protein. Now I
want to see whether that region binds to zinc ions or not and what is the
effect of ion binding to the topology of the protein .. Can this be done
using gromacs and how ??

Regards

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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