date:20091020

wuxiao wrote:
> Dear GMXers,
>When I perfomed a MD simulation, it always teminated after about 700 
> ps with the message:
> /Fatal error: 2 particles communicated to PME node 0 are more than a 
> cell length out of the domain decomposition cell of their charge group/
>I utilized the GROMACS-4.0.5. I have searched the maillist to find 
> some similar posts but they can not yet cope with this issues. Could you 
> give me some clues, please?

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

Mark
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[gmx-users] Fatal error: 2 particles communicated to PME node 0 are more than a cell length out of the domain decomposition cell of their charge group

2009-10-20 Thread wuxiao


Dear GMXers,

   When I perfomed a MD simulation, it always teminated after about 700 ps with 
the message:

Fatal error: 2 particles communicated to PME node 0 are more than a cell length 
out of the domain decomposition cell of their charge group

   I utilized the GROMACS-4.0.5. I have searched the maillist to find some 
similar posts but they can not yet cope with this issues. Could you give me 
some clues, please?

  Best wishes,

  Chaofu Wu, Dr.
  
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Re: [gmx-users] why are the values of the LJ interaction energy negative and the values of the Coulomb interaction energy positive between two group.

Jinyao Wang wrote:
> Hi gmx-users,
>I have calculated the interaction energy between two group. But I find 
> that the values of the LJ interaction energy are negative and the values of 
> the Coulomb interaction energy are positive between two group. So I think the 
> LJ interaction is attractive and the Coulomb interaction is repulsive. Is it 
> correct for my consideration of the interaction ?  

Maybe. That conclusion would assume
a) that you've calculated it correctly,
b) that the model physics is robust with respect to such a decomposition
when it almost certainly wasn't parameterized for such a property, and
c) the decomposed interaction energy means anything.

Mark
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[gmx-users] why are the values of the LJ interaction energy negative and the values of the Coulomb interaction energy positive between two group.

2009-10-20 Thread Jinyao Wang

Hi gmx-users,
   I have calculated the interaction energy between two group. But I find that 
the values of the LJ interaction energy are negative and the values of the 
Coulomb interaction energy are positive between two group. So I think the LJ 
interaction is attractive and the Coulomb interaction is repulsive. Is it 
correct for my consideration of the interaction ?  





Jinyao Wang
wan...@ciac.jl.cn
　　2009-10-21
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Re: [gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field




Pablo Englebienne wrote:


Thanks for confirming this, Justin.

I decided not to use the user-contributed CHCl3 box because the topology 
is not consistent with the GROMOS atom types: the CH is united atom 
(although the mass is 12.01100, it should probably be 13.01900?), while 
in G53a5 there are parameters for C, H and Cl. Has someone ever used 
this box successfully?


I was able to equilibrate the box in NVT (100-200ps gives a stable 
simulation), although it exploded at constant pressure. After looking at 
some references on the mailing lists (both GMX and AMBER), I tried 
increasing tau_p from 2.0 to 5.0 and that yielded a stable 100 ps 
simulation, although the system later (continuing for further ~150 ps) 
started to oscillate wildly in temperature and pressure.


What is the effect of increasing tau_p? Besides making the dynamics 
stable, would changing its value affect the outcome of the simulation in 
any other way?


By increasing tau_p you are reducing the stringency of the pressure coupling, 
i.e. allowing the system to change a bit more between coordinate scaling.  By 
decreasing the frequency of coordinate scaling in extremis, you would lose the 
benefit of pressure coupling and achieve an NVT ensemble, with the box 
dimensions being essentially static.  In the case of a tau_p of 2.0 vs. 5.0, you 
should not have this problem.


If the provided box uses a united-atom CH, I would suspect it is not suitable 
for GROMOS96 parameters, as you have discovered.  In all G96 variants, the H is 
explicitly represented.  You might consider coming up with your own box.  Start 
with a coordinate file for one molecule, use genconf to generate a box, and 
equilibrate.


If you want any further information about diagnosing the current problem, 
posting the .mdp file would be helpful.


-Justin



Thanks again!
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--


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


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Re: [gmx-users] how to mimick explicit hydrogen bonding


ms wrote:

Hi,

I need to implement a FF which includes directional hydrogen bonding. It
seems however, to my understanding, that Gromacs has no simple way to
include an explicitly directional contribution. All I can find is that,
in standard force fields, h-bond terms are implicitly described by
coulombic and vdw interactions, but I am a bit puzzled by how these
terms are combined to give a directional interaction.


There's nothing directional about the physics of a hydrogen bond, unless 
your model makes it so. There'd be nothing intrinsically valid or 
invalid with that either, so long as you parameterized the force field 
under that assumption. If using rigid water models and/or other atomic 
constraints where H-bonded atoms can't have a geometric distortion, I 
suppose such a model might be necessary. It's still far from clear that 
H-bonding is sufficiently different from other electrostatic 
interactions to warrant special treatment (and thus reparameterization 
of charges).



Can anyone give me hints on how to describe a directional
hydrogen-bond-like interaction?


You would not achieve this in GROMACS without code modification. A 
special non-bonded list for H-bonded water (and maybe H-bonded 
non-water) that didn't call the standard water inner loops would be 
required.


MArk
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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD


Justin A. Lemkul wrote:


I have also added a Perl script to the GROMACS site (the VMD page):

http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD

The user provides an input topology file, and a .psf file is written, 
which can be loaded as data for the structure in VMD.  The !NBOND 
section seems to be the most important in this regard, so the other 
sections are a bit rough, but it seems to work alright.


The caveat is the topology must be one generated by MARTINI, in order to 
satisfy all the pattern matching and the order of the topology.  It 
should be fairly easy to modify the program further to accommodate other 
layouts, but I haven't had the need to do so.


I added text to the above page describing both scripts, which are 
attached. I'd have done that yesterday but the website was 
intermittently down.


Mark


Nicolas Sapay wrote:

Hello Thomas,

I have a tcl script in my personal script library that might do what 
you want to do. I didn't use it for quite a while, but it was working 
well as far as I remember. I think it has been adapted from a script 
available on the VMD website, but I don't remember exactly its 
history. It doesn't seem too difficult to understand. You should be 
able to modify it for your own purpose, if needed.


Cheers,
Nicolas


Thomas Schmidt a écrit :

Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?

Thomas

  


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[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

2009-10-20 Thread Pablo Englebienne

I'm trying to simulate a small molecule in a chloroform box using the
GROMOS G53a5 forcefield. I realized that the parameters for the
solvent

are present in the ffG53a5.rtp file, however I could not find a CHCl3
solvent box included in GROMACS. I did find, however, a CHCl3 solvent
box equilibrated by PeiQuan Chen
(http://lists.gromacs.org/pipermail/gmx-users/2003-May/005572.html)
at

http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies
.

I also saw mention of a box for the Amber forcefield, that is now
included in AmberTools (amber10/dat/solvents/cform/cform.pdb and
chcl3_equil.pdb.1). I took this one and I'm equilibrating it to use
it

later.

In the mean time, I wanted to know if I overlooked something, and
there

is a CHCl3 box to use with the GROMOS forcefield?

Not one that is officially distributed. If it was, it would be the
/share/gromacs/top subdirectory with other solvent topologies and
structures.
Probably your best bet is to use the one in the User Contributions
section,

unless you feel the need to create your own and start from scratch.

Thanks for confirming this, Justin.

I decided not to use the user-contributed CHCl3 box because the
topology is not consistent with the GROMOS atom types: the CH is
united atom (although the mass is 12.01100, it should probably be
13.01900?), while in G53a5 there are parameters for C, H and Cl. Has
someone ever used this box successfully?

I was able to equilibrate the box in NVT (100-200ps gives a stable
simulation), although it exploded at constant pressure. After looking
at some references on the mailing lists (both GMX and AMBER), I tried
increasing tau_p from 2.0 to 5.0 and that yielded a stable 100 ps
simulation, although the system later (continuing for further ~150 ps)
started to oscillate wildly in temperature and pressure.

What is the effect of increasing tau_p? Besides making the dynamics
stable, would changing its value affect the outcome of the simulation
in any other way?

Thanks again!
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Re: [gmx-users] non-standard atom names




Stefano Meliga wrote:

Hello,

I noticed that the command editconf -i structure.gro -o structure.pdb 
produce a pdb file in which some atom names are not standard.


In particular the delta carbon on ILE:

"CD  ILE" should be "CD1 ILE";

and the oxigens of the C-terminus

"O1" should be "O "
"O2" should be "OXT".

This is particularly annoying when GROMACS' output pdb is then used in 
input of other software, e.g. FIRST.


You might want to fix this.



I think "should be" is a matter of perspective.  The atoms are named according 
to GROMACS convention, and are used consistently within all force field files 
(.rtp, .tdb, etc).  If you are aware of inconsistencies with other programs, I 
would think a few simple find-and-replace commands in a text editor (or 
scripting, awk, sed, etc) would solve the problem, without a re-write of 
numerous GROMACS files (and code?).


-Justin


Sincerely,

Stefano




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--


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


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Re: [gmx-users] Long Simulation Time




Chih-Ying Lin wrote:



HI
 i was reading somewhere..  "simulation will break / terminate when 
the simulation is running so so long "...


Did anyone read the same information?
Please refer me the related information since I have no idea where I 
read this information.


How long is long ?
How to avoid this?



I've never heard of such a thing.  Unless you can produce the source, no one can 
comment on its validity.  I've had jobs that run for weeks of computing time 
without problem, and I know others whose jobs are even longer.


The only potentially related information I can think of is using mdrun -maxh, 
which will terminate the run if it exceeds the specified value.


Unless you're actually seeing a problem with long simulations inexplicably 
dying, I wouldn't think there's a reason to worry.


-Justin



Thank you
Lin




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


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Re: [gmx-users] Long Simulation Time

2009-10-20 Thread Tsjerk Wassenaar

Hi Lin,

That is likely related to running with a scheduler that only allows a
limited time for processes (the wall time). Under 'normal' conditions
the simulation will not break due to long running times. It may break
due to a full disk, which can be related to a long running time :p

Cheers,

Tsjerk

On Tue, Oct 20, 2009 at 6:53 PM, Chih-Ying Lin  wrote:
>
>
> HI
>  i was reading somewhere..  "simulation will break / terminate when the
> simulation is running so so long "...
> Did anyone read the same information?
> Please refer me the related information since I have no idea where I read
> this information.
> How long is long ?
> How to avoid this?
>
> Thank you
> Lin
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] Long Simulation Time

2009-10-20 Thread Chih-Ying Lin

HI
 i was reading somewhere..  "simulation will break / terminate when the
simulation is running so so long "...

Did anyone read the same information?
Please refer me the related information since I have no idea where I read
this information.

How long is long ?
How to avoid this?


Thank you
Lin
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[gmx-users] non-standard atom names

2009-10-20 Thread Stefano Meliga


Hello,

I noticed that the command editconf -i structure.gro -o structure.pdb 
produce a pdb file in which some atom names are not standard.


In particular the delta carbon on ILE:

"CD  ILE" should be "CD1 ILE";

and the oxigens of the C-terminus

"O1" should be "O "
"O2" should be "OXT".

This is particularly annoying when GROMACS' output pdb is then used in 
input of other software, e.g. FIRST.


You might want to fix this.

Sincerely,

Stefano




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Re: [gmx-users] Chloroform (CHCl3) solvent box for G53a5 force field

Pablo Englebienne wrote:

Hi all,

I'm trying to simulate a small molecule in a chloroform box using the
GROMOS G53a5 forcefield. I realized that the parameters for the solvent
are present in the ffG53a5.rtp file, however I could not find a CHCl3
solvent box included in GROMACS. I did find, however, a CHCl3 solvent
box equilibrated by PeiQuan Chen
(http://lists.gromacs.org/pipermail/gmx-users/2003-May/005572.html) at
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies
.

In the mean time, I wanted to know if I overlooked something, and there
is a CHCl3 box to use with the GROMOS forcefield?

Not one that is officially distributed. If it was, it would be the
/share/gromacs/top subdirectory with other solvent topologies and structures.
Probably your best bet is to use the one in the User Contributions section,
unless you feel the need to create your own and start from scratch.

-Justin

Thanks!

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

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[gmx-users] Chloroform (CHCl3) solvent box for G53a5 force field

2009-10-20 Thread Pablo Englebienne


Hi all,

I'm trying to simulate a small molecule in a chloroform box using the 
GROMOS G53a5 forcefield. I realized that the parameters for the solvent 
are present in the ffG53a5.rtp file, however I could not find a CHCl3 
solvent box included in GROMACS. I did find, however, a CHCl3 solvent 
box equilibrated by PeiQuan Chen 
(http://lists.gromacs.org/pipermail/gmx-users/2003-May/005572.html) at 
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies 
.


I also saw mention of a box for the Amber forcefield, that is now 
included in AmberTools (amber10/dat/solvents/cform/cform.pdb and 
chcl3_equil.pdb.1). I took this one and I'm equilibrating it to use it 
later.


In the mean time, I wanted to know if I overlooked something, and there 
is a CHCl3 box to use with the GROMOS forcefield?


Thanks!

--
Pablo Englebienne, PhD
Institute of Complex Molecular Systems (ICMS)
Eindhoven University of Technology, TU/e
PO Box 513, HG -1.26
5600 MB Eindhoven, The Netherlands
Tel +31 40 247 5349

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[gmx-users] CMAP request

2009-10-20 Thread Pär Bjelkmar


Hi Supid,


We are trying to convert CHARMM force field for MTSSL (a small
molecule which is used as EPR label) into gromacs
format. But in CHARMM they have CMAP. I checked the gromacs mailing
archive and found that there is a gromacs
CVS where CMAP implementation is done.


Yes, the code is in the git master branch and is officially released  
as of version 4.1. You'd need a rtp entry of MTSSL for this to work  
with CMAP terms defined as for the amino acids (you can get the  
CHARMM27 ff files supporting CMAP from me if you send me an e-mail).  
Don't know if the CHARMM community has generalized the use of the CMAP  
term for something else than a peptide though. I mean CMAP is a  
correlation term between protein backbone phi and psi angles and MTSSL  
doesn't seem to be a peptide, right?



It will be very helpful for us if we get a copy of the code.


/Pär


<><><><><><><><><><><><><><><><><><>
Pär Bjelkmar, PhD student   

Stockholm Center for Biomembrane Research,
Stockholm Bioinformatics Center,
Department of Biochemistry and Biophysics,
Stockholm University

Tel:+46-8-16 2746   
Fax: +46-8-15 3679  
E-mail: bjelk...@cbr.su.se  
Home: http://www.dbb.su.se/User:Bjelkmar
<><><><><><><><><><><><><><><><><><>

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[gmx-users] Re: converting proper dihedrals into ryckaert-bellemans

2009-10-20 Thread Alan

Dear Carla,

Let me suggest you the wikis at acpypi.googlecode.com.

And then let me ask why amber94 and not amber99sb? And why not trying
acpypi in the link above as I guess it can do pretty much what you
want with much less pain?

Cheers,
Alan

On Tue, Oct 20, 2009 at 15:55,   wrote:
>
> Hi everyone,
> I'm using the amber94 force field in gromacs. I need to add topology of a
> new molecule for my MD simulation.
> I saw this line "propers treated as RBs in GROMACS to use combine multiple
> AMBER torsions per quartet" in my ffamber94bon.itp file.
> So it seems that I have to convert my proper dihedrals parameters into RB
> parameters, in order to run my simulation.
> Does anyone have an idea of how can I do this, to have the right parameters
> for my molecule?
>
> Thanks a lot
>
> Carla

-- 
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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[gmx-users] Re: 1. Normal mode analysis of pure water (simon sangma)

2009-10-20 Thread Gerrit Groenhof

If you are interested in the IR spectrum of water, all you need to do  
is a simulation of a flexible water model (not flexspc btw), save  
every fs, compute the dipole moment, compute the powerspectrum of that  
dipole moment and check for the peaks.


Gerrit



(tip3p_flex for instance, by skinner)




  1. Normal mode analysis of pure water (simon sangma)
  2. Normal mode analysis of pure water (simon sangma)
  3. Re: Normal mode analysis of pure water (Justin A. Lemkul)
  4. Re: AMBER force fields in gromacs program (Justin A. Lemkul)
  5. Re: Error during NVT equillibration with nvt.log file (ram bio)
  6. Re: Error during NVT equillibration with nvt.log file
 (Justin A. Lemkul)


--

Message: 1
Date: Tue, 20 Oct 2009 19:46:56 +0530
From: simon sangma 
Subject: [gmx-users] Normal mode analysis of pure water
To: gmx-users@gromacs.org
Message-ID:
<93e0339c0910200716x52cc241bq2861cc0638d7...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi Berk,
I want to determine the vibrational frequencies of water  
(close
to the experimentally observed values for the three modes). And then  
extend

the analogy for more complex systems.

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Re: [gmx-users] Error during NVT equillibration with nvt.log file

Dear Justin,

Thanks, will be back after some trials.

Ram

On Tue, Oct 20, 2009 at 8:16 PM, Justin A. Lemkul  wrote:
>
>
> ram bio wrote:
>>
>> Dear Justin,
>>
>> Thanks for the advice and suggestions,  will look into the plots and
>> try to run a further NPT equillibration, (here you mean equilibration
>> phase 2 ? without annealing, as in the tutorial)..
>>
>
> Yes, normal NPT.
>
> -Justin
>
>> Please let me know.
>>
>> Ram
>>
>> On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul  wrote:
>>>
>>> ram bio wrote:

 Dear Justion,

 When I executed the command g_energy -f anneal_npt1.edr, the output
 for temperature and pressure were as under:

 Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets
 All averages are exact over 51 steps

 Energy  Average   RMSD Fluct.  Drift
  Tot-Drift


 ---
 Temperature  161.4193.1199  0   0.645591
  322.796
 Heat Capacity Cv:   24.906 J/mol K (factor = 0.332832)

 Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets
 All averages are exact over 51 steps

 Energy  Average   RMSD Fluct.  Drift
  Tot-Drift


 ---
 Pressure (bar) -7.96937115.169114.406  0.0916656
  45.8329

 i am unable to understand from these parameters, whether the system is
 ok for future steps.
>>>
>>> Because simply looking at averages is less useful than looking at the
>>> plots.
>>>  I asked whether the temperature had stabilized, not what it's average
>>> value
>>> was. Consider this - you're constantly increasing the temperature, so an
>>> average is useless.  Look at the plot that g_energy gives you and make
>>> sure
>>> the increase is as you would expect.  Probably a further NPT
>>> equilibration
>>> is needed to make sure that the temperature will remain stable without
>>> the
>>> influence of annealing.
>>>
>>> Same thing for pressure - look at the plot.  Wide fluctuations will
>>> occur,
>>> so that's not a problem.  The trend is what is important (i.e., running
>>> average in xmgrace).  Is the pressure leveling off?  The average is more
>>> meaningful here, and it looks a bit low, but as I advise in my tutorial,
>>> equilibrating membrane systems takes a *long* time, anyway.
>>>
>>> -Justin
>>>
 Regarding the gaps in the lipid bilayers,now when i visualized the
 .trr file in the VMD there were no gaps in the lipid bilayer, that is
 they did not move apart.

 Please help.

 Thanks

 Ram






 On Tue, Oct 20, 2009 at 7:40 PM, Justin A. Lemkul 
 wrote:
>
> ram bio wrote:
>
> 
>
>> Now as i would like to proceed further, please suggest me how to
>> confirm that the simulated annealing was proper and also please let me
>> know can i now go to npt equillibration using the output of simulated
>> annealing as input to npt equilibration.
>>
> Like you would anything else.  Have the temperature and pressure
> stabilized?
>  Is your structure reasonable (no gaps, etc)?
>
> -Justin
>
>> Like I am going to use the following command to run the npt
>> equillibration:
>>
>> grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n
>> index.ndx -o npt.tpr
>>
>> Thanks,
>>
>> Ram
>>
>>
>>
>>
>> On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul 
>> wrote:
>>>
>>> ram bio wrote:

 Dear Justin,

 Thanks and I tried your suggestion, that is minimizing the system
 without restraints and increasing the Fmax to 1000, the mdp file
 used
 is as follows:

>>> Note that I only suggested EM, not necessarily Fmax < 1000.  You
>>> original
>>> post contained an even lower Fmax, suggesting that you can do better
>>> than
>>> 1000.  The parameters in my tutorial are somewhat generic; you should
>>> alter
>>> them to suit your needs.
>>>
>>> 
>>>
>>> Please note that the headers of log files are typically unnecessary
>>> when
>>> posting the .mdp file.
>>>
 please suggest me is it ok to remove the constraints and run the NVT
 equillibration.

>>> You can try it, but I doubt it will make a difference.  Your
>>> simulation
>>> is
>>> crashing before it is even starting, making it very difficult to
>>> diagnose.
>>>  You probably need to re-build the system, using as rigorous criteria
>>> as
>>> possible during the InflateGRO steps to ensure that you don't have
>>> any
>>> improper atomic overlap.  In my experience

[gmx-users] converting proper dihedrals into ryckaert-bellemans

2009-10-20 Thread Carla Jamous

Hi everyone,
I'm using the amber94 force field in gromacs. I need to add topology of a
new molecule for my MD simulation.
I saw this line "propers treated as RBs in GROMACS to use combine multiple
AMBER torsions per quartet" in my ffamber94bon.itp file.
So it seems that I have to convert my proper dihedrals parameters into RB
parameters, in order to run my simulation.
Does anyone have an idea of how can I do this, to have the right parameters
for my molecule?

Thanks a lot

Carla
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[gmx-users] CMAP request

2009-10-20 Thread Sudip Roy


Dear Users,

 We are trying to convert CHARMM force field for MTSSL (a small 
molecule which is used as EPR label) into gromacs
format. But in CHARMM they have CMAP. I checked the gromacs mailing 
archive and found that there is a gromacs

CVS where CMAP implementation is done.

It will be very helpful for us if we get a copy of the code.

Please suggest me if I should mail it to developers list.

Thanking you.

Sudip

--
**

Dr. Sudip Roy
Physical Chemistry and Material Science Division
Scientist C
National Chemical Laboratory
Pune 411008
India 


Tel.  +91 2590 2735 Office
Email s@ncl.res.in


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Re: [gmx-users] multiple processor running of gromacs-4.0.4

2009-10-20 Thread Jianhui Tian

Hi Mark,

You are right that treating electrostatics and vdw without cutoff and use
multiple processors to speed up doesn't make any sense.
Using cutoff for electrostatics and vdw without using pbc and pme, the
system can't run on parallel (using flag -pd doesn't work either), but works
on single node.
Using cutoff for electrostatics and vdw with pbc and pme, the system can run
on parallel.
Thanks for the clarifications.

Jianhui

Jianhui Tian wrote:
> Hi,
>
> I have a small system of fullerene ball with waters. I want to
> simulation the system without pbc and pme, treating the coulomb and vdw
> without cutoff. The system can be run on single processor. But when I
> try to run it with multiple processors, it can't proceed. I am including
> the error message at the end of this mail.

Those messages are generic failure messages from the MPI system. The
stack trace therein suggests you should read the stderr and/or log file
to get some diagnostic information from GROMACS. Possibly your system is
blowing up because you've started from an unsuitable configuration.

> There are some of my guesses for the possible reason of the error:
> 1. Do we have to use pbc and pme to use multiple processors for
simulation?

Wouldn't think so. However because you have no cut-offs, there will be
no advantage to DD because there is no data locality - every processor
needs the position of every atom. mdrun -pd may work. It strikes me as
possible that this scenario doesn't work in parallel on GROMACS.

> 2. Can wen use restraints when use multiple processors?

Yes.

> 3. If a molecule is "divided" into two parts in domain decomposition,
> will this be a problem for simulation?

No, that's routine.

Mark

> Thanks for any suggestion about this error message.
>
> logfile:--

> [0,1,1]: OpenIB on host compute-1-12.local was unable to find any HCAs.
> Another transport will be used instead, although this may result in
> lower performance.
> --
> --
> [0,1,0]: OpenIB on host compute-1-12.local was unable to find any HCAs.
> Another transport will be used instead, although this may result in
> lower performance.
> --
> NNODES=2, MYRANK=0, HOSTNAME=compute-1-12.local
> NODEID=0 argc=13
> NNODES=2, MYRANK=1, HOSTNAME=compute-1-12.local
> NODEID=1 argc=13
> .
> .
> .
> .
> Reading file
> /data/disk04/tianj/trp_remd_091012/equilibrium/test/trp_full_run1.tpr,
> VERSION 4.0 (single precision)
> [compute-1-12:08033] *** Process received signal ***
> [compute-1-12:08033] Signal: Segmentation fault (11)
> [compute-1-12:08033] Signal code: Address not mapped (1)
> [compute-1-12:08033] Failing at address: 0xc0
> [compute-1-12:08033] [ 0] /lib64/libpthread.so.0 [0x378fe0de80]
> [compute-1-12:08033] [ 1] /lib64/libc.so.6(_IO_vfprintf+0x39)
[0x378f642309]
> [compute-1-12:08033] [ 2] /lib64/libc.so.6(_IO_fprintf+0x88)
[0x378f64cf68]
> [compute-1-12:08033] [ 3]
> /usr/local/gromacs-4.0.4/bin/mdrun_sm(mk_mshift+0x315) [0x516593]
> [compute-1-12:08033] [ 4] /usr/local/gromacs-4.0.4/bin/mdrun_sm [0x45fa97]
> [compute-1-12:08033] [ 5]
> /usr/local/gromacs-4.0.4/bin/mdrun_sm(dd_bonded_cg_distance+0x36c)
> [0x45ff53]
> [compute-1-12:08033] [ 6]
> /usr/local/gromacs-4.0.4/bin/mdrun_sm(init_domain_decomposition+0x780)
> [0x44d10c]
> [compute-1-12:08033] [ 7]
> /usr/local/gromacs-4.0.4/bin/mdrun_sm(mdrunner+0x89c) [0x429f6e]
> [compute-1-12:08033] [ 8]
> /usr/local/gromacs-4.0.4/bin/mdrun_sm(main+0x7ba) [0x4306b6]
> [compute-1-12:08033] [ 9] /lib64/libc.so.6(__libc_start_main+0xf4)
> [0x378f61d8b4]
> [compute-1-12:08033] [10] /usr/local/gromacs-4.0.4/bin/mdrun_sm [0x4199a9]
> [compute-1-12:08033] *** End of error message ***
> mpirun noticed that job rank 0 with PID 8033 on node compute-1-12.local
> exited on signal 11 (Segmentation fault).
> 1 additional process aborted (not shown)
>
>
> 
>
> ___
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Re: [gmx-users] Error during NVT equillibration with nvt.log file




ram bio wrote:

Dear Justin,

Thanks for the advice and suggestions,  will look into the plots and
try to run a further NPT equillibration, (here you mean equilibration
phase 2 ? without annealing, as in the tutorial)..



Yes, normal NPT.

-Justin


Please let me know.

Ram

On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul  wrote:


ram bio wrote:

Dear Justion,

When I executed the command g_energy -f anneal_npt1.edr, the output
for temperature and pressure were as under:

Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets
All averages are exact over 51 steps

Energy  Average   RMSD Fluct.  Drift
 Tot-Drift

---
Temperature  161.4193.1199  0   0.645591
 322.796
Heat Capacity Cv:   24.906 J/mol K (factor = 0.332832)

Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets
All averages are exact over 51 steps

Energy  Average   RMSD Fluct.  Drift
 Tot-Drift

---
Pressure (bar) -7.96937115.169114.406  0.0916656
 45.8329

i am unable to understand from these parameters, whether the system is
ok for future steps.

Because simply looking at averages is less useful than looking at the plots.
 I asked whether the temperature had stabilized, not what it's average value
was. Consider this - you're constantly increasing the temperature, so an
average is useless.  Look at the plot that g_energy gives you and make sure
the increase is as you would expect.  Probably a further NPT equilibration
is needed to make sure that the temperature will remain stable without the
influence of annealing.

Same thing for pressure - look at the plot.  Wide fluctuations will occur,
so that's not a problem.  The trend is what is important (i.e., running
average in xmgrace).  Is the pressure leveling off?  The average is more
meaningful here, and it looks a bit low, but as I advise in my tutorial,
equilibrating membrane systems takes a *long* time, anyway.

-Justin


Regarding the gaps in the lipid bilayers,now when i visualized the
.trr file in the VMD there were no gaps in the lipid bilayer, that is
they did not move apart.

Please help.

Thanks

Ram






On Tue, Oct 20, 2009 at 7:40 PM, Justin A. Lemkul  wrote:

ram bio wrote:




Now as i would like to proceed further, please suggest me how to
confirm that the simulated annealing was proper and also please let me
know can i now go to npt equillibration using the output of simulated
annealing as input to npt equilibration.


Like you would anything else.  Have the temperature and pressure
stabilized?
 Is your structure reasonable (no gaps, etc)?

-Justin


Like I am going to use the following command to run the npt
equillibration:

grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n
index.ndx -o npt.tpr

Thanks,

Ram




On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul 
wrote:

ram bio wrote:

Dear Justin,

Thanks and I tried your suggestion, that is minimizing the system
without restraints and increasing the Fmax to 1000, the mdp file used
is as follows:


Note that I only suggested EM, not necessarily Fmax < 1000.  You
original
post contained an even lower Fmax, suggesting that you can do better
than
1000.  The parameters in my tutorial are somewhat generic; you should
alter
them to suit your needs.



Please note that the headers of log files are typically unnecessary
when
posting the .mdp file.


please suggest me is it ok to remove the constraints and run the NVT
equillibration.


You can try it, but I doubt it will make a difference.  Your simulation
is
crashing before it is even starting, making it very difficult to
diagnose.
 You probably need to re-build the system, using as rigorous criteria
as
possible during the InflateGRO steps to ensure that you don't have any
improper atomic overlap.  In my experience, if the simulation is
failing
at
step 0, there is no hope for coaxing the system into working.  The
configuration simply isn't reasonable.

-Justin


Thanks

Ram







On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul 
wrote:

ram bio wrote:

Dear Gromacs users,

I am doing protein in lipid-bilayer simulation and i am following
the
procedure as per justin tutorial. I am able to insert the protein in
lipid bilayer and minimize the system as per Inflategro
procedure,during the total procedure the system was minimized in
every
step.Then, I solvated and ionized sytem and minimized using the
following mdp file:

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
define = -DSTRONG_POSRES
integrator  = steep ; Algorithm (steep = steepest
descent
minimization)
emtol   = 500.0 ; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm
emstep

Re: [gmx-users] Error during NVT equillibration with nvt.log file

Dear Justin,

Thanks for the advice and suggestions,  will look into the plots and
try to run a further NPT equillibration, (here you mean equilibration
phase 2 ? without annealing, as in the tutorial)..

Please let me know.

Ram

On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul  wrote:
>
>
> ram bio wrote:
>>
>> Dear Justion,
>>
>> When I executed the command g_energy -f anneal_npt1.edr, the output
>> for temperature and pressure were as under:
>>
>> Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets
>> All averages are exact over 51 steps
>>
>> Energy  Average   RMSD Fluct.  Drift
>>  Tot-Drift
>>
>> ---
>> Temperature  161.4193.1199  0   0.645591
>>  322.796
>> Heat Capacity Cv:   24.906 J/mol K (factor = 0.332832)
>>
>> Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets
>> All averages are exact over 51 steps
>>
>> Energy  Average   RMSD Fluct.  Drift
>>  Tot-Drift
>>
>> ---
>> Pressure (bar) -7.96937115.169114.406  0.0916656
>>  45.8329
>>
>> i am unable to understand from these parameters, whether the system is
>> ok for future steps.
>
> Because simply looking at averages is less useful than looking at the plots.
>  I asked whether the temperature had stabilized, not what it's average value
> was. Consider this - you're constantly increasing the temperature, so an
> average is useless.  Look at the plot that g_energy gives you and make sure
> the increase is as you would expect.  Probably a further NPT equilibration
> is needed to make sure that the temperature will remain stable without the
> influence of annealing.
>
> Same thing for pressure - look at the plot.  Wide fluctuations will occur,
> so that's not a problem.  The trend is what is important (i.e., running
> average in xmgrace).  Is the pressure leveling off?  The average is more
> meaningful here, and it looks a bit low, but as I advise in my tutorial,
> equilibrating membrane systems takes a *long* time, anyway.
>
> -Justin
>
>> Regarding the gaps in the lipid bilayers,now when i visualized the
>> .trr file in the VMD there were no gaps in the lipid bilayer, that is
>> they did not move apart.
>>
>> Please help.
>>
>> Thanks
>>
>> Ram
>>
>>
>>
>>
>>
>>
>> On Tue, Oct 20, 2009 at 7:40 PM, Justin A. Lemkul  wrote:
>>>
>>> ram bio wrote:
>>>
>>> 
>>>
 Now as i would like to proceed further, please suggest me how to
 confirm that the simulated annealing was proper and also please let me
 know can i now go to npt equillibration using the output of simulated
 annealing as input to npt equilibration.

>>> Like you would anything else.  Have the temperature and pressure
>>> stabilized?
>>>  Is your structure reasonable (no gaps, etc)?
>>>
>>> -Justin
>>>
 Like I am going to use the following command to run the npt
 equillibration:

 grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n
 index.ndx -o npt.tpr

 Thanks,

 Ram




 On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul 
 wrote:
>
> ram bio wrote:
>>
>> Dear Justin,
>>
>> Thanks and I tried your suggestion, that is minimizing the system
>> without restraints and increasing the Fmax to 1000, the mdp file used
>> is as follows:
>>
> Note that I only suggested EM, not necessarily Fmax < 1000.  You
> original
> post contained an even lower Fmax, suggesting that you can do better
> than
> 1000.  The parameters in my tutorial are somewhat generic; you should
> alter
> them to suit your needs.
>
> 
>
> Please note that the headers of log files are typically unnecessary
> when
> posting the .mdp file.
>
>> please suggest me is it ok to remove the constraints and run the NVT
>> equillibration.
>>
> You can try it, but I doubt it will make a difference.  Your simulation
> is
> crashing before it is even starting, making it very difficult to
> diagnose.
>  You probably need to re-build the system, using as rigorous criteria
> as
> possible during the InflateGRO steps to ensure that you don't have any
> improper atomic overlap.  In my experience, if the simulation is
> failing
> at
> step 0, there is no hope for coaxing the system into working.  The
> configuration simply isn't reasonable.
>
> -Justin
>
>> Thanks
>>
>> Ram
>>
>>
>>
>>
>>
>>
>>
>> On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul 
>> wrote:
>>>
>>> ram bio wrote:

 Dear Gromacs users,

 I am doing protein in lipid-bilayer simulation and i am following
 the
 procedur

[gmx-users] Re: AMBER force fields in gromacs program

2009-10-20 Thread Alan

As long as not GMX 3.x, the wikis are still valid, no matter which GMX
4.0.x you use.

Alan

PS: thinking twice, the wikis should even work with GMX 3.x as long as
one uses the respective ffamber port.

On Tue, Oct 20, 2009 at 14:38,   wrote:
>
> dear  Alan
> your suggestion is true. but I Use  gromacs 4.0.3

-- 
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD



I have also added a Perl script to the GROMACS site (the VMD page):

http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD

The user provides an input topology file, and a .psf file is written, which can 
be loaded as data for the structure in VMD.  The !NBOND section seems to be the 
most important in this regard, so the other sections are a bit rough, but it 
seems to work alright.


The caveat is the topology must be one generated by MARTINI, in order to satisfy 
all the pattern matching and the order of the topology.  It should be fairly 
easy to modify the program further to accommodate other layouts, but I haven't 
had the need to do so.


-Justin

Nicolas Sapay wrote:

Hello Thomas,

I have a tcl script in my personal script library that might do what you 
want to do. I didn't use it for quite a while, but it was working well 
as far as I remember. I think it has been adapted from a script 
available on the VMD website, but I don't remember exactly its history. 
It doesn't seem too difficult to understand. You should be able to 
modify it for your own purpose, if needed.


Cheers,
Nicolas


Thomas Schmidt a écrit :

Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?

Thomas

  


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


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Re: [gmx-users] Error during NVT equillibration with nvt.log file




ram bio wrote:

Dear Justion,

When I executed the command g_energy -f anneal_npt1.edr, the output
for temperature and pressure were as under:

Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets
All averages are exact over 51 steps

Energy  Average   RMSD Fluct.  Drift  Tot-Drift
---
Temperature  161.4193.1199  0   0.645591322.796
Heat Capacity Cv:   24.906 J/mol K (factor = 0.332832)

Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets
All averages are exact over 51 steps

Energy  Average   RMSD Fluct.  Drift  Tot-Drift
---
Pressure (bar) -7.96937115.169114.406  0.091665645.8329

i am unable to understand from these parameters, whether the system is
ok for future steps.


Because simply looking at averages is less useful than looking at the plots.  I 
asked whether the temperature had stabilized, not what it's average value was. 
Consider this - you're constantly increasing the temperature, so an average is 
useless.  Look at the plot that g_energy gives you and make sure the increase is 
as you would expect.  Probably a further NPT equilibration is needed to make 
sure that the temperature will remain stable without the influence of annealing.


Same thing for pressure - look at the plot.  Wide fluctuations will occur, so 
that's not a problem.  The trend is what is important (i.e., running average in 
xmgrace).  Is the pressure leveling off?  The average is more meaningful here, 
and it looks a bit low, but as I advise in my tutorial, equilibrating membrane 
systems takes a *long* time, anyway.


-Justin


Regarding the gaps in the lipid bilayers,now when i visualized the
.trr file in the VMD there were no gaps in the lipid bilayer, that is
they did not move apart.

Please help.

Thanks

Ram






On Tue, Oct 20, 2009 at 7:40 PM, Justin A. Lemkul  wrote:


ram bio wrote:




Now as i would like to proceed further, please suggest me how to
confirm that the simulated annealing was proper and also please let me
know can i now go to npt equillibration using the output of simulated
annealing as input to npt equilibration.


Like you would anything else.  Have the temperature and pressure stabilized?
 Is your structure reasonable (no gaps, etc)?

-Justin


Like I am going to use the following command to run the npt
equillibration:

grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n
index.ndx -o npt.tpr

Thanks,

Ram




On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul 
wrote:

ram bio wrote:

Dear Justin,

Thanks and I tried your suggestion, that is minimizing the system
without restraints and increasing the Fmax to 1000, the mdp file used
is as follows:


Note that I only suggested EM, not necessarily Fmax < 1000.  You original
post contained an even lower Fmax, suggesting that you can do better than
1000.  The parameters in my tutorial are somewhat generic; you should
alter
them to suit your needs.



Please note that the headers of log files are typically unnecessary when
posting the .mdp file.


please suggest me is it ok to remove the constraints and run the NVT
equillibration.


You can try it, but I doubt it will make a difference.  Your simulation
is
crashing before it is even starting, making it very difficult to
diagnose.
 You probably need to re-build the system, using as rigorous criteria as
possible during the InflateGRO steps to ensure that you don't have any
improper atomic overlap.  In my experience, if the simulation is failing
at
step 0, there is no hope for coaxing the system into working.  The
configuration simply isn't reasonable.

-Justin


Thanks

Ram







On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul 
wrote:

ram bio wrote:

Dear Gromacs users,

I am doing protein in lipid-bilayer simulation and i am following the
procedure as per justin tutorial. I am able to insert the protein in
lipid bilayer and minimize the system as per Inflategro
procedure,during the total procedure the system was minimized in every
step.Then, I solvated and ionized sytem and minimized using the
following mdp file:

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
define = -DSTRONG_POSRES
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 500.0 ; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization)
steps to perform

; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor
list and long range forces
ns_t

Re: [gmx-users] AMBER force fields in gromacs program




leila karami wrote:

dear  Alan
your suggestion is true. but I Use  gromacs 4.0.3



This version difference (4.0.3 vs 4.0.5) is inconsequential for what you're 
doing.  Otherwise, upgrade to the newest version - it has the latest features 
and bug fixes.


-Justin





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


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Re: [gmx-users] Error during NVT equillibration with nvt.log file

Dear Justion,

When I executed the command g_energy -f anneal_npt1.edr, the output
for temperature and pressure were as under:

Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets
All averages are exact over 51 steps

Energy  Average   RMSD Fluct.  Drift  Tot-Drift
---
Temperature  161.4193.1199  0   0.645591322.796
Heat Capacity Cv:   24.906 J/mol K (factor = 0.332832)

Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets
All averages are exact over 51 steps

Energy  Average   RMSD Fluct.  Drift  Tot-Drift
---
Pressure (bar) -7.96937115.169114.406  0.091665645.8329

i am unable to understand from these parameters, whether the system is
ok for future steps.
Regarding the gaps in the lipid bilayers,now when i visualized the
.trr file in the VMD there were no gaps in the lipid bilayer, that is
they did not move apart.

Please help.

Thanks

Ram






On Tue, Oct 20, 2009 at 7:40 PM, Justin A. Lemkul  wrote:
>
>
> ram bio wrote:
>
> 
>
>> Now as i would like to proceed further, please suggest me how to
>> confirm that the simulated annealing was proper and also please let me
>> know can i now go to npt equillibration using the output of simulated
>> annealing as input to npt equilibration.
>>
>
> Like you would anything else.  Have the temperature and pressure stabilized?
>  Is your structure reasonable (no gaps, etc)?
>
> -Justin
>
>> Like I am going to use the following command to run the npt
>> equillibration:
>>
>> grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n
>> index.ndx -o npt.tpr
>>
>> Thanks,
>>
>> Ram
>>
>>
>>
>>
>> On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul 
>> wrote:
>>>
>>> ram bio wrote:

 Dear Justin,

 Thanks and I tried your suggestion, that is minimizing the system
 without restraints and increasing the Fmax to 1000, the mdp file used
 is as follows:

>>> Note that I only suggested EM, not necessarily Fmax < 1000.  You original
>>> post contained an even lower Fmax, suggesting that you can do better than
>>> 1000.  The parameters in my tutorial are somewhat generic; you should
>>> alter
>>> them to suit your needs.
>>>
>>> 
>>>
>>> Please note that the headers of log files are typically unnecessary when
>>> posting the .mdp file.
>>>
 please suggest me is it ok to remove the constraints and run the NVT
 equillibration.

>>> You can try it, but I doubt it will make a difference.  Your simulation
>>> is
>>> crashing before it is even starting, making it very difficult to
>>> diagnose.
>>>  You probably need to re-build the system, using as rigorous criteria as
>>> possible during the InflateGRO steps to ensure that you don't have any
>>> improper atomic overlap.  In my experience, if the simulation is failing
>>> at
>>> step 0, there is no hope for coaxing the system into working.  The
>>> configuration simply isn't reasonable.
>>>
>>> -Justin
>>>
 Thanks

 Ram







 On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul 
 wrote:
>
> ram bio wrote:
>>
>> Dear Gromacs users,
>>
>> I am doing protein in lipid-bilayer simulation and i am following the
>> procedure as per justin tutorial. I am able to insert the protein in
>> lipid bilayer and minimize the system as per Inflategro
>> procedure,during the total procedure the system was minimized in every
>> step.Then, I solvated and ionized sytem and minimized using the
>> following mdp file:
>>
>> ; minim.mdp - used as input into grompp to generate em.tpr
>> ; Parameters describing what to do, when to stop and what to save
>> define = -DSTRONG_POSRES
>> integrator  = steep ; Algorithm (steep = steepest descent
>> minimization)
>> emtol   = 500.0 ; Stop minimization when the maximum
>> force < 1000.0 kJ/mol/nm
>> emstep  = 0.01  ; Energy step size
>> nsteps  = 5 ; Maximum number of (minimization)
>> steps to perform
>>
>> ; Parameters describing how to find the neighbors of each atom and how
>> to calculate the interactions
>> nstlist = 1 ; Frequency to update the neighbor
>> list and long range forces
>> ns_type = grid  ; Method to determine neighbor list
>> (simple, grid)
>> rlist   = 1.2   ; Cut-off for making neighbor list
>> (short range forces)
>> coulombtype = PME   ; Treatment of long range
>> electrostatic interactions
>> rcoulomb= 1.2   ; Short-range electrostatic cut-off
>> rvdw= 1.2   ; Short-range Van der Waa

Re: [gmx-users] Normal mode analysis of pure water




simon sangma wrote:

Hi  Justin,
Are you suggesting that after thorough energy 
minimization, seperate .mdp file is to be used for NMA? In that case how 
would that output file (energy minimised file) be taken as an input file 
for the grompp and mdrun command (for NMA)? What extension would the 
file have (.what) ?




Yes, they are done in separate steps.  I think you need to do some tutorial 
material on the workflow of a GROMACS procedure.  Run energy minimization (in 
double precision), and the output of EM is your input for NMA (the minimized 
structure).


-Justin





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


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[gmx-users] Normal mode analysis of pure water

Hi Berk,
 I want to determine the vibrational frequencies of water (close
to the experimentally observed values for the three modes). And then extend
the analogy for more complex systems.
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[gmx-users] Normal mode analysis of pure water

Hi  Justin,
Are you suggesting that after thorough energy minimization,
seperate .mdp file is to be used for NMA? In that case how would that output
file (energy minimised file) be taken as an input file for the grompp and
mdrun command (for NMA)? What extension would the file have (.what) ?
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Re: [gmx-users] Error during NVT equillibration with nvt.log file




ram bio wrote:




Now as i would like to proceed further, please suggest me how to
confirm that the simulated annealing was proper and also please let me
know can i now go to npt equillibration using the output of simulated
annealing as input to npt equilibration.



Like you would anything else.  Have the temperature and pressure stabilized?  Is 
your structure reasonable (no gaps, etc)?


-Justin


Like I am going to use the following command to run the npt equillibration:

grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n
index.ndx -o npt.tpr

Thanks,

Ram




On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul  wrote:


ram bio wrote:

Dear Justin,

Thanks and I tried your suggestion, that is minimizing the system
without restraints and increasing the Fmax to 1000, the mdp file used
is as follows:


Note that I only suggested EM, not necessarily Fmax < 1000.  You original
post contained an even lower Fmax, suggesting that you can do better than
1000.  The parameters in my tutorial are somewhat generic; you should alter
them to suit your needs.



Please note that the headers of log files are typically unnecessary when
posting the .mdp file.


please suggest me is it ok to remove the constraints and run the NVT
equillibration.


You can try it, but I doubt it will make a difference.  Your simulation is
crashing before it is even starting, making it very difficult to diagnose.
 You probably need to re-build the system, using as rigorous criteria as
possible during the InflateGRO steps to ensure that you don't have any
improper atomic overlap.  In my experience, if the simulation is failing at
step 0, there is no hope for coaxing the system into working.  The
configuration simply isn't reasonable.

-Justin


Thanks

Ram







On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul  wrote:

ram bio wrote:

Dear Gromacs users,

I am doing protein in lipid-bilayer simulation and i am following the
procedure as per justin tutorial. I am able to insert the protein in
lipid bilayer and minimize the system as per Inflategro
procedure,during the total procedure the system was minimized in every
step.Then, I solvated and ionized sytem and minimized using the
following mdp file:

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
define = -DSTRONG_POSRES
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 500.0 ; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization)
steps to perform

; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor
list and long range forces
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
rlist   = 1.2   ; Cut-off for making neighbor list
(short range forces)
coulombtype = PME   ; Treatment of long range
electrostatic interactions
rcoulomb= 1.2   ; Short-range electrostatic cut-off
rvdw= 1.2   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)

the output was as follows:

Steepest Descents converged to Fmax < 500 in 4770 steps
Potential Energy  = -3.8820288e+05
Maximum force =  4.4803549e+02 on atom 3573
Norm of force =  1.7854408e+01

As the potential energy and Fmax values were agreeable , I proceeded
to equillibrate the system using NVT.


Did you minimize the structure without restraints, prior to NVT?




Angle   G96AngleProper Dih. Ryckaert-Bell.  Improper
Dih.
  2.20077e+048.54042e+036.78950e+034.34650e+03
 3.03266e+03
LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb
(SR)
  4.76527e+035.50236e+048.36617e+06   -2.20019e+03
-4.46844e+05
 Coul. recip. Position Rest.  PotentialKinetic En.   Total
Energy
 -1.65524e+051.07769e+017.85612e+065.88813e+10
 5.88892e+10
 Conserved En.Temperature Pressure (bar)  Cons. rmsd ()
  5.88892e+102.23805e+081.21713e+093.10245e+01


In my experience, the combination of an astronomically high temperature
and
a repulsive temperature is indicative of restraining an unrestrainable
starting structure.  Try the EM I suggested above.  Other than that, as
I've
suggested before, see the Advanced Troubleshooting page I created in the
tutorial.

-Justin


Please help me to proceed further and let me know where are the
mistakes lying and how to overcome them.

Thanks in advance,

Ram
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Re: [gmx-users] Error during NVT equillibration with nvt.log file

Dear Justin,

Thanks.

I tried to equilibrate the system in NVT ensemble without constraints,
the equilibration completed, but the lipid layers moved apart, so i
tried to do simulated annealing procedure mentioned in the trouble
shooting section of the tutorial and here also i was able to
equilibrate only with the constraints = none option in anneal_npt.mdp
file (below).

title   = Simulated Annealing
define  = -DPOSRES -DPOSRES_LIPID
integrator  = md
dt  = 0.001 
nsteps  = 50
continuation= no
constraints = none  
constraint-algorithm = lincs
lincs-iter  = 1 
lincs-order = 4 
nstxout = 1000  
nstvout = 1000  
nstfout = 1000  
nstenergy   = 1000  
nstlist = 5 
ns_type = grid  
rlist   = 1.2
rcoulomb= 1.2   
rvdw= 1.2   
coulombtype = PME   
pme_order   = 4 
fourierspacing  = 0.16  
Tcoupl  = Berendsen 
tc_grps = Protein DPPC SOL_CL-  
tau_t   = 0.1   0.1 0.1 
ref_t   = 323   323 323 
Pcoupl  = Berendsen 
Pcoupltype  = semiisotropic 
ref_p   = 1.0 1.0   
compressibility = 4.5e-5 4.5e-5 
gen_vel = no
pbc = xyz   
DispCorr= EnerPres  
nstcomm = 1
comm-mode   = Linear
comm-grps   = Protein_DPPC SOL_CL-
annealing   = single single single  
annealing_npoints   = 2 2 2 
annealing_time  = 0 500 0 500 0 500 
annealing_temp  = 0 323 0 323 0 323 

Now as i would like to proceed further, please suggest me how to
confirm that the simulated annealing was proper and also please let me
know can i now go to npt equillibration using the output of simulated
annealing as input to npt equilibration.

Like I am going to use the following command to run the npt equillibration:

grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n
index.ndx -o npt.tpr

Thanks,

Ram




On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul  wrote:
>
>
> ram bio wrote:
>>
>> Dear Justin,
>>
>> Thanks and I tried your suggestion, that is minimizing the system
>> without restraints and increasing the Fmax to 1000, the mdp file used
>> is as follows:
>>
>
> Note that I only suggested EM, not necessarily Fmax < 1000.  You original
> post contained an even lower Fmax, suggesting that you can do better than
> 1000.  The parameters in my tutorial are somewhat generic; you should alter
> them to suit your needs.
>
> 
>
> Please note that the headers of log files are typically unnecessary when
> posting the .mdp file.
>
>> please suggest me is it ok to remove the constraints and run the NVT
>> equillibration.
>>
>
> You can try it, but I doubt it will make a difference.  Your simulation is
> crashing before it is even starting, making it very difficult to diagnose.
>  You probably need to re-build the system, using as rigorous criteria as
> possible during the InflateGRO steps to ensure that you don't have any
> improper atomic overlap.  In my experience, if the simulation is failing at
> step 0, there is no hope for coaxing the system into working.  The
> configuration simply isn't reasonable.
>
> -Justin
>
>> Thanks
>>
>> Ram
>>
>>
>>
>>
>>
>>
>>
>> On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul  wrote:
>>>
>>> ram bio wrote:

 Dear Gromacs users,

 I am doing protein in lipid-bilayer simulation and i am following the
 procedure as per justin tutorial. I am able to insert the protein in
 lipid bilayer and minimize the system as per Inflategro
 procedure,during the total procedure the system was minimized in every
 step.Then, I solvated and ionized sytem and minimized using the
 following mdp file:

 ; minim.mdp - used as input into grompp to generate em.tpr
 ; Parameters describing what to do, when to stop and what to save
 define = -DSTRONG_POSRES
 integrator  = steep ; Algorithm (steep = steepest descent
 minimization)
 emtol   = 500.0 ; Stop minimization when the maximum
 force < 1000.0 kJ/mol/nm
 emstep  = 0.01  ; Energy step size
 nsteps  = 5 ; Maximum number of (minimization)
 steps to perform

 ; Parameters describing how to find the neighbors of each atom and how
 to calculate the interactions
 nstlist = 1 ; Frequency to update the neighbor
 list and long range forces
 ns_type = grid  ; Method to determine neighbor list
 (simple, grid)
 rlist   = 1.2   ; Cut-off for making neighbor list
 (short range forces)
 coulombtype = PME   ; Treatment of long range
 electrostatic interact

RE: [gmx-users] Normal mode analysis of pure water

2009-10-20 Thread Berk Hess


You could get better help if you tell us what information you want to get out 
of this analysis.

NMA gives you a harmonic description of the potential energy around a minimum 
of the system.
For water the minimum is ice, so you would get the modes of a certain ice state.

Berk

Date: Tue, 20 Oct 2009 19:20:19 +0530
From: simoniitc...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Normal mode analysis of pure water

Hi Berk,
 You mentioned that standard NMA techniques will not work for the 
liquid water  system. Could you suggest the alternatives then?
  
_
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[gmx-users] Normal mode analysis of pure water

Hi Berk,
 You mentioned that standard NMA techniques will not work for
the liquid water  system. Could you suggest the alternatives then?
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RE: [gmx-users] Normal mode analysis of pure water

2009-10-20 Thread Berk Hess


This is wasting a large amount of CPU time.
Water is solid (ice) at 0 K.
A plain normal mode analysis would give you the normal modes of ice.
You can do a normal mode analysis of liquid water without minimization,
but the standard NMA techniques will not work.

Berk

Date: Tue, 20 Oct 2009 18:33:43 +0530
From: simoniitc...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Normal mode analysis of pure water

Hi,
I encountered the following remarks during normal mode analysis of pure 
water. Can someone please suggest a solution.
 mdrun_d -v -s water.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log -mtx 
nm.mtx
Getting Loaded...

Reading file water.tpr, VERSION 4.0.4 (double precision)
Loaded with Money

Non-cutoff electrostatics used, forcing full Hessian format.
Allocating Hessian memory...

starting normal mode calculation 'Pure Water'

648 steps.

Maximum force: 2.74758e+03
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.

Finished step 648 out of 648

Writing Hessian...

gcq#258: "In the End Science Comes Down to Praying" (P. v.d. Berg)

g_nmeig_d -f nm.mtx -s water.tpr -of eigenfreq.xvg -ol eigenval.xvg -v 
eigenvec.trr


Reading file water.tpr, VERSION 4.0.4 (double precision)
Reading file water.tpr, VERSION 4.0.4 (double precision)
Reading double precision matrix generated by Gromacs VERSION 4.0.4
Full matrix storage format, nrow=1944, ncols=1944


Diagonalizing to find vectors 1 through 50...

One of the lowest 6 eigenvalues has a non-zero value.
This could mean that the reference structure was not
properly energy minimized.
Writing eigenvalues...

Writing eigenfrequencies - negative eigenvalues will be set to zero.

Writing average structure & eigenvectors 1--50 to eigenvec.trr

gcq#132: "Shit Happens" (Pulp Fiction)


The eigenfreq is 0 which is the problem


The .mdp file used was;
;   User spoel (236)
;   Wed Nov  3 17:12:44 1993
;   Input file
;
cpp =
define  =  -DFLEXIBLE
constraints =  none
integrator  =  nm

nsteps  =  1
;
;   Energy minimizing stuff
;
emtol   =  0.01
emstep  =  0.01
coulombtype =  PME
nstcomm =  1
ns_type =  grid

rlist   =  0.9
rcoulomb=  0.9
rvdw=  0.9
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no




  
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Re: [gmx-users] Normal mode analysis of pure water




simon sangma wrote:

Hi  Justin,
I tried  altering  the  .mdp file  (integrator  =  
steep  instead  of nm) for energy  minimization. But in that case the 
mdrun did not generate the Hessian matrix (nm.mtx) inspite of using the 
command twice.




Energy minimization is not the same thing as Normal Mode Analysis.  You have to 
energy minimize your system (thoroughly!) first, then run NMA.


-Justin





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--


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


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[gmx-users] Normal mode analysis of pure water

Hi  Justin,
I tried  altering  the  .mdp file  (integrator  =  steep
instead  of nm) for energy  minimization. But in that case the mdrun did not
generate the Hessian matrix (nm.mtx) inspite of using the command twice.
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Re: [gmx-users] Normal mode analysis of pure water




simon sangma wrote:

Hi,
I encountered the following remarks during normal mode analysis of 
pure water. Can someone please suggest a solution.


You've been told twice already what the likely solution is:




Maximum force: 2.74758e+03
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.





One of the lowest 6 eigenvalues has a non-zero value.
This could mean that the reference structure was not
properly energy minimized.


-Justin

--


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


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[gmx-users] Normal mode analysis of pure water