Re: [gmx-users] Reg trr file

[Justin A. Lemkul]

On 5/22/12 7:17 AM, Ramya LN wrote:

Thank you Justin. But if i want to extend my simulation, i need trr file...
right?then how should i proceed?



You do not need a .trr file to extend a simulation unless you are using an 
ancient version of Gromacs.  See the following:


http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4

-Justin


On Mon, May 21, 2012 at 11:18 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



On 5/21/12 7:47 AM, Ramya LN wrote:

Hello all,
I am doing protein-ligand dynamics using GROMACS. i could get all the 
final
files after simulation like gro,edr, log files. But i couldnt get the 
trr
file.Can anyone of you please tell me wht should i do to get this or
tell me at
what step i have done this mistake.


A .trr file will not be produced if nstxout, nstvout, and nstfout are all
set to zero in the .mdp file.  You can create a .trr file from an .xtc file,
but its precision will only be as good as the .xtc and it will not contain
velocities or forces, so there's not really any point to doing that ;)

-Justin

--
==__==

Justin A. Lemkul, Ph.D.
Research Scientist
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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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
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Re: [gmx-users] Reg trr file

[Ramya LN]

Thank you Justin. But if i want to extend my simulation, i need trr file...
right?then how should i proceed?

On Mon, May 21, 2012 at 11:18 PM, Justin A. Lemkul  wrote:

>
>
> On 5/21/12 7:47 AM, Ramya LN wrote:
>
>> Hello all,
>> I am doing protein-ligand dynamics using GROMACS. i could get all the
>> final
>> files after simulation like gro,edr, log files. But i couldnt get the trr
>> file.Can anyone of you please tell me wht should i do to get this or tell
>> me at
>> what step i have done this mistake.
>>
>>
> A .trr file will not be produced if nstxout, nstvout, and nstfout are all
> set to zero in the .mdp file.  You can create a .trr file from an .xtc
> file, but its precision will only be as good as the .xtc and it will not
> contain velocities or forces, so there's not really any point to doing that
> ;)
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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] Regarding error.

[Dylan Smith]

Hi Suryanarayana,

http://www.gromacs.org/Documentation/Errors is where i'd start. But to help 
you along this error suggests that you have a different number of atoms in 
your coordinate file(.gro) than your topology(.top) suggests. Often this can 
be caused by adding or removing ions or solvent without modifying your .top 
file.


Regards,
Dylan Smith

On 2012-05-22 15:03, Seera Suryanarayana wrote:

Dear all gromacs users,
 I tried the
grompp and i got the following error.

Fatal error:
number of coordinates in coordinate file (1UZ9_ion.gro, 41103)
 does not match topology (1UZ9.top, 41100)

Is there any explanation why is thid happening?

I would appreciate any help. Iam new in using MD and gromac in particular.

Suryanarayana Seera,
PhD student,
Hyderabad,
India.


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[gmx-users] Regarding error.

[Seera Suryanarayana]

Dear all gromacs users,
 I tried the grompp and i got the following
error.


Fatal error:
number of coordinates in coordinate file (1UZ9_ion.gro, 41103)
 does not match topology (1UZ9.top, 41100)



Is there any explanation why is thid happening?

I would appreciate any help. Iam new in using MD and gromac in particular.

Suryanarayana Seera,
PhD student,
Hyderabad,
India.
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Re: [gmx-users] intermolecular H bond selection

[Erik Marklund]

21 maj 2012 kl. 06.54 skrev Anirban:

> 
> 
> On Mon, May 21, 2012 at 3:09 AM, mu xiaojia  wrote:
> Thanks for prompt answering but I may need to clarify my question and sorry 
> for the understanding,
> 
> For example, I have dipeptides like Ala-Ala, how to ask g_hbond only 
> calculate the h bonds between Ala on different dipeptides instead of counting 
> all the possible h bonds between Ala(intermolecularly and intramolecularly)
> 
> 
> Make two groups with make_ndx that contains the residue numbers (or specific 
> atom numbers) of the ALA residues between which you want to count the H bonds 
> and then select these group numbers with g_hbond.
> 
> -Anirban

And if you have many alanines you might have to call g_hbond many times (think 
in the lines of scripting). Or invoke g_hbond once with the index group 
consisting of all alanines chosen twice and decompose the hbonding matrix (-hbm 
-hbn) yourself (python/perl).

Best,

Erik

>  
> Thanks very  much!
> 
> 
> On Fri, May 18, 2012 at 7:57 PM, Justin A. Lemkul  wrote:
> 
> 
> On 5/18/12 7:22 PM, mu xiaojia wrote:
> Hi gmx-users,
> 
> I have a question might be explained before but I cannot understand from the
> previous , how to calculation the intermolecular h-bonds between two 
> molecules?
> I saw someone mentioned using a second tpr file, but how to do it 
> specifically?
> Thanks very much!
> 
> 
> g_hbond asks for two index groups to be selected.  Assign each molecule to an 
> index group and select them when prompted.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
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Re: [gmx-users] Large forces on HIS hydrogen atoms

[Justin A. Lemkul]

On 5/21/12 8:10 PM, patrick wintrode wrote:

Hi.

I've been trying to build my system in gromacs and have run into a problem. On
my initial energy minimization after building the .go and .top files, I
inevitably get 1 atom that doesn't get below the specified fmax (fmax of 10 in
my case: the force on the atom is around 60-90). This remains true after
multiple rounds of minimization using both steepest descent and CG algorithms.
The atom in question is always a hydrogen at the D1 or E2 position in one of the
histidines. I've tried both letting pdb2gmx assign the histidine protonation
states and using proPKA to assign them and then making pdb2gmx use those
assignments with the -his tag.

So far nothing has worked. Any suggestions?



An emtol of 10 is very low for normal applications, and you're unlikely to 
achieve it unless you're using double precision, a very small emstep, and/or 
several rounds of steep/cg/l-bfgs minimization algorithms.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Large forces on HIS hydrogen atoms

[patrick wintrode]

Hi.

I've been trying to build my system in gromacs and have run into a problem. On 
my initial energy minimization after building the .go and .top files, I 
inevitably get 1 atom that doesn't get below the specified fmax (fmax of 10 in 
my case: the force on the atom is around 60-90). This remains true after 
multiple rounds of minimization using both steepest descent and CG algorithms. 
The atom in question is always a hydrogen at the D1 or E2 position in one of 
the histidines. I've tried both letting pdb2gmx assign the histidine 
protonation states and using proPKA to assign them and then making pdb2gmx use 
those assignments with the -his tag.

So far nothing has worked. Any suggestions?
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Re: [gmx-users] RE: Re: Wierd results from Umbrella sampling (Justin A. Lemkul)

[Justin A. Lemkul]

On 5/21/12 10:05 AM, Du Jiangfeng (BIOCH) wrote:

Please don't reply to the entire digest message; copy and paste only the 
relevant parts.



On 5/16/12 4:08 AM, Du Jiangfeng (BIOCH) wrote:

Dear Sir/Madam,

I have performed umbrella pulling and umbrella sampling my protein from a
DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve
suddenly turns to zero at the last 1 nm) and the histograph does not show any
overlap. Actually, I did it strictly based on Justin's tutorial, with the
sample spacing of 0.2 nm.



Can you provide images of what your histograms and PMF profile look like?


What energetic term is this?  A summation can decrease if the values being added
are all negative.

The energetic term should be binding energy.
Even there are some samples with the negative energies but the energy curve 
shouldn't go to zero (I calculated them by hand).



I don't understand what this means.  Binding energy is not stored in the .edr 
file, and I'm not clear what you calculated yourself.




Followings are some lines from the end of histograph file:

Distance(nm) 5.455761 0   0   0   0   0   0   0   0 
  0   0   0   0   0   0   0   0   0   0 
  8 5.483663  0   0   0   0
0 0   0   0   0   0   0   0   0   0   0 
  0   0   0   8 5.511565  0   0   0   0   0 
  0   0   0   0   0   0   0   0   0   0 
  0   0   0   12
  5.539467 0   0   0   0   0   0   0   0   
0   0   0   0   0   0   0   0   0   0   
4 5.567369  0   0   0   0   0   0   0   0   
0   0
0 0   0   0   0   0   0   0   2


I am really depressed because it took me quiet a long time to sampling but it
seems in vain... I really no idea to find out what went wrong.



Nor do we.  What is in your .mdp file?  How many windows are you using?  What is
the total desired length of the reaction coordinate, and what are the initial
and final COM distances that you are restraining?  What are your box dimensions?

-Justin

My box dimensions are  x: 7.94677  y: 7.94677  z: 13.48094 (nm)
The initial COM of DOPC(lipids) is at z=3.5 nm;
The initial COM of my protein is at z= 6.65nm.
The desired length is 3.6 nm, but it moved 3.4 nm along z-dimension.
So I used 19 windows for 3.4 nm movement (0.17 nm / window)

In pulling.mdp:
dt= 2 fs;  nsteps=1 ns; nstxout=10 ps; nstvout=10ps
rlist/rcoulomb/ rvdw= 1.4
Tcoupl= v-rescale;  Pcoupl= Parrinello-Rahman
; Pull code
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance>  0
pull_ngroups= 1
pull_group0 = DOPC
pull_group1 = protein
pull_rate1  = 0.0036  ; 0.0036 nm per ps = 3.6 nm per ns
pull_k1 = 1300  ; kJ mol^-1 nm^-2

In umbrella sampling.mdp:
nsteps=9.5 ns; pull_rate1= 0.0; pull_k1= 1000
other parameters are same as pulling.mdp.


Thank you for your help, above are my parameters.



In principle, this setup should work fine.  What does grompp say about the 
restrained distances?  Does it agree with what you've calculated above in terms 
of COM distances?


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] concatenate log files

[Justin A. Lemkul]

On 5/21/12 7:25 PM, Andreas Zink wrote:

Hi,

what is the easiest way to concatenate .log files? Is there a tool like trjcat
for trajectory files? Or do I have to do it by hand?

I recently had to restart a REMD simulation from checkpoint files after it
crashed. I did not use the append option and now have two log files for each
replica. I want to concatenate the log files in order to run the demux script on
them. (See postprocessing section at
http://www.gromacs.org/Documentation/How-tos/REMD)


Since it's just a text file, use the Unix 'cat' command:

cat log1.log log2.log > full.log

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] top/itp file to show parameters explicitly

[Justin A. Lemkul]

On 5/21/12 2:43 PM, Alan wrote:

Hi there,

Is there an option in pdb2gmx that when generating the top/itp file, it could
show the parameters explicitly? e.g.:

Instead of:
[ dihedrals ]
;  aiajakal functc0c1c2
c3
 5131112 4
11151314 4
15232122 4
21252324 4
25323133 4

(my hard hand modifications)

[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
;i  j  k  l   func   phase kd  pn
  5 13 11 12  4   180.00  43.93200   2 ; CA- N-
C- O
 11 15 13 14  4   180.00   4.60240   2 ;  C-CA-
N- H
 15 23 21 22  4   180.00  43.93200   2 ; CA- N-
C- O
 21 25 23 24  4   180.00   4.60240   2 ;  C-CA-
N- H
 25 32 31 33  4   180.00  43.93200   2 ; CA-   OC1-
C-   OC2

I mean, if the parameters that are hiding in e.g. ...gromacs/top/amber99sb.ff
could be showed in the top/itp file for human readers, that would be great.



You can obtain these parameters (I believe) by running grompp with the -pp 
option.  If you think it would be a useful feature for pdb2gmx, file a feature 
request on redmine.gromacs.org.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Reg trr file

[Justin A. Lemkul]

On 5/21/12 7:47 AM, Ramya LN wrote:

Hello all,
I am doing protein-ligand dynamics using GROMACS. i could get all the final
files after simulation like gro,edr, log files. But i couldnt get the trr
file.Can anyone of you please tell me wht should i do to get this or tell me at
what step i have done this mistake.



A .trr file will not be produced if nstxout, nstvout, and nstfout are all set to 
zero in the .mdp file.  You can create a .trr file from an .xtc file, but its 
precision will only be as good as the .xtc and it will not contain velocities or 
forces, so there's not really any point to doing that ;)


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Lysozyme tutorial-error with moleculetype

[Justin A. Lemkul]

On 5/20/12 8:18 AM, delara aghaie wrote:

Dear Gromacs Users
I am doing Justin's Lysozyme tutorial. In EM step I got the error with molecule
type. (I am using Gromacs, 4.0.5)
It was about Cl and Na. I noticed that because I have selected OPLS forcefield,
I should change the name of Cl and Na in my .top file to Na+ and Cl-.
I did this and again when using grompp to create *.tpr file for energy
minimization, it says that
-
WARNING 1 [file topol.top, line 18272]:
8 non-matching atom names
atom names from topol.top will be used
atom names from 1AKI_solv_ions.gro will be ignored
--
Should I change the ions name in .gro file also to Cl-? is it only for atom name
or also for atom number (coulumn 2 in .gro file)?



The names specified in the topology (and thus supplied to -pname and -nname) 
must match the [moleculetype] name(s) specified in ions.itp.  Previous versions 
of Gromacs (before 4.5) had a haphazard naming scheme that was standardized for 
4.5.  In the case of 4.0.5, you'll have to look up the proper names - genion 
will add them correctly if you do, otherwise you will also have to modify the 
residue and atom names in the coordinate file.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Re: BAR calculations with tabulated non-bonded potentials

[Justin A. Lemkul]

On 5/20/12 2:30 AM, jrustad wrote:


Justin A. Lemkul wrote



You don't need the pull code if the two atoms are in the same
[moleculetype] - a
"molecule" in Gromacs is any set of atoms; they don't necessarily have to
make
chemical sense.  The only problem I see is that if you have two atoms in
the
same location, while simultaneously turning one "on" and the other "off,"
you
will likely develop strong repulsive interactions between them such that
the
constraints may fail and your atoms will be displaced from the desired
location.
   I can't say for sure whether it will be a problem, but if you've got
atom A
existing at 20% and atom B trying to exist at 80% in the exact same
location,
that sounds like a recipe for trouble.




OK, thanks very much  for the advice, however, I'm not following something
here-
maybe I am just being dense:

I thought the point was that the Fe2+ and Fe3+ ions cannot be in the same
molecule, because the lookup tables for their short ranged interactions need
to be assigned using energygrps, which seem to apply to molecules not atom
types.  If the tables could be applied to atom types rather than molecules
(which makes more sense to me anyway), then there would be no problems.



You can assign energygrps to any valid group, though I honestly have no 
experience using such groups with tables.  It may work differently.



I thought it was possible in GMX to completely switch off all interactions
(including coulomb and vdw) between selected molecules.  If so, then when
one "turns on" while the other "turns off" they never interact, correct?

Maybe I am wrong that it is possible to exclude all interactions between two
given molecules?



Forgive me, the enegrygrp_excl option slipped my mind when I wrote that last 
message, so yes, it should be possible to exclude their interactions.


-Justin

--


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Research Scientist
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] concatenate log files

[Andreas Zink]

Hi,

what is the easiest way to concatenate .log files? Is there a tool like 
trjcat for trajectory files? Or do I have to do it by hand?


I recently had to restart a REMD simulation from checkpoint files after 
it crashed. I did not use the append option and now have two log files 
for each replica. I want to concatenate the log files in order to run 
the demux script on them. (See postprocessing section at 
http://www.gromacs.org/Documentation/How-tos/REMD)


Thanks in advance,
Andi
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Re: [gmx-users] constraints between protein ligand - metal chelation

[R.S.K.Vijayan]

Many thanks for your response

On Mon, May 21, 2012 at 12:01 PM, francesco oteri  wrote:

> You are right Peter
>
> 2012/5/21 Peter C. Lai 
>
> This approach still requires the system to be parameterized as a single
>> moleculetype, doesn't it?
>>
>> On 2012-05-20 04:42:26PM +0200, francesco oteri wrote:
>> > Hi,
>> > if you are able to define atom couples able to mantein the structure of
>> > your complex,
>> > you can insert in .top file a set of bond using function 6 (see table at
>> > pag 125 of the user manual).
>> > For example, let atom 1 and 100 are at distance 0.6nm, you can insert in
>> > .top a row like
>> >
>> > 1 100 6 0.6 1000
>> >
>> > you impose a bond between the two atoms having as eauilibrium distance
>> > 0.6nm and
>> > force strenght 1000J.
>> >
>> > Function 6 doesn't implie the generation of angles and dihedrals so it
>> is
>> > the right choice
>> > to impose distance restraints
>> >
>> >
>> > Francesco
>> > 2012/5/20 R.S.K.Vijayan 
>> >
>> > > Many  thanks for your response. No special reasons for parametrizing
>> the
>> > > ligand and the protein as a separate system. I dont think that the
>> ligand
>> > > and protein can be parametrized as a single system, but will
>> definitely try
>> > > doing it as a single system and see if it works.
>> > > Regards
>> > > Vijayan.R
>> > >
>> > >
>> > > On Sat, May 19, 2012 at 10:23 PM, Peter C. Lai  wrote:
>> > >
>> > >> Is there a particular reason why the ligand has been parameterized
>> as a
>> > >> separate moleculetype from the protein in your case? I prefer to
>> treat
>> > >> coordination bonds as "real bonds" instead of relying on
>> electrostatic
>> > >> interactions anyway, since it is the only way to conservatively
>> ensure the
>> > >> coordination geometry is preserved (like for Zn, where QM predicts a
>> > >> tetrahedral geometry but Zn free ions will result in an octahedral
>> > >> geometry).
>> > >> In any case, even if you stick with freeion Zn, you can paramaterize
>> the
>> > >> complex as a single moleculetype and use distance restraints there,
>> can't
>> > >> you?
>> > >>
>> > >>
>> > >> On 2012-05-19 09:42:25PM -0400, R.S.K.Vijayan wrote:
>> > >> > Dear Gromacs users
>> > >> >
>> > >> > I was wondering if there exists any technique that sets
>> > >> > distance restraint between specified ligand (atoms) and the
>> > >> protein(atoms)
>> > >> > in Gromacs.  I am simulating a system which contains metal ions
>> > >> coordinated
>> > >> > to the Ligand. I looked in to the mailing list and Gromacs manual
>> and
>> > >> > figured out that  *genrster*  can be employed, to
>> > >> > set distance, position and dihedral restraints. Unfortunately i
>> also
>> > >> > stumbled on the fact  that restraints between systems is not
>> possible.
>> > >> >
>> > >> > Since force fields are not good at handling chelation  between
>> metal
>> > >> atoms,
>> > >> > i find that the metals drifting away from the coordinated  ligand
>> atoms
>> > >> > during the course of simulation, hence i introduced position
>> constraints
>> > >> > for the metal and ended up realizing  that the coordination
>> distance
>> > >> > between the ligand and the metal exceeds the permissible range and
>> the
>> > >> > angles between the chelating atoms gets distorted  and some
>> coordinating
>> > >> > residues like Histidine and Aspartic  acid also moves away from the
>> > >> metal.
>> > >> >
>> > >> > Hence, i was wondering if l anyone knows of any method (apart from
>> > >> > QM/MM) that can help to set distance restraints between the protein
>> > >> (metal
>> > >> > ion ) and the  ligand, also any suggestion that could help in
>> handling
>> > >> > ligand metal chelation is welcomed.
>> > >> > Thanking in advance
>> > >> >
>> > >> >
>> > >> > Regards
>> > >> >
>> > >> > Vijayan.R
>> > >>
>> > >> > --
>> > >> > gmx-users mailing listgmx-users@gromacs.org
>> > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > >> > Please search the archive at
>> > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > >> > Please don't post (un)subscribe requests to the list. Use the
>> > >> > www interface or send it to gmx-users-requ...@gromacs.org.
>> > >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > >>
>> > >>
>> > >> --
>> > >> ==
>> > >> Peter C. Lai| University of Alabama-Birmingham
>> > >> Programmer/Analyst  | KAUL 752A
>> > >> Genetics, Div. of Research  | 705 South 20th Street
>> > >> p...@uab.edu | Birmingham AL 35294-4461
>> > >> (205) 690-0808|
>> > >> ==
>> > >>
>> > >> --
>> > >> gmx-users mailing listgmx-users@gromacs.org
>> > >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > >> Please search the archive at
>> > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

Re: [gmx-users] constraints between protein ligand - metal chelation

[francesco oteri]

You are right Peter

2012/5/21 Peter C. Lai 

> This approach still requires the system to be parameterized as a single
> moleculetype, doesn't it?
>
> On 2012-05-20 04:42:26PM +0200, francesco oteri wrote:
> > Hi,
> > if you are able to define atom couples able to mantein the structure of
> > your complex,
> > you can insert in .top file a set of bond using function 6 (see table at
> > pag 125 of the user manual).
> > For example, let atom 1 and 100 are at distance 0.6nm, you can insert in
> > .top a row like
> >
> > 1 100 6 0.6 1000
> >
> > you impose a bond between the two atoms having as eauilibrium distance
> > 0.6nm and
> > force strenght 1000J.
> >
> > Function 6 doesn't implie the generation of angles and dihedrals so it is
> > the right choice
> > to impose distance restraints
> >
> >
> > Francesco
> > 2012/5/20 R.S.K.Vijayan 
> >
> > > Many  thanks for your response. No special reasons for parametrizing
> the
> > > ligand and the protein as a separate system. I dont think that the
> ligand
> > > and protein can be parametrized as a single system, but will
> definitely try
> > > doing it as a single system and see if it works.
> > > Regards
> > > Vijayan.R
> > >
> > >
> > > On Sat, May 19, 2012 at 10:23 PM, Peter C. Lai  wrote:
> > >
> > >> Is there a particular reason why the ligand has been parameterized as
> a
> > >> separate moleculetype from the protein in your case? I prefer to treat
> > >> coordination bonds as "real bonds" instead of relying on electrostatic
> > >> interactions anyway, since it is the only way to conservatively
> ensure the
> > >> coordination geometry is preserved (like for Zn, where QM predicts a
> > >> tetrahedral geometry but Zn free ions will result in an octahedral
> > >> geometry).
> > >> In any case, even if you stick with freeion Zn, you can paramaterize
> the
> > >> complex as a single moleculetype and use distance restraints there,
> can't
> > >> you?
> > >>
> > >>
> > >> On 2012-05-19 09:42:25PM -0400, R.S.K.Vijayan wrote:
> > >> > Dear Gromacs users
> > >> >
> > >> > I was wondering if there exists any technique that sets
> > >> > distance restraint between specified ligand (atoms) and the
> > >> protein(atoms)
> > >> > in Gromacs.  I am simulating a system which contains metal ions
> > >> coordinated
> > >> > to the Ligand. I looked in to the mailing list and Gromacs manual
> and
> > >> > figured out that  *genrster*  can be employed, to
> > >> > set distance, position and dihedral restraints. Unfortunately i also
> > >> > stumbled on the fact  that restraints between systems is not
> possible.
> > >> >
> > >> > Since force fields are not good at handling chelation  between metal
> > >> atoms,
> > >> > i find that the metals drifting away from the coordinated  ligand
> atoms
> > >> > during the course of simulation, hence i introduced position
> constraints
> > >> > for the metal and ended up realizing  that the coordination distance
> > >> > between the ligand and the metal exceeds the permissible range and
> the
> > >> > angles between the chelating atoms gets distorted  and some
> coordinating
> > >> > residues like Histidine and Aspartic  acid also moves away from the
> > >> metal.
> > >> >
> > >> > Hence, i was wondering if l anyone knows of any method (apart from
> > >> > QM/MM) that can help to set distance restraints between the protein
> > >> (metal
> > >> > ion ) and the  ligand, also any suggestion that could help in
> handling
> > >> > ligand metal chelation is welcomed.
> > >> > Thanking in advance
> > >> >
> > >> >
> > >> > Regards
> > >> >
> > >> > Vijayan.R
> > >>
> > >> > --
> > >> > gmx-users mailing listgmx-users@gromacs.org
> > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > >> > Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > >> > Please don't post (un)subscribe requests to the list. Use the
> > >> > www interface or send it to gmx-users-requ...@gromacs.org.
> > >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >>
> > >> --
> > >> ==
> > >> Peter C. Lai| University of Alabama-Birmingham
> > >> Programmer/Analyst  | KAUL 752A
> > >> Genetics, Div. of Research  | 705 South 20th Street
> > >> p...@uab.edu | Birmingham AL 35294-4461
> > >> (205) 690-0808|
> > >> ==
> > >>
> > >> --
> > >> gmx-users mailing listgmx-users@gromacs.org
> > >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> > >> Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > >> Please don't post (un)subscribe requests to the list. Use the
> > >> www interface or send it to gmx-users-requ...@gromacs.org.
> > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >
> > >
> > > --
>

Re: [gmx-users] constraints between protein ligand - metal chelation

[Peter C. Lai]

This approach still requires the system to be parameterized as a single
moleculetype, doesn't it?

On 2012-05-20 04:42:26PM +0200, francesco oteri wrote:
> Hi,
> if you are able to define atom couples able to mantein the structure of
> your complex,
> you can insert in .top file a set of bond using function 6 (see table at
> pag 125 of the user manual).
> For example, let atom 1 and 100 are at distance 0.6nm, you can insert in
> .top a row like
> 
> 1 100 6 0.6 1000
> 
> you impose a bond between the two atoms having as eauilibrium distance
> 0.6nm and
> force strenght 1000J.
> 
> Function 6 doesn't implie the generation of angles and dihedrals so it is
> the right choice
> to impose distance restraints
> 
> 
> Francesco
> 2012/5/20 R.S.K.Vijayan 
> 
> > Many  thanks for your response. No special reasons for parametrizing the
> > ligand and the protein as a separate system. I dont think that the ligand
> > and protein can be parametrized as a single system, but will definitely try
> > doing it as a single system and see if it works.
> > Regards
> > Vijayan.R
> >
> >
> > On Sat, May 19, 2012 at 10:23 PM, Peter C. Lai  wrote:
> >
> >> Is there a particular reason why the ligand has been parameterized as a
> >> separate moleculetype from the protein in your case? I prefer to treat
> >> coordination bonds as "real bonds" instead of relying on electrostatic
> >> interactions anyway, since it is the only way to conservatively ensure the
> >> coordination geometry is preserved (like for Zn, where QM predicts a
> >> tetrahedral geometry but Zn free ions will result in an octahedral
> >> geometry).
> >> In any case, even if you stick with freeion Zn, you can paramaterize the
> >> complex as a single moleculetype and use distance restraints there, can't
> >> you?
> >>
> >>
> >> On 2012-05-19 09:42:25PM -0400, R.S.K.Vijayan wrote:
> >> > Dear Gromacs users
> >> >
> >> > I was wondering if there exists any technique that sets
> >> > distance restraint between specified ligand (atoms) and the
> >> protein(atoms)
> >> > in Gromacs.  I am simulating a system which contains metal ions
> >> coordinated
> >> > to the Ligand. I looked in to the mailing list and Gromacs manual and
> >> > figured out that  *genrster*  can be employed, to
> >> > set distance, position and dihedral restraints. Unfortunately i also
> >> > stumbled on the fact  that restraints between systems is not possible.
> >> >
> >> > Since force fields are not good at handling chelation  between metal
> >> atoms,
> >> > i find that the metals drifting away from the coordinated  ligand atoms
> >> > during the course of simulation, hence i introduced position constraints
> >> > for the metal and ended up realizing  that the coordination distance
> >> > between the ligand and the metal exceeds the permissible range and the
> >> > angles between the chelating atoms gets distorted  and some coordinating
> >> > residues like Histidine and Aspartic  acid also moves away from the
> >> metal.
> >> >
> >> > Hence, i was wondering if l anyone knows of any method (apart from
> >> > QM/MM) that can help to set distance restraints between the protein
> >> (metal
> >> > ion ) and the  ligand, also any suggestion that could help in handling
> >> > ligand metal chelation is welcomed.
> >> > Thanking in advance
> >> >
> >> >
> >> > Regards
> >> >
> >> > Vijayan.R
> >>
> >> > --
> >> > gmx-users mailing listgmx-users@gromacs.org
> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> > Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> > Please don't post (un)subscribe requests to the list. Use the
> >> > www interface or send it to gmx-users-requ...@gromacs.org.
> >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >>
> >> --
> >> ==
> >> Peter C. Lai| University of Alabama-Birmingham
> >> Programmer/Analyst  | KAUL 752A
> >> Genetics, Div. of Research  | 705 South 20th Street
> >> p...@uab.edu | Birmingham AL 35294-4461
> >> (205) 690-0808|
> >> ==
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface

Re: [gmx-users] Coarse grained for Proteins

[XAvier Periole]

The choice of CG force field is (as for atomistic) rather strongly  
dependent on the problem your are looking at. Martini is far from  
being perfect  but it is really good at many things and proteins are  
not so bad but don't expect folding (yet).


I am not aware of other CG FF adapted to GMX.

On May 21, 2012, at 5:22 PM, Steven Neumann wrote:


Dear Gmx Users,

Which coarse grained force filed would you suggest for studying  
proteins in GMX? I have heard that Martini is not the best for such  
a system e.g. proteins interactions in water.


thanks,

Steven
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[gmx-users] Coarse grained for Proteins

[Steven Neumann]

Dear Gmx Users,

Which coarse grained force filed would you suggest for studying proteins in
GMX? I have heard that Martini is not the best for such a system e.g.
proteins interactions in water.

thanks,

Steven
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Re: [gmx-users] MARTINI parameters for dodecyl maltoside (DDM)

[XAvier Periole]

Thee are not yet parameters for DDM but indeed the parameters for both  
the head and the tail are defined separately. It would be very useful  
to combine them and start building a detergent parameter library ...  
the topologies would have to be tested against experimental and/or  
atomistic data. I believe there must be an enormous amount of data on  
the phase behavior of DDM and other thermodynamic data.


On May 21, 2012, at 3:35 PM, Dariush Mohammadyani wrote:

Sure, this is the way to make forcefield for your molecule. Also,  
please check literature.


Good luck,
Dariush



On Mon, May 21, 2012 at 9:26 AM, francesco oteri > wrote:

Hi Dariush,
I've checked but it seems there no parameters for my detergent.

Actully there are parameters for the polar head and the lipidic  
tail, so it is worth trying to merge them

to have the correct representation!

Francesco

2012/5/21 Dariush Mohammadyani 
Have you checked MARTINI website?
http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters

Dariush




Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
USA



On Sun, May 20, 2012 at 1:01 PM, francesco oteri > wrote:

Dear gromacs users,
does someone of you know whether parameters for the detergent  
dodecyl-beta-maltoside

are avalaible in MARTINI forcefield?

Thank you in advance,
Francesco

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--
Cordiali saluti, Dr.Oteri Francesco

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[gmx-users] Polarization term in non-boded potential - Regd

[ramesh cheerla]

Hi all,

 I am planing to use Gromacs for the simulation of my system,
for which the non-bonded interaction potential has the polarization term
as  -Dij/(rij**4) in addition to the Bucking ham potential and
electrostatic interactions.  So the non-bonded potential  will appear as

   U(r)NB = A exp( -rij B) - C/rij**6 - D/rij**4 +
qiqj/rij   Here the units for the polarization term is  nm^4 Kcal/mol
How can I handle this kind of potentials in gromacs ? Can I use tabulated
potential for this ?

Please help me in this regard,

Thank you in advance.

Regards,
Ramesh Cheerla.
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Re: [gmx-users] top/itp file to show parameters explicitly

[Javier Cerezo]

The actual parameters are listed in the ffbonded.itp file located in the 
folder of the corresponding force field, under [ dihedraltypes ] section.


Javier

El 21/05/12 14:43, Alan escribió:

Hi there,

Is there an option in pdb2gmx that when generating the top/itp file, 
it could show the parameters explicitly? e.g.:


Instead of:
[ dihedrals ]
;  aiajakal functc0c1   
 c2c3

5131112 4
   11151314 4
   15232122 4
   21252324 4
   25323133 4

(my hard hand modifications)

[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
;i  j  k  l   func   phase kd  pn
 5 13 11 12  4   180.00  43.93200   2 ; CA-   
  N- C- O
11 15 13 14  4   180.00   4.60240   2 ;  C-   
 CA- N- H
15 23 21 22  4   180.00  43.93200   2 ; CA-   
  N- C- O
21 25 23 24  4   180.00   4.60240   2 ;  C-   
 CA- N- H
25 32 31 33  4   180.00  43.93200   2 ; CA-   
OC1- C-   OC2


I mean, if the parameters that are hiding in e.g. 
...gromacs/top/amber99sb.ff could be showed in the top/itp file for 
human readers, that would be great.


Thanks,

Alan

--
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Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588





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Physical Chemistry
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Re: [gmx-users] MARTINI parameters for dodecyl maltoside (DDM)

[Dariush Mohammadyani]

Sure, this is the way to make forcefield for your molecule. Also, please
check literature.

Good luck,
Dariush



On Mon, May 21, 2012 at 9:26 AM, francesco oteri
wrote:

> Hi Dariush,
> I've checked but it seems there no parameters for my detergent.
>
> Actully there are parameters for the polar head and the lipidic tail, so
> it is worth trying to merge them
> to have the correct representation!
>
> Francesco
>
> 2012/5/21 Dariush Mohammadyani 
>
>> Have you checked MARTINI website?
>> http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters
>>
>> Dariush
>>
>>
>>
>>
>> Kind Regards,
>> Dariush Mohammadyani
>> Department of Structural Biology
>> University of Pittsburgh School of Medicine
>> Biomedical Science Tower 3
>> 3501 Fifth Avenue
>> Pittsburgh, PA 15261
>> USA
>>
>>
>>
>> On Sun, May 20, 2012 at 1:01 PM, francesco oteri <
>> francesco.ot...@gmail.com> wrote:
>>
>>> Dear gromacs users,
>>> does someone of you know whether parameters for the detergent
>>> dodecyl-beta-maltoside
>>> are avalaible in MARTINI forcefield?
>>>
>>> Thank you in advance,
>>> Francesco
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>
>>
>>
>>
>>
>> --
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>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>
> --
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Re: [gmx-users] MARTINI parameters for dodecyl maltoside (DDM)

[francesco oteri]

Hi Dariush,
I've checked but it seems there no parameters for my detergent.

Actully there are parameters for the polar head and the lipidic tail, so it
is worth trying to merge them
to have the correct representation!

Francesco

2012/5/21 Dariush Mohammadyani 

> Have you checked MARTINI website?
> http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters
>
> Dariush
>
>
>
>
> Kind Regards,
> Dariush Mohammadyani
> Department of Structural Biology
> University of Pittsburgh School of Medicine
> Biomedical Science Tower 3
> 3501 Fifth Avenue
> Pittsburgh, PA 15261
> USA
>
>
>
> On Sun, May 20, 2012 at 1:01 PM, francesco oteri <
> francesco.ot...@gmail.com> wrote:
>
>> Dear gromacs users,
>> does someone of you know whether parameters for the detergent
>> dodecyl-beta-maltoside
>> are avalaible in MARTINI forcefield?
>>
>> Thank you in advance,
>> Francesco
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
>
> --
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-- 
Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] MARTINI parameters for dodecyl maltoside (DDM)

[Dariush Mohammadyani]

Have you checked MARTINI website?
http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters

Dariush




Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
USA



On Sun, May 20, 2012 at 1:01 PM, francesco oteri
wrote:

> Dear gromacs users,
> does someone of you know whether parameters for the detergent
> dodecyl-beta-maltoside
> are avalaible in MARTINI forcefield?
>
> Thank you in advance,
> Francesco
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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RE: [gmx-users] constraints hbonds with 4.6

[Berk Hess]

Hi,

I swapped two arguments to a function call. I have fixed it and it should 
appear soon
in the public repository. You can find the fix below.

Cheers,

Berk

diff --git a/src/kernel/topshake.c b/src/kernel/topshake.c
index c5f3957..78961c5 100644
--- a/src/kernel/topshake.c
+++ b/src/kernel/topshake.c
@@ -204,7 +204,7 @@ void make_shake (t_params plist[],t_atoms 
*atoms,gpp_atomtype_t at,int nshake)
p.C1 = pr->param[i].C2;
add_param_to_list (&(plist[F_CONSTR]),&p);
  } else {
-copy_bond(pr,i,j++); 
+ copy_bond(pr,j++,i); 
  }
}
pr->nr = j;


> Date: Mon, 21 May 2012 11:13:46 +0200
> From: sebastian.wa...@physik.uni-freiburg.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] constraints hbonds with 4.6
> 
> Hi all together,
> 
> I am testing the 4.6 dev version of gromacs with heterogeneous
> acceleration (force field: amber99-ildn) on a 95 residue protein (all
> atom model) in SPCE and run into major troubles using in the .mdp file
> option constraints = hbonds with the default lincs parameters. The
> system is exploding with the standard lincs warning (relative constraint
> deviation after LINCS ..). Everything is working fine with the
> option constraints = all-bonds or when I constrain all bonds with
> hydrogen atoms manually in the .top file (which is a lot of effort).
> Using gmxdump to search the .tpr file for the constraints I can't find
> the bond constraints using the constraints = hbonds. Therefore I am
> wondering if the very useful option is not included in the 4.6 version
> of grompp or if there is something equal I don't know anything about.
> 
> Thank a lot for any response
> 
> Sebastian
>  
> 
> -- 
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[gmx-users] Protein_Protein Simulation -reg

[rethina malliga]

Respected Gromacs Developers,

I am Rethinamalliga Gunasekaran, using different modules of GROMACS for my
project and its guiding me profoundly.

Thank you for developing such a tool and also for your well guiding
tutorial.

I need to perform Protein Protein simulation and I tried with GROMACS with
the tutorial for Protein-Ligand simulation.

Can I use the tutorial for Protein-Ligand for Protein-Protein Simulation?

I got the error in ions adding step insisting to check the coordinate file
in topol.top and solv.gro.

Kindly help me to do Protein Protein simulation via GROMACS.

My thanks in advance.

Sincerely,
Rethina Malliga Gunasekaran,
Department Of BioInformatics,
Science Block,
Alagappa University,
Karaikudi – 630 004, India.
http://alagappauniversity.academia.edu/RethinamalligaGunasekaran/

**
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[gmx-users] top/itp file to show parameters explicitly

[Alan]

Hi there,

Is there an option in pdb2gmx that when generating the top/itp file, it
could show the parameters explicitly? e.g.:

Instead of:
[ dihedrals ]
;  aiajakal functc0c1c2
   c3
5131112 4
   11151314 4
   15232122 4
   21252324 4
   25323133 4

(my hard hand modifications)

[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
;i  j  k  l   func   phase kd  pn
 5 13 11 12  4   180.00  43.93200   2 ; CA- N-
C- O
11 15 13 14  4   180.00   4.60240   2 ;  C-CA-
N- H
15 23 21 22  4   180.00  43.93200   2 ; CA- N-
C- O
21 25 23 24  4   180.00   4.60240   2 ;  C-CA-
N- H
25 32 31 33  4   180.00  43.93200   2 ; CA-   OC1-
C-   OC2

I mean, if the parameters that are hiding in e.g.
...gromacs/top/amber99sb.ff could be showed in the top/itp file for human
readers, that would be great.

Thanks,

Alan

-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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Re: [gmx-users] What is the autocorrelation time

[Patrick Fuchs]

Hi Erik,
your examples on H-bond acfs are interesting. I'm wondering about the 
"distinct features which are non-exponential" in your examples. What do 
you mean exactly? Could these features be due to rare (H-bonding) 
events, or in other words to poor sampling?
Intuitively, I'd say that the interpretation of the acf (at least for 
the decay and the decorelation) is always valid unless maybe if you have 
very poor statistics.

Ciao,

Patrick

Le 20/05/2012 16:12, Erik Marklund a écrit :

Dear Chris,

As I see it there one can interpret the acf and correlatation time
further for certain types of data. I'll use the h-bond autocorrelation
function as an example. Here the data is time series of logical true and
false, represented as ones and zeros. This type of acf can be direcly
interpreted as a probablity, and some quantities derived from the acf
can bear further meaning because of this.

I also thought that the nature of the data may be such there is a
non-exponential part, which makes the autocorreltaion time less valid,
or less connected to other intuitive concepts. Again, the h-bond acf has
distinct features which are non-exponential and the autocorreltaion time
derived from such acfs may in fact be misleading when the h-bond
kinetics is to be determined.

Hope that makes sense. I's be happy to hear from you if you disagree.

Best,

Erik

19 maj 2012 kl. 04.01 skrev Christopher Neale:


Dear Erik:

I thought about your comment for a while and I have come to understand
that you are correct. The exponential (or integral) autocorrelation
time is a mathematical construct and is defined as such. What I was
looking for was an interpretation of the autocorrelation time in terms
of the time required to decorrelate the sampling.

As to whether or not this will depend on the nature of the data, I
don't really understand your conjecture. If the interpretation of the
autocorrelation time depends on the nature of the data, then that
implies to me that a single scalar value is useless in this case. I
don't understand how it could be useful to represent the
autocorrelation time by a single number if that number does not mean
anything on its own. If you have time, I would appreciate if you could
elaborate on this point.

Thank you,
Chris.

-- original message --

Aren't you looking for an interpretation rather than a definition? And
will this not depend on the nature of the data?

Best,

Erik

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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 6688 fax: +46 18 511 755
er...@xray.bmc.uu.se 
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--
___
Patrick FUCHS
Dynamique des Structures et Interactions des Macromolécules Biologiques
INTS, INSERM UMR-S665, Université Paris Diderot,
6 rue Alexandre Cabanel, 75015 Paris
Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19
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Re: [gmx-users] Regarding error.

[Javier Cerezo]

Hi Seera

As the error message is telling you, the molecule type CU1 is defined 
more than once along your topology. Check it, locate the [ moleculetype 
] sections and verify that CU1 is defined only once. If that does not 
solve the problem, you can post you topology here so that we can try to 
identify the source for the error.


Javier

El 21/05/12 10:55, Seera Suryanarayana escribió:

Dear all gromacs users,
   I tried the grompp and i got the 
following error.




Fatal error:
moleculetype CU1 is redefined.

Is there any explanation why is thid happening?

I would appreciate any help. Iam new in using MD and gromac in particular.


Suryanarayana Seera,
PhD student,
HYderabad,
India.




--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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[gmx-users] constraints hbonds with 4.6

[SebastianWaltz]

Hi all together,

I am testing the 4.6 dev version of gromacs with heterogeneous
acceleration (force field: amber99-ildn) on a 95 residue protein (all
atom model) in SPCE and run into major troubles using in the .mdp file
option constraints = hbonds with the default lincs parameters. The
system is exploding with the standard lincs warning (relative constraint
deviation after LINCS ..). Everything is working fine with the
option constraints = all-bonds or when I constrain all bonds with
hydrogen atoms manually in the .top file (which is a lot of effort).
Using gmxdump to search the .tpr file for the constraints I can't find
the bond constraints using the constraints = hbonds. Therefore I am
wondering if the very useful option is not included in the 4.6 version
of grompp or if there is something equal I don't know anything about.

Thank a lot for any response

Sebastian
 

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[gmx-users] Regarding error.

[Seera Suryanarayana]

Dear all gromacs users,
   I tried the grompp and i got the
following error.



Fatal error:
moleculetype CU1 is redefined.

Is there any explanation why is thid happening?

I would appreciate any help. Iam new in using MD and gromac in particular.


Suryanarayana Seera,
PhD student,
HYderabad,
India.
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[gmx-users] RE: Re: Wierd results from Umbrella sampling (Justin A. Lemkul)

[Du Jiangfeng (BIOCH)]

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of gmx-users-requ...@gromacs.org [gmx-users-requ...@gromacs.org]
Sent: Wednesday, May 16, 2012 2:59 PM
To: gmx-users@gromacs.org
Subject: gmx-users Digest, Vol 97, Issue 120

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When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."


Today's Topics:

   1. Re: grompp Unkown bond_atomtype C2 (Justin A. Lemkul)
   2. Re: grompp Unkown bond_atomtype C2 (Lara Bunte)
   3. Re: grompp Unkown bond_atomtype C2 (Justin A. Lemkul)
   4. Re: Wierd results from Umbrella sampling (Justin A. Lemkul)
   5. (no subject) (rama david)
   6. Re: (no subject) (Justin A. Lemkul)
   7. forcefields for lipids (Shima Arasteh)


--

Message: 1
Date: Wed, 16 May 2012 07:22:31 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] grompp Unkown bond_atomtype C2
To: Lara Bunte ,   Discussion list for GROMACS
users 
Message-ID: <4fb38df7.2060...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 5/16/12 3:56 AM, Lara Bunte wrote:
> Hi
>
> After:
>
> pdb2gmx -f mymol.pdb -water tip3p
> editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro
>
> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
>
>
> I typed:
>
>
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>
>
> where em.mdp is my energy minimization file and I got:
>
> Fatal error:
> Unknown bond_atomtype C2
>
>
> What is here the problem? All atom types should be declared by me, I guess.
>

You're making use of an atom type called "C2" in some bonded interaction, but
such an atom type doesn't exist.  You need to define it.

-Justin

--


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




--

Message: 2
Date: Wed, 16 May 2012 13:05:24 +0100 (BST)
From: Lara Bunte 
Subject: Re: [gmx-users] grompp Unkown bond_atomtype C2
To: "jalem...@vt.edu" 
Cc: "gmx-users@gromacs.org" 
Message-ID:
<1337169924.86371.yahoomail...@web29405.mail.ird.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1

Hi


in my .rtp file I wrote in the [ atoms ] block

C2?? CN1A??? 0.7481?? 1


but in the atomtypes.atp file I wrote

CN1A??? 12.01100


So I declared it. So what do you mean with "such an atom type doesn't exist"?

Greetings
Lara






- Urspr?ngliche Message -
Von: Justin A. Lemkul 
An: Lara Bunte ; Discussion list for GROMACS users 

CC:
Gesendet: 13:22 Mittwoch, 16.Mai 2012
Betreff: Re: [gmx-users] grompp Unkown bond_atomtype C2



On 5/16/12 3:56 AM, Lara Bunte wrote:
> Hi
>
> After:
>
> pdb2gmx -f mymol.pdb -water tip3p
> editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro
>
> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
>
>
> I typed:
>
>
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>
>
> where em.mdp is my energy minimization file and I got:
>
> Fatal error:
> Unknown bond_atomtype C2
>
>
> What is here the problem? All atom types should be declared by me, I guess.
>

You're making use of an atom type called "C2" in some bonded interaction, but
such an atom type doesn't exist.? You need to define it.

-Justin

--


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





--

Message: 3
Date: Wed, 16 May 2012 08:08:29 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] grompp Unkown bond_atomtype C2
To: Discussion list for GROMACS users 
Message-ID: <4fb398bd.6010...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 5/16/12 8:05 AM, Lara Bunte wrote:
> Hi
>
>
> in my .rtp file I wrote in the [ atoms ] block
>
> C2   CN1A0.7481   1
>
>
> but in the atomtypes.atp file I wrote
>
> CN1A12.01100
>
>
> So I declared it. So what do you mean with "such an atom type doesn't exist"?
>

Neither of those actions constitutes what you need.  Your atom name is C2, while
its type is CN1A.  Apparently somewhere in the bonded parameters you've assigned
C2 as a type, which is wrong.  You need to be using CN1A if adding a new bonded
parameter.  The CN1A atom type already exists in the force field so you don't
ne