Re: [gmx-users] problem with solvent box in gromacs 4.5.4

[Tsjerk Wassenaar]

Hi,

> The triclinic representation is used for all boxes in Gromacs as it is the
> most compact.  One needs to invoke trjconv with "-pbc mol -ur compact" to
> obtain the expected visualization.

Well, it's not the most compact (otherwise -ur compact would yield you
a brick again), but it's the easiest, and the easiest to build with a
rectangular bricklet of solvent. Mind that this is explained in quite
some detail in the manual, in numerous posts in the user list
archives, and in tutorial material. Oh, and also do note that there is
no need to do any conversion with trjconv, unless you aim at pretty
visualization.

Cheers,

Tsjerk

>
> -Justin
>
>> On Tue, May 22, 2012 at 9:27 AM, patrick wintrode > > wrote:
>>
>>    After generating my protein .gro and .top files and doing the initial
>> energy
>>    minimization, I used the following series of commands:
>>
>>    editconf -f protein-vacuum.gro -o protein-PBC.gro -bt dodecahedron -d
>> 1.2
>>
>>    genbox -cp protein-PBC.gro -cs spc216.gro -p protein.top -o
>> protein-water.gro
>>
>>    I then use editconf to convert protein-water.gro to a pdb file. When I
>> open this
>>    file in PyMol, the water box is cubic rather than dodecahedral.
>>
>>    Has any one else encountered this?
>>
>>    Thanks.
>>
>>
>>    --
>>    gmx-users mailing list gmx-users@gromacs.org
>> 
>>
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>
> --
> 
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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RE: [gmx-users] Chemical Potential

[Marzinek, Jan]

Hi Fabian,

The tpi integrator will caluclate it for you when you simply add the extra 
molecule to your gro and topology:

http://www.mail-archive.com/gmx-users@gromacs.org/msg50610.html

Best,

Jan


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Fabian Casteblanco [fabian.castebla...@gmail.com]
Sent: Tuesday, May 22, 2012 11:54 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Chemical Potential

Hello community,

I'm just trying to explore what kind of calculations one can do on
polymer systems (pure or in water) in order to validate the force
field works accurately for that system.  I know there are basics such
as density, volume, dH of vaporization, isothermal compressibility,
heat capacity, etc.   I've been reading about the particle insertion
method to calculate chemical potentials.  Since the chemical potential
is simply the change in gibbs as the number of particles changes,  can
one use the g_bar method to simply insert/delete a molecule to/from
the system?

Anybody know an article where this or something similar was done?  Thanks.

--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering
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[gmx-users] g_rms -bm

[Kowsar Bagherzadeh]

Dear Users, 
I am trying to analyze a ligand-protein simulation results. I read in the 
manual that using g_rms command with –bm option produces a matrix of average 
bond angle deviations. And only bonds between atoms in the comparison groups 
are considered.  Does it mean that it is for the bonds and their angles that 
are already in existence? (Not the ones that may be formed throughout 
simulation, I mean the ligand may for example interact with residues through 
H-bonds) .I have made a group in my index file named Active site (including 
only the active site residues), and I have a LIG group as well. If I choose 
these two groups for g_rms with this command:
g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx
Does it show me how the ligand affects the active site residues bond angles?
And one more question, how can I study the ligand orientation in the active 
site?
Sogol-- 
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[gmx-users] Gromacs files to simulate SiO2 film

[Alexey Lyulin]

Dear all,
would it be possible to send me the necessary files in order to start the 
Gromacs simulations of thin film of SiO_2 (preferably amorphous)?

Do people use Gromacs force fields for this, or BKS potential?

Thanks a lot in advance,
Yours, alexey

*
Dr. Alexey V. Lyulin
Assistant Professor
Theory of Polymers and Soft Matter (TPS)
Eindhoven University of Technology
Postbus 513 5600 MB Eindhoven
The Netherlands
http://www.phys.tue.nl
* 


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[gmx-users] RE: Re: Wierd results from Umbrella sampling (Justin A. Lemkul)(Thomas Schlesier)

[Du Jiangfeng (BIOCH)]

I increased the potential to 2350 instead of 1000 in my md_umbrella.mdp (the 
other parameters kept unchanged), then the movement of my protein was less than 
the previous one, which we can see from pullx.xvg (attached). But it still not 
reach to the designed region. So I am going to increase the potential higher 
again.

It still does not work if I switched on the LINCS. The error is that the number 
of constraint is more than the number of freedom.

I am running another trail with high potential (let's say 3000, ok?) and dt=2 
ft, which value is definitely not recommended by Martini developers.

With Regards,

Jiangfeng.



Message: 3
Date: Tue, 22 May 2012 18:53:54 +0200
From: Thomas Schlesier 
Subject: [gmx-users] Re: Wierd results from Umbrella sampling,  (Justin
A. Lemkul)
To: 
Message-ID: <4fbbc4a2.9020...@uni-mainz.de>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed

I never worked with the MARTINI (or other coarse-grained) force field,
but this in the umbrella.mdp

title   = Umbrella pulling simulation
integrator  = md
dt  = 0.019

looks suspicious. The dt is about an order of magnitude greater than one
uses in normal (bond-)constrainted md-simulations. I know that in
coarse-grained simulations the potentials are smoother than in atomistic
force fields and one therefore could use a higher timestep, but i don't
know if you can go so high.
Anyway you should look for the umbrella potential. If the force constant
and the timestep are both too high you could get problems:
Assume a particle in a harmonic well. If the force constant is high and
the timestep too high, you wont sample the harmonic well, but 'jump'
each time from one side to the other (high force + great timestep ->
long movement).
So i would test it first with a timestep of 0.002 (same as you used for
pulling sim).





--

Message: 4
Date: Tue, 22 May 2012 19:15:41 +0200
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Re: Wierd results from Umbrella sampling,
(Justin A. Lemkul)
To: Discussion list for GROMACS users 
Message-ID: <4fbbc9bd.8070...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 5/22/12 6:53 PM, Thomas Schlesier wrote:
> I never worked with the MARTINI (or other coarse-grained) force field, but 
> this
> in the umbrella.mdp
>
> title = Umbrella pulling simulation
> integrator = md
> dt = 0.019
>
> looks suspicious. The dt is about an order of magnitude greater than one uses 
> in
> normal (bond-)constrainted md-simulations. I know that in coarse-grained
> simulations the potentials are smoother than in atomistic force fields and one
> therefore could use a higher timestep, but i don't know if you can go so high.
> Anyway you should look for the umbrella potential. If the force constant and 
> the
> timestep are both too high you could get problems:
> Assume a particle in a harmonic well. If the force constant is high and the
> timestep too high, you wont sample the harmonic well, but 'jump' each time 
> from
> one side to the other (high force + great timestep -> long movement).
> So i would test it first with a timestep of 0.002 (same as you used for 
> pulling
> sim).
>

Testing this would be good, though the MARTINI developers routinely report
timesteps of 20-40 fs as "normal" use.  I have never obtained stable
trajectories above 20 fs, but I also do not do much coarse graining.  It could
very well be that the pull code is not stable with such an integration step.

-Justin

>
> Am 22.05.2012 18:37, schrieb gmx-users-requ...@gromacs.org:
>> Thank you for your reply, Thomas. Under your explanation, I am well 
>> understood
>> of the terms: pull_k and pull_rate.
>> Here I upload both md_umbrella.mdp and md_pulling.mdp.
>> I have to mention that it is coarse gained system with Martini force field.
>>
>> At the same time, i am going to run a simulation without pull code but with
>> LINCS constraint, and also run another system with a huge pull_k but without
>> LINCS. Hope I could get some interesting information.
>>
>> With Regards,
>>
>> Jiangfeng.
>>
>> Message: 3
>> Date: Tue, 22 May 2012 16:36:47 +0200
>> From: Thomas Schlesier
>> Subject: [gmx-users] Re: Wierd results from Umbrella, sampling (Justin
>> A. Lemkul)
>> To:
>> Message-ID:<4fbba47f.5010...@uni-mainz.de>
>> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>>
>> Think it would be best to show the .mdp file, else we can only guess
>> what the parameters are.
>> From the histogram it looks like that the force constant of the
>> restraining potential is too low, since the histograms are really wide,
>> but pull_k1=1000 is a 'normal' value.
>> On thing which confueses me is you said that fluctuations from g_dist
>> are about 0.4nm, but in the histogram i looks like the distance
>> fluctuates about 1nm or even more. for this be sure, that you compare
>> the right distances -> if you pull only in z-direction, the only look
>> into the z-direction from the 

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

[Alan]

Thanks Justin, you were right. In the end gmxdump helped to clear some
doubts but I wished it would be less painfully.

Cheers,

Alan

On 22 May 2012 12:36, Justin A. Lemkul  wrote:

>
>
> On 5/22/12 12:46 PM, Alan wrote:
>
>> Hi Justin, your suggestion got close. However, let me give an example.
>> You can
>> use the Gly-Gly-Gly example I am attaching and do this:
>>
>> pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top  -water none
>> /sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o aGGG.tpr -pp
>> aGGGp.top
>>
>> if you look at aGGGp.top I can't find which parameters were used for
>>
>> [ dihedrals ]
>> ;  aiajakal functc0c1c2
>>c3c4c5
>> 2 1 5 6 9
>>
>> I.e., for proper dihedral (H1- N-CA-   HA1), I can't find
>> in amber99sb.ff/forcefield.itp any combination that handles parameters for
>> X-N-CA-X or X-CA-N-X, so how grompp is interpreting this dihedral?
>>
>>
> Make sure you're looking at types, not names.  The type sequence here is
> H-N3-CT-HP, which I think is mapped to this dihedral:
>
>  X   CT  N3  X 9   0.0  0.65084 3  ; JCC,7,(1986),230
>
> Running gmxdump on the .tpr file will show it for sure; I had assumed it
> would be in the post-processed topology as well, but I guess not.
>
> -Justin
>
>  Thanks,
>>
>> Alan
>>
>> On 21 May 2012 18:50, Justin A. Lemkul > > wrote:
>>
>>
>>
>>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 functc0c1
>>c2
>>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
>>
>> 
>> >
>>
>>==**__==
>>--
>>gmx-users mailing list gmx-users@gromacs.org > gmx-users@gromacs.org>
>>
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>>
>>
>> 
>> >
>>Please search the archive at
>>
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>>
>>
>> >
>> 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
>>
>>
>> 
>> >
>>
>>
>>
>>
>> --
>> Alan Wilter SOUSA da SILVA, DSc
>> Bioinformatician, UniProt - PANDA, EMBL-EBI
>> CB10 1SD, Hinxton, Cambridge, UK
>> +44 1223 49 4588
>>
>>

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

[Mark Abraham]

On 23/05/2012 6:42 PM, Alan wrote:
Thanks Justin, you were right. In the end gmxdump helped to clear some 
doubts but I wished it would be less painfully.


One useful approach is to simplify the system as much as possible before 
producing the .tpr and using gmxdump. The necessary cross-referencing is 
easier to see when the complexity of the contents is low.


Mark



Cheers,

Alan

On 22 May 2012 12:36, Justin A. Lemkul > wrote:




On 5/22/12 12:46 PM, Alan wrote:

Hi Justin, your suggestion got close. However, let me give an
example. You can
use the Gly-Gly-Gly example I am attaching and do this:

pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top
 -water none
/sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o aGGG.tpr
-pp aGGGp.top

if you look at aGGGp.top I can't find which parameters were
used for

[ dihedrals ]
;  aiajakal functc0c1
   c2

   c3c4c5
2 1 5 6 9

I.e., for proper dihedral (H1- N-CA-   HA1), I can't find
in amber99sb.ff/forcefield.itp any combination that handles
parameters for
X-N-CA-X or X-CA-N-X, so how grompp is interpreting this dihedral?


Make sure you're looking at types, not names.  The type sequence
here is H-N3-CT-HP, which I think is mapped to this dihedral:

 X   CT  N3  X 9   0.0  0.65084 3  ; JCC,7,(1986),230

Running gmxdump on the .tpr file will show it for sure; I had
assumed it would be in the post-processed topology as well, but I
guess not.

-Justin

Thanks,

Alan

On 21 May 2012 18:50, Justin A. Lemkul mailto:jalem...@vt.edu>
>> wrote:



   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 functc0  
 c1c2

   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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 >
http://lists.gromacs.org/__mailman/listinfo/gmx-users


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 before
posting!
 

[gmx-users] Re: Gromacs files to simulate SiO2 film

[jrustad]

Dear Alexey,
The answer to this question partly depends on your application- for example,
is it important for the surface of the amorphous SiO2 to be able to undergo
reactions like Si-O-Si + H2O = 2SiOH? 

Regards,
Jim Rustad

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[gmx-users] H3 of NPRO missing in AMBER force field

[SebastianWaltz]

Hallo together,

in the amino acid data base file (aminoacids.rtp) of the amber99sb-ildn
force field the H3 hydrogen of NPRO is missing.
Would be nice if someone could add the missing parameters or pose them.

Thanks a lot

Sebastian
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Re: [gmx-users] Re: Gromacs files to simulate SiO2 film

[Alexey Lyulin]

hi Jim,
first of all, thanks for the answer.
No, for me it is not important. Our task is to simulate natural rubber 
between two silica surfaces, i.e, no water will be present.

Do you have some initial files?

thanks, alexey

*
Dr. Alexey V. Lyulin
Assistant Professor
Theory of Polymers and Soft Matter (TPS)
Eindhoven University of Technology
Postbus 513 5600 MB Eindhoven
The Netherlands
http://www.phys.tue.nl
*
- Original Message - 
From: "jrustad" 

To: 
Sent: Wednesday, May 23, 2012 12:12 PM
Subject: [gmx-users] Re: Gromacs files to simulate SiO2 film


Dear Alexey,
The answer to this question partly depends on your application- for example,
is it important for the surface of the amorphous SiO2 to be able to undergo
reactions like Si-O-Si + H2O = 2SiOH?

Regards,
Jim Rustad

--
View this message in context: 
http://gromacs.5086.n6.nabble.com/Gromacs-files-to-simulate-SiO2-film-tp4997666p4997670.html

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[gmx-users] Re: Gromacs files to simulate SiO2 film

[jrustad]

Alexey
I have a quartz(101) surface and a gromacs BKS input file that might get you
started at least.
Cheers
Jim

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[gmx-users] Fatal error: atom C not found in buiding block 19NH2 while combining tdb and rtp

[ankita oindrila]

 i am stimulting an AMP protein in water.

this is the error i get on my first step..

pdb2gmx -f 1PG1_1.pdb -o 1PG1_1_processed.gro -water spce

error:

Fatal error: atom C not found in buiding block 19NH2 while combining
tdb and rtp

please HELP!!
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Re: [gmx-users] H3 of NPRO missing in AMBER force field

[Justin A. Lemkul]

On 5/23/12 12:17 PM, SebastianWaltz wrote:

Hallo together,

in the amino acid data base file (aminoacids.rtp) of the amber99sb-ildn
force field the H3 hydrogen of NPRO is missing.
Would be nice if someone could add the missing parameters or pose them.



There is no H3 in NPRO.  It is a secondary amine, so three H atoms would give it 
five bonds.


-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] Fatal error: atom C not found in buiding block 19NH2 while combining tdb and rtp

[Justin A. Lemkul]

On 5/23/12 1:26 PM, ankita oindrila wrote:

  i am stimulting an AMP protein in water.

this is the error i get on my first step..

pdb2gmx -f 1PG1_1.pdb -o 1PG1_1_processed.gro -water spce

error:

Fatal error: atom C not found in buiding block 19NH2 while combining
tdb and rtp

please HELP!!


I suspect you're not selecting your termini correctly.  If NH2 is a capping 
residue, you need to interactively select termini (using the -ter option) and 
specify them as "None."  Otherwise, pdb2gmx treats all residues as normal amino 
acids and tries to build normal amino and carboxylate termini.


-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] Re: Wierd results from Umbrella sampling

[Thomas Schlesier]

The picture of pullx.xvg is not really helpful. The reason is that in 
pullx.xvg the second column (after the time) is the position of the 
reference group (which naturally moves; but it's not the thing in which 
wie are interested) and the third column is the distance from the 
reference group to the pulled group (this is the one which interestes you).
Another thing you could try is to pull in all 3 dimensions, if you pull 
only in the z-direction your pulled group can move freely in the x-y 
plane and wouldn't be affected by the umbrella potential. But i think 
for the histogram only the direction in which one pulls are accounted 
for, so the wide histograms are somewhat strange.
For the problems with the constraints i have absolute no idea, never had 
this error message. Even don't know if the problems you get from there 
follow you into the pull-mode simulation. Does the constraint simulation 
run without the pull-code, or do you get there the same problem?

greetings
thomas




I increased the potential to 2350 instead of 1000 in my md_umbrella.mdp (the 
other parameters kept unchanged), then the movement of my protein was less than 
the previous one, which we can see from pullx.xvg (attached). But it still not 
reach to the designed region. So I am going to increase the potential higher 
again.

It still does not work if I switched on the LINCS. The error is that the number 
of constraint is more than the number of freedom.

I am running another trail with high potential (let's say 3000, ok?) and dt=2 
ft, which value is definitely not recommended by Martini developers.

With Regards,

Jiangfeng.



Message: 3
Date: Tue, 22 May 2012 18:53:54 +0200
From: Thomas Schlesier
Subject: [gmx-users] Re: Wierd results from Umbrella sampling,  (Justin
 A. Lemkul)
To:
Message-ID:<4fbbc4a2.9020...@uni-mainz.de>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed

I never worked with the MARTINI (or other coarse-grained) force field,
but this in the umbrella.mdp

title   = Umbrella pulling simulation
integrator  = md
dt  = 0.019

looks suspicious. The dt is about an order of magnitude greater than one
uses in normal (bond-)constrainted md-simulations. I know that in
coarse-grained simulations the potentials are smoother than in atomistic
force fields and one therefore could use a higher timestep, but i don't
know if you can go so high.
Anyway you should look for the umbrella potential. If the force constant
and the timestep are both too high you could get problems:
Assume a particle in a harmonic well. If the force constant is high and
the timestep too high, you wont sample the harmonic well, but 'jump'
each time from one side to the other (high force + great timestep ->
long movement).
So i would test it first with a timestep of 0.002 (same as you used for
pulling sim).





--

Message: 4
Date: Tue, 22 May 2012 19:15:41 +0200
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Re: Wierd results from Umbrella sampling,
 (Justin A. Lemkul)
To: Discussion list for GROMACS users
Message-ID:<4fbbc9bd.8070...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 5/22/12 6:53 PM, Thomas Schlesier wrote:

I never worked with the MARTINI (or other coarse-grained) force field, but this
in the umbrella.mdp

title = Umbrella pulling simulation
integrator = md
dt = 0.019

looks suspicious. The dt is about an order of magnitude greater than one uses in
normal (bond-)constrainted md-simulations. I know that in coarse-grained
simulations the potentials are smoother than in atomistic force fields and one
therefore could use a higher timestep, but i don't know if you can go so high.
Anyway you should look for the umbrella potential. If the force constant and the
timestep are both too high you could get problems:
Assume a particle in a harmonic well. If the force constant is high and the
timestep too high, you wont sample the harmonic well, but 'jump' each time from
one side to the other (high force + great timestep ->  long movement).
So i would test it first with a timestep of 0.002 (same as you used for pulling
sim).



Testing this would be good, though the MARTINI developers routinely report
timesteps of 20-40 fs as "normal" use.  I have never obtained stable
trajectories above 20 fs, but I also do not do much coarse graining.  It could
very well be that the pull code is not stable with such an integration step.

-Justin



Am 22.05.2012 18:37, schrieb gmx-users-requ...@gromacs.org:

Thank you for your reply, Thomas. Under your explanation, I am well understood
of the terms: pull_k and pull_rate.
Here I upload both md_umbrella.mdp and md_pulling.mdp.
I have to mention that it is coarse gained system with Martini force field.

At the same time, i am going to run a simulation without pull code but with
LINCS constraint, and also run another system with a huge pull_k but without
LINCS. Hope I could get some interesting information.

With Regards,

[gmx-users] g_polystat

[Leandro]

Dear GMX-users,

I am trying to use g_polystat in order to calculate persistence length of
DNA oligomer, 60bp. From g_polystat -h I understood that this function
provides the persistence length measures in number of bonds between
consequtive atoms making DNA backbone. Using this function I obtain an
average number of bonds equal to 0.3. What can this mean? Does it mean that
the length of one bond is larger than DNA persistence length? Could anyone
explain me please how I can properly interpret the "number of bonds" which
is the output parameter of g_polystat? Thank you.

Regards,
Leandro  

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[gmx-users] Re: Chemical Potential

[Fabian Casteblanco]

Thank you Jan.

-Fabian

On Tue, May 22, 2012 at 6:54 PM, Fabian Casteblanco
 wrote:
> Hello community,
>
> I'm just trying to explore what kind of calculations one can do on
> polymer systems (pure or in water) in order to validate the force
> field works accurately for that system.  I know there are basics such
> as density, volume, dH of vaporization, isothermal compressibility,
> heat capacity, etc.   I've been reading about the particle insertion
> method to calculate chemical potentials.  Since the chemical potential
> is simply the change in gibbs as the number of particles changes,  can
> one use the g_bar method to simply insert/delete a molecule to/from
> the system?
>
> Anybody know an article where this or something similar was done?  Thanks.
>
> --
> Best regards,
>
> Fabian F. Casteblanco
> Rutgers University --
> Chemical Engineering



-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering
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Re: [gmx-users] What is the autocorrelation time

[Erik Marklund]

Hi Patrick,

There is a fast decay of the hbond acf for liquid water on a 100-200 fs 
timescale that traditionally is associated with the librational motion of water 
molecules. There's a good paper by Omer Markovich and Noam Agmon in J. Chem. 
Phys. 129 084505 2008 where this effect is discussed, although it's not the 
main focus of that paper. Then, after 10 ps or so, there's a regime where the 
acf falls of as a power law. As a consequence the correlation time is not 
really derived from a purely exponential acf and the interpretation might be 
misleading to some extent if you imply exponential behaviour.

Best,

Erik

21 maj 2012 kl. 14.07 skrev 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
>>> 
>>> --
>>> gmx-users mailing list gmx-users@gromacs.org
>>> 
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>> www interface or send it to gmx-users-requ...@gromacs.org.
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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 
>> http://www2.icm.uu.se/molbio/elflab/index.html
>> 
>> 
>> 
> 
> -- 
> ___
> 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
> E-mail address: patrick.fu...@univ-paris-diderot.fr
> Web Site: http://www.dsimb.inserm.fr/~fuchs
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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---
Erik Marklund, PhD
Dept.

[gmx-users] Justin umbrella sampling tutorial......

[rama david]

Hi Gromacs Friends,

   I am performing justin tutorial for umbrella sampling ..
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
I encounter with following problem while using the disatances.pl script

1. After command perl distances.pl  I got following message ...


   Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 30.
   readline() on closed filehandle IN at distances.pl line 16.
  What may be reason for these ..
2. What is the groups.txt ??
   Where it will find ?? Why it is needed??
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[gmx-users] RE: Re: Wierd results from Umbrella sampling (Thomas Schlesier)

[Du Jiangfeng (BIOCH)]

Dear Thomas,

I just finished the run of 2ft with potential 3000. It is much better than 
previous ones. But it still has 1 nm fluctuation along z-axis. I am going to 
increase potential to 5000, crazy :)

For the pullx.xvg, I mistaken the second column as the COM position of pulled 
group, the third column as the COM distance of pulled group with reference 
group. I agree, you are right, the second column should be for reference group, 
for which the trend between second column and third column can prove (one curve 
increases with the other curve decreasing, roughly). However, the second column 
value in my system, which is supposed to be for reference group, fits my pulled 
group perfectly, and I am quiet sure that the COM position of my reference is 
smaller than 5, but the value from second column is between 6 to 7 nm. 

I am also going to try 3 dimension constraint as you suggested.

By the way, I applied position constraint to my reference group in the last 
trail, so I am sure the COM of reference doesn't move at all. 

Thanks a lot,

Jiangfeng.


Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
The Netherlands


--

Message: 8
Date: Wed, 23 May 2012 14:19:36 +0200
From: Thomas Schlesier 
Subject: [gmx-users] Re: Wierd results from Umbrella sampling
To: 
Message-ID: <4fbcd5d8.6090...@uni-mainz.de>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed

The picture of pullx.xvg is not really helpful. The reason is that in
pullx.xvg the second column (after the time) is the position of the
reference group (which naturally moves; but it's not the thing in which
wie are interested) and the third column is the distance from the
reference group to the pulled group (this is the one which interestes you).
Another thing you could try is to pull in all 3 dimensions, if you pull
only in the z-direction your pulled group can move freely in the x-y
plane and wouldn't be affected by the umbrella potential. But i think
for the histogram only the direction in which one pulls are accounted
for, so the wide histograms are somewhat strange.
For the problems with the constraints i have absolute no idea, never had
this error message. Even don't know if the problems you get from there
follow you into the pull-mode simulation. Does the constraint simulation
run without the pull-code, or do you get there the same problem?
greetings
thomas



> I increased the potential to 2350 instead of 1000 in my md_umbrella.mdp (the 
> other parameters kept unchanged), then the movement of my protein was less 
> than the previous one, which we can see from pullx.xvg (attached). But it 
> still not reach to the designed region. So I am going to increase the 
> potential higher again.
>
> It still does not work if I switched on the LINCS. The error is that the 
> number of constraint is more than the number of freedom.
>
> I am running another trail with high potential (let's say 3000, ok?) and dt=2 
> ft, which value is definitely not recommended by Martini developers.
>
> With Regards,
>
> Jiangfeng.
>
>
>
> Message: 3
> Date: Tue, 22 May 2012 18:53:54 +0200
> From: Thomas Schlesier
> Subject: [gmx-users] Re: Wierd results from Umbrella sampling,  (Justin
>  A. Lemkul)
> To:
> Message-ID:<4fbbc4a2.9020...@uni-mainz.de>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>
> I never worked with the MARTINI (or other coarse-grained) force field,
> but this in the umbrella.mdp
>
> title   = Umbrella pulling simulation
> integrator  = md
> dt  = 0.019
>
> looks suspicious. The dt is about an order of magnitude greater than one
> uses in normal (bond-)constrainted md-simulations. I know that in
> coarse-grained simulations the potentials are smoother than in atomistic
> force fields and one therefore could use a higher timestep, but i don't
> know if you can go so high.
> Anyway you should look for the umbrella potential. If the force constant
> and the timestep are both too high you could get problems:
> Assume a particle in a harmonic well. If the force constant is high and
> the timestep too high, you wont sample the harmonic well, but 'jump'
> each time from one side to the other (high force + great timestep ->
> long movement).
> So i would test it first with a timestep of 0.002 (same as you used for
> pulling sim).
>
>
>
>
>
> --
>
> Message: 4
> Date: Tue, 22 May 2012 19:15:41 +0200
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] Re: Wierd results from Umbrella sampling,
>  (Justin A. Lemkul)
> To: Discussion list for GROMACS users
> Message-ID:<4fbbc9bd.8070...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 5/22/12 6:53 PM, Thomas Schlesier wrote:
>> I never worked with the MARTINI (or other coarse-gra

[gmx-users] RE: Justin umbrella sampling tutorial...... (rama david)

[Du Jiangfeng (BIOCH)]

For your second problem: you have to create this file by writing the group 
numbers, which inform the script to decide which two groups to be selected for 
distance calculation. 

If you made it, you first problem would probably be solved.

Good luck,
Jiangfeng.

Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
The Netherlands


Message: 4
Date: Wed, 23 May 2012 19:18:56 +0530
From: rama david 
Subject: [gmx-users] Justin umbrella sampling tutorial..
To: Discussion list for GROMACS users 
Message-ID:

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

Hi Gromacs Friends,

   I am performing justin tutorial for umbrella sampling ..
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
I encounter with following problem while using the disatances.pl script

1. After command perl distances.pl  I got following message ...


   Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 30.
   readline() on closed filehandle IN at distances.pl line 16.
  What may be reason for these ..
2. What is the groups.txt ??
   Where it will find ?? Why it is needed??
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Re: [gmx-users] H3 of NPRO missing in AMBER force field

[SebastianWaltz]

On 05/23/2012 02:16 PM, Justin A. Lemkul wrote:
>
>
> On 5/23/12 12:17 PM, SebastianWaltz wrote:
>> Hallo together,
>>
>> in the amino acid data base file (aminoacids.rtp) of the amber99sb-ildn
>> force field the H3 hydrogen of NPRO is missing.
>> Would be nice if someone could add the missing parameters or pose them.
>>
>
> There is no H3 in NPRO.  It is a secondary amine, so three H atoms
> would give it five bonds.
>
> -Justin
>
As far as I remember the NPRO (like the NLEU) in the amber force field
stands for the protonated N-termini of PRO and therefore should have
three hydrogens like NLEU NALA and so on.

Thanks

Sebastina


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Re: [gmx-users] RE: Justin umbrella sampling tutorial...... (rama david)

[rama david]

On Wed, May 23, 2012 at 7:30 PM, Du Jiangfeng (BIOCH) <
j...@maastrichtuniversity.nl> wrote:

> For your second problem: you have to create this file by writing the group
> numbers, which inform the script to decide which two groups
>
> Thank you... Du Jiangfeng


Yes problem get solve!!!

Thank you

With Best Wishes,
Rama David
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[gmx-users] BAR and non-bonded tables revisited

[jrustad]

All

Thanks much for your previous help.  I now have the calculation running.
However I get suspicious results that make me think that BAR may not be
integrated with tables correctly.

In this problem I am trying to change an Mg ion into an Fe ion (really its a
ferrous iron to a ferric iron, but I’m calling the ferrous iron “Mg” for
convenience

Here are the relevant fragments of my current top file:

[ atomtypes ]

;name   mass  chargeptype   AB

O  15.99940 -1.2   A   0.0  0.0
Na 22.99000  0.6   A   0.0  0.0  
Si 28.08000  2.4   A   0.0  0.0
Ca 40.07800  1.2   A   0.0  0.0
Al 26.98200  1.8   A   0.0  0.0
Mg 55.30500  1.2   A   0.0  0.0
Fe 55.30500  1.8   A   0.0  0.0

;(The tables “table_O_Fe.xvg” and “table_O_Mg.xvg” exist and are read in
without problems)


[ nonbond_params ] ; these now give the multipliers for the tables columns

; i j   func   C6  C12 
OO 1 4.0904959800   2.12268E-09
OSi1 32.8584684009.64853E-11
ONa1 2.2541869930   4.82427E-10
OCa1  2.9149186000   4.82427E-10
OAl1 34.8872656408.68368E-11
OMg1  7.542  1.92800E-10
OFe1 40.4255242401.92800E-10



. . .

 

Now I have defined a molecule type for the changing ion labeled “Cr” in the
.gro file, which transforms from atom type Mg to atom type Fe

[ moleculetype ]
; name nrexcl
Cr 0
[ atoms ]

; nr   type   resnr  residue   atom   cgnr   charge  mass TypeB  ChargeB 
MassB
1   Mg 1 MgMg  2   1.2   55.3050   Fe1.8  
55.305

 . . .

And the relevant portion of my .mdp file for lambda=0

 

coulombtype  = PME-Switch
rcoulomb = 1.0
vdw_type = User

.  .  .

free-energy  = yes
couple-moltype   = Cr
init-lambda  = 0.0
foreign-lambda   =  0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
couple-lambda0   = vdw-q
couple-lambda1   = vdw-q

 
It runs fine, but when I look at the RDF for the changing ion (Cr), it does
not go smoothly between Mg and Fe as lambda goes from 0  to 1, but, at
lambda=1, the peak position is pushed way further out than either Mg (~0.2
nm) and Fe (~0.19 nm) (it’s not an aqueous system b.t.w.) and sits at 0.23
nm or more.
At lambda=0, everything looks OK (i.e. the "Cr" ion gives the same g(r) as
the "Mg" ion)

So it makes me wonder if the short-ranged interactions in the tables are
simply being added together without regard for what the lambda value is? 
(i.e. at lambda =1, we still get the entire short range interaction for the
"A" state added to that of the "B" state).

Is it possible that there is a bug in the integration of non-bonded tables
into the free energy capability?
Or do I misunderstand how the lambda is applied in this "mutating" type free
energy problem?

Thanks for all the help already, and for any further insight anyone can
provide.  I can show a picture if the RDFs if you want to see them.

 
James R. Rustad, Ph.D.
Research Associate, Corning, Inc.
Professor Emeritus, UC Davis

Corning Incorporated
One Science Center Drive
SP TD 01-1
Corning, NY 14831



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[gmx-users] Protein moves out of box after several simulations, how to fix it?

[Marc Hömberger]

Hallo,

I have several (12) simulations running in which I simulate a protein
in a water box (cubic 9x9x9). For all simulations I can  see the
following:
After a few simulations (total time of 7.6ns) the protein moves out of
the water box - for all the twelve simulations. Since the following
simulation is started with the output .gro file of the prior
simulation the protein moves further and further out of the box.  I
have no idea if this is a problem because of periodic boundaries or if
this is a problem with my vmd installation. Can anyone give me a hint
what I could to to fix this and not have to restart all the runs?

I am using a script I used before and I am doing everything like last
time but last time I did not see this behavior of the protein. I am
using vmd to look at the protein and its trajectory (commands see
below)

FYI the commands I use to setup the simulations (just an example of two):
grompp -f md2.mdp -c Protein-struct_md1.gro -p Protein.top -o Protein_md2.tpr
mdrun -nt 3 -s Protein_md2.tpr -o Protein_md2.trr -x Protein_md2.xtc
-c Protein-struct_md2.gro -g Protein_md2.log
grompp -f md3.mdp -c Protein-struct_md2.gro -p Protein.top -o Protein_md3.tpr
mdrun -nt 3 -s Protein_md3.tpr -o Protein_md3.trr -x Protein_md3.xtc
-c Protein-struct_md3.gro -g Protein_md3.log
and so on and so forth.

GROMACS version is 4.5.5
VMD version is 1.9.1.

Thanks in advance
Marc Hoemberger
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Re: [gmx-users] Justin umbrella sampling tutorial......

[Justin A. Lemkul]

On 5/23/12 3:48 PM, rama david wrote:

Hi Gromacs Friends,

I am performing justin tutorial for umbrella sampling ..
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
I encounter with following problem while using the disatances.pl
 script

1. After command perl distances.pl   I got following
message ...


Use of uninitialized value $distance in concatenation (.) or string at
distances.pl  line 30.
readline() on closed filehandle IN at distances.pl 
line 16.
   What may be reason for these ..


The required input doesn't exist.  Either you omitted a step or you're executing 
the script in the wrong directory.



2. What is the groups.txt ??
Where it will find ?? Why it is needed??



This is stated in the tutorial.

-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] H3 of NPRO missing in AMBER force field

[Justin A. Lemkul]

On 5/23/12 4:08 PM, SebastianWaltz wrote:

On 05/23/2012 02:16 PM, Justin A. Lemkul wrote:



On 5/23/12 12:17 PM, SebastianWaltz wrote:

Hallo together,

in the amino acid data base file (aminoacids.rtp) of the amber99sb-ildn
force field the H3 hydrogen of NPRO is missing.
Would be nice if someone could add the missing parameters or pose them.



There is no H3 in NPRO.  It is a secondary amine, so three H atoms
would give it five bonds.

-Justin


As far as I remember the NPRO (like the NLEU) in the amber force field
stands for the protonated N-termini of PRO and therefore should have
three hydrogens like NLEU NALA and so on.



The "N" prefix simply means it is at the N-terminus, not necessarily that it is 
protonated, though the typical forms of the terminal amino acids bear a net 
charge in this group.


Back to the original question - have a look at the structure of proline; it is 
quite different from every other amino acid since it contains a secondary amine.


http://en.wikipedia.org/wiki/Proline

-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] Protein moves out of box after several simulations, how to fix it?

[Justin A. Lemkul]

On 5/23/12 5:30 PM, Marc Hömberger wrote:

Hallo,

I have several (12) simulations running in which I simulate a protein
in a water box (cubic 9x9x9). For all simulations I can  see the
following:
After a few simulations (total time of 7.6ns) the protein moves out of
the water box - for all the twelve simulations. Since the following
simulation is started with the output .gro file of the prior
simulation the protein moves further and further out of the box.  I
have no idea if this is a problem because of periodic boundaries or if
this is a problem with my vmd installation. Can anyone give me a hint
what I could to to fix this and not have to restart all the runs?



Your observations are consistent with 100% normal (and expected) behavior. 
There is no "outside" of a periodic box.  Check out the first two bullet points 
here and the explanation that follows:


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


I am using a script I used before and I am doing everything like last
time but last time I did not see this behavior of the protein. I am
using vmd to look at the protein and its trajectory (commands see
below)



Whether or not a molecule stays near the perceived "center" of the unit cell is 
simply a matter of probability.  Given sufficient simulation time, all proteins 
in water will cross at least one periodic boundary.  Such is the nature of 
diffusion.


-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] Gromacs installed , but no directory /bin under it

[aiqunhuang]

Hi everybody,
I am installing  Gromacs,  in the shell it is said that Gromacs has been 
installed :
GROMACS is installed under /home/Program/gromacs-4.5.
but I couldn't find the directory bin under /gromacs-4.5, I don't know I have 
installed successfully or not, any one could help?
Here is the commands which I used to install Gromacs, my system is Ubuntu 
11.10, gcc complier.
There are some errors in config.log saying: gcc: fatal error no imput files. 
I don't know if this matters or not, i tried to fix the fatal errors in log 
file, but I didn't get anywhere. 
In the last part of showing up in the shell it says something like this:
 /usr/bin/install -c -m 644 'xpm2ps.1' 
'/home/Program/gromacs-4.5/share/man/man1/xpm2ps_mpi.1'
but I couldn't find man/man1 under /gromacs-4.5/share/, anyone could 
help?installation commands:1)  tar -zxvf fftw-3.3.1.tar.gz  tar �Czxvf 
gromacs-4.5.tar.gz  tar -zxvf lam-7.1.4.tar.gz (2) cd lam-7.1.3 ./configure 
--prefix=/home/Program/lam-7.1.4 --with-rsh="ssh-x"make sudo  make 
install (3)  export PATH=$PATH:/home/Program/lam-7.1.4/bin(4)  cd 
fftw-3.3.1  ./configure --enable-float --enable-mpi 
--prefix=/home/Program/fftw-3.3.1  make  make install (3) export 
CPPFLAGS=-I/home/Program/fftw-3.3.1/include  export 
LDFLAGS=-L/home/Program/fftw-3.3.1/lib (4) cd gromacs-4.5 ./configure 
--prefix=/home/Program/gromacs-4.5 --enable-mpi --program-suffix=_mpi make  
sudo make install Here below are the last  part of  output in the shell 
after I run "sudo make install" /usr/bin/install -c -m 644 'trjorder.1' 
'/home/Program/gromacs-4.5/share/man/man1/trjorder_mpi.1' /usr/bin/install -c 
-m 644 'xpm2ps.1' '/home/Program/gromacs-4.5/sha
 re/man/man1/xpm2ps_mpi.1'make[3]: Leaving directory 
`/home/qunzi/Program/gromacs-4.5/man/man1'make[2]: Leaving directory 
`/home/qunzi/Program/gromacs-4.5/man/man1'Making install in man7make[2]: 
Entering directory `/home/qunzi/Program/gromacs-4.5/man/man7'make[3]: Entering 
directory `/home/qunzi/Program/gromacs-4.5/man/man7'make[3]: Nothing to be done 
for `install-exec-am'.test -z "/home/Program/gromacs-4.5/share/man/man7" || 
/bin/mkdir -p "/home/Program/gromacs-4.5/share/man/man7" /usr/bin/install -c -m 
644 'gromacs.7' 
'/home/Program/gromacs-4.5/share/man/man7/gromacs_mpi.7'make[3]: Leaving 
directory `/home/qunzi/Program/gromacs-4.5/man/man7'make[2]: Leaving directory 
`/home/qunzi/Program/gromacs-4.5/man/man7'make[2]: Entering directory 
`/home/qunzi/Program/gromacs-4.5/man'make[3]: Entering directory 
`/home/qunzi/Program/gromacs-4.5/man'make[3]: Nothing to be done for 
`install-exec-am'.make[3]: Nothing to be done for `install-data-am'.make[3]: 
Leaving directory `/home/qunzi/
 Program/gromacs-4.5/man'make[2]: Leaving directory 
`/home/qunzi/Program/gromacs-4.5/man'make[1]: Leaving directory 
`/home/qunzi/Program/gromacs-4.5/man'make[1]: Entering directory 
`/home/qunzi/Program/gromacs-4.5'make[2]: Entering directory 
`/home/qunzi/Program/gromacs-4.5'make  install-exec-hookmake[3]: Entering 
directory `/home/qunzi/Program/gromacs-4.5'
GROMACS is installed under /home/Program/gromacs-4.5.Make sure to update your 
PATH and MANPATH to find theprograms and unix manual pages, and possibly 
LD_LIBRARY_PATHor /etc/ld.so.conf if you are using dynamic libraries.
Please run "make tests" now to verify your installation.
If you want links to the executables in /usr/local/bin,you can issue "make 
links" now.make[3]: Leaving directory `/home/qunzi/Program/gromacs-4.5'make[2]: 
Nothing to be done for `install-data-am'.make[2]: Leaving directory 
`/home/qunzi/Program/gromacs-4.5'make[1]: Leaving directory 
`/home/qunzi/Program/gromacs-4.5'qunzi@qunzi-AO722:~/Program/gromacs-4.5$ 
lsacinclude.m4  AUTHORS config configure COPYING-GPU  
include  Makefile man  shareaclocal.m4cmake   
config.log configure.ac  Doxyfile INSTALL-GPU  Makefile.am  README   
srcadmin CMakeLists.txt  config.status  COPYING   Doxyfile.in  
libtool  Makefile.in  scripts  
testsqunzi@qunzi-AO722:~/Program/gromacs-4.5$ echo 
$PATH/opt/intel/bin:/opt/intel/bin:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/home/Program/lam-7.1.4/binqunzi@qunzi-AO722:~/Program/gromacs-4.5$
 make testsmake: `tests' is up to date.qunzi@qunzi-A
 O722:~/Program/gromacs-4.5$ make testsmake: `tests' is up to 
date.qunzi@qunzi-AO722:~/Program/gromacs-4.5$ man mdrun_mpiNo manual entry for 
mdrun_mpiSee 'man 7 undocumented' for help when manual pages are not 
available.qunzi@qunzi-AO722:~/Program/gromacs-4.5$ man mdrun_mpi.1No manual 
entry for mdrun_mpi.1qunzi@qunzi-AO722:~/Program/gromacs-4.5$ 


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[gmx-users] Re: Distance restraints not working

[tdgrant1]

There are a few possibilities. 
> 
> 1. Numbering in [distance_restraints] is not based on .gro numbering.  The
> atom 
> numbers supplied are only relevant within the [moleculetype] to which they 
> belong, much like [position_restraints].  Also make sure that the 
> [distance_restraints] block is in the correct location in the topology. 
> 
> 2. You've omitted the dihre_fc keyword, though it is set to 1000 by
> default. 
> Check the mdout.mdp file or your .tpr file to ensure that you have a
> sensible 
> value here.  Setting values of fac that high are unnecessary.
> 

Thanks for your help. I have it working now.  It actually turned out to be a
typo.

I have an unrelated question though.  After running the temperature and
pressure equilibration, grompp tells me my md run will produce ~150 GB of
data.  I'd really like to avoid such an enormous amount of data.  The system
is ~300,000 atoms and I will be running 20 ns of simulation (~3 days on our
cluster according to the equilibration output).  Can I simply change the
output control from saving the various files at every 2 ps to every, say, 20
ps?  I realize it's a large jump compared to 2 ps, but 150 GB is a lot of
data.  Will changing the output control so drastically adversely affect the
simulation in any way?

-Tom

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Re: [gmx-users] Re: Distance restraints not working

[Justin A. Lemkul]

On 5/23/12 8:26 PM, tdgrant1 wrote:


There are a few possibilities.


1. Numbering in [distance_restraints] is not based on .gro numbering.  The
atom
numbers supplied are only relevant within the [moleculetype] to which they
belong, much like [position_restraints].  Also make sure that the
[distance_restraints] block is in the correct location in the topology.

2. You've omitted the dihre_fc keyword, though it is set to 1000 by
default.
Check the mdout.mdp file or your .tpr file to ensure that you have a
sensible
value here.  Setting values of fac that high are unnecessary.



Thanks for your help. I have it working now.  It actually turned out to be a
typo.

I have an unrelated question though.  After running the temperature and
pressure equilibration, grompp tells me my md run will produce ~150 GB of
data.  I'd really like to avoid such an enormous amount of data.  The system
is ~300,000 atoms and I will be running 20 ns of simulation (~3 days on our
cluster according to the equilibration output).  Can I simply change the
output control from saving the various files at every 2 ps to every, say, 20
ps?  I realize it's a large jump compared to 2 ps, but 150 GB is a lot of
data.  Will changing the output control so drastically adversely affect the
simulation in any way?



Saving output has no bearing on the simulation result.  Writing every 2 ps is 
probably drastic overkill for most situations.  You should also evaluate what it 
is you need to save, and in what precision.  For instance, if you only need 
coordinate information, most analysis can be conducted on .xtc files, which take 
less space.  If you don't need velocities or forces, you can set nstvout and 
nstfout to zero.  If you only care about .xtc precision for coordinates, you can 
eliminate the .trr file altogether by also setting nstxout to zero.


-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] Gromacs installed , but no directory /bin under it

[Justin A. Lemkul]

On 5/23/12 7:55 PM, aiqunhu...@knights.ucf.edu wrote:



Hi everybody,

I am installing Gromacs, in the shell it is said that Gromacs has been 
installed :

GROMACS is installed under /home/Program/gromacs-4.5.

but I couldn't find the directory bin under /gromacs-4.5, I don't know I have
installed su! c cessfully or not, any one could help?

Here is the commands which I used to install Gromacs, my system is Ubuntu 11.10,
gcc complier.

There are some errors in config.log saying: gcc: fatal error no imput files. !



With respect to what?


I don't know if this matters or not, i tried to fix the fatal errors in log
file, but I didn't get anywhere.



What were the errors and what did you do to fix them?  Anything catastrophic 
should have been printed in a more obvious form to the terminal.



In the last part of showing up in the shell it says something like this:

/usr/bin/install -c -m 644 'xpm2ps.1'
'/home/Program/gromacs-4.5/share/man/man1/xpm2ps_mpi.1'

but I couldn't find man/man1 under /gromacs-4.5/share/, anyone could help?
installation commands:
1) tar -zxvf fftw-3.3.1.tar.gz
tar –zxvf gromacs-4.5.tar.gz
tar -zxvf lam-7.1.4.tar.gz
(2) cd lam-7.1.3 ./configure --prefix=/home/Program/la! m -7.1.4 
--with-rsh="ssh-x"
make
sudo make install
(3)export PATH=$PATH:/home/Program/lam-7.1.4/bin

(4) cd fftw-3.3.1
./configure --enable-float --enable-mpi --prefix=/home/Program/fftw-3.3.1


You don't need an MPI-enabled version of FFTW.


make
make install
(3)export CPPFLAGS=-I/home/Program/fftw-3.3.1/include
export LDFLAGS=-L/home/Program/fftw-3.3.1/lib

(4) cd gromacs-4.5 ./configure --prefix=/home/Program/gromacs-4.5 --enable-mpi
--program-suffix=_mpi
make


You should not compile the complete Gromacs distribution with MPI.  There is no 
need for it; only mdrun is MPI-aware, and in version 4.5 and onward, can make 
use of threads instead, if your architecture supports it.



sudo make install


You likely don't need superuser privileges to write in the /home directory or 
subdirectories thereof.  Note as well that you're attempting to write to 
/home/Program/gromacs-4.5, but the output below indicates you're looking in 
/home/qunzi/Program/gromacs-4.5; I suspect this is your problem.  You're either 
installing or looking in the wrong place.  I would also recommend you not 
install Gromacs within the source tree - choose a new location for the 
installation and consider installing version 4.5.5 rather than an old version (4.5).


-Justin


*Here below are the last &n! bs p;part of output in the shell after I run "sudo
make install"*
/usr/bin/install -c -m 644 'trjorder.1'
'/home/Program/gromacs-4.5/share/man/man1/trjorder_mpi.1'
/usr/bin/install -c -m 644 'xpm2ps.1'
'/home/Program/gromacs-4.5/share/man/man1/xpm2ps_mpi.1'
make[3]: Leaving directory `/home/qunzi/Program/gromacs-4.5/man/man1'
make[2]: Leaving directory `/home/qunzi/Program/gromacs-4.5/man/man1'
Making install in man7
make[2]: Entering directory `/home/qunzi/Program/gromacs-4.5/man/man7'
make[3]: Entering directory `/home/qunzi/Program/gromacs-4.5/man/man7'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/home/Program/gromacs-4.5/share/man/man7" || /bin/mkdir -p
"/home/Program/gromacs-4.5/share/man/man7"
/usr/bin/install -c -m 644 'gromacs.7'
'/home/Program/gromacs-4.5/share/man/man7/gromacs_mpi.7'
make[3]: Leaving directory `/home/qunzi/Program/gromacs-4.5/man/man7'
make[2]: Leaving directory `/home/qunzi/Program/gromacs-4.5/man/man7'
make[2]: Entering directory `/home/qunzi/Program/gromacs-4.5/man'
make[3]: Entering directory `/home/qunzi/Program/gromacs-4.5/man'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory ! `/h ome/qunzi/Program/gromacs-4.5/man'
make[2]: Leaving directory `/home/qunzi/Program/gromacs-4.5/man'
make[1]: Leaving directory `/home/qunzi/Program/gromacs-4.5/man'
make[1]: Entering directory `/home/qunzi/Program/gromacs-4.5'
make[2]: Entering directory `/home/qunzi/Program/gromacs-4.5'
make install-exec-hook
make[3]: Entering directory `/home/qunzi/Program/gromacs-4.5'

GROMACS is installed under /home/Program/gromacs-4.5.
Make sure to update your PATH and MANPATH to find the
programs and unix manual pages, and possibly LD_LIBRARY_PATH
or /etc/ld.so.conf if you are using dynamic libraries.

Please run "make tests" now to verify your installation.

If you want links to the executables in /usr/local/bin,
you can issue "make links" now.
make[3]: Leaving directory `/home/qunzi/Program/gromacs-4.5'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/qunzi/Program/gromacs-4.5'
make[1]: Leaving directory `/home/qunzi/Program/gromacs-4.5'
qunzi@qunzi-AO722:~/Program/gromacs-4.5$ ls
acinclude.m4 AUTHORS config configure COPYING-GPU include Makefile man share
aclocal.m4 cmake config.log configure.ac Doxyfile ! ; INSTALL-GPU Makefile.am
README src
admin CMakeLists.txt config.status COPYING Doxyfile.in libtool Mak

Re: [gmx-users] Gromacs installed , but no directory /bin under it

[Justin A. Lemkul]

On 5/23/12 9:37 PM, aiqunhu...@knights.ucf.edu wrote:

Hi Justin, thanks a lot for replying.
Regarding your question, in the beginning there were errors like this in 
config.log:

" cc: error: unrecognized option '-V'
cc: fatal error: no input files
compilation terminated.
configure:4343: $? = 4
configure:4332: cc -qversion >&5
cc: error: unrecognized option '-qversion'
cc: fatal error: no input files
...
configure:6186: checking how to run the C preprocessor
configure:6217: mpicc -E -I/home/Program/fftw-3.3.1/include conftest.c
configure:6217: $? = 0
configure:6231: mpicc -E -I/home/Program/fftw-3.3.1/include conftest.c
conftest.c:21:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
mpicc: No such file o! r directory
configure:6231: $? = 1
configure: failed program was:
...

Thread model: posix
gcc version 4.6.1 (Ubuntu/Linaro 4.6.1-9ubuntu3)
configure:9684: $? = 0
configure:9673: mpicc -V >&5
gcc: error: unrecognized option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:9684: $? = 4
configure:9673: mpicc -qversion >&5
gcc: error: unrecognized option '-qversion'
gcc: fatal error: no input files
compilation terminated
.

fatal error: libxml/parser.h: No such file or directory "

I searched a little and found this page
http://verahill.blogspot.com/2012/01/debian-testing-64-whee!
zy-compiling_20.html

 to
run this command
/sudo apt-get install libxml2-dev /
/and fixed the last fatal error: /libxml/parser.h: No such file or directory
but I did't do anything about the other errors



libxml is an optional package.


In the first beginning I tried to install 4.5.5, but I didn't succeed. I got
something like this"*** No rule to make target `../gmxlib/libgmx_mpi.la', needed
by `libmd_mpi.la'"
I tried both enable shared and disable shared for cofiguring Gromacs4.5.5. It
didn't succeed.



This comes from the above error regarding mpicc not being found.  I see you 
installed lam previously.  Don't use it.  There are newer and better packages, 
and likely you can easily install an Ubuntu package for a modern version of 
OpenMPI that will be automatically configured for your environment.



Ok, since there are more threads, I won't use mpi. can I ask you that what do
you mean by " not
 > install Gromacs within the source tree "? Can I create a new folder like
/home/program and install FFTW and Gromacs and everything needed in the
/home/program?



You can install programs wherever you like.  What I was saying was to choose an 
installation such that binaries are not installed as a subdirectory of the 
source code.  If you're not planning on doing any development, the source just 
gunks up disk space, since all you're after is the executables.


For instance, you may find it useful to install all your programs in some 
subdirectory within $HOME.  Just be careful to specify the locations correctly. 
 After sending my last message, I noticed a number of inconsistencies in your 
commands that likely refer to nonexistent directories.


-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] Restarting a run

[Shyno Mathew]

Dear Gromacs users,

I have question about restarts
First I did 50 ns (time step 2fs, total steps 25*10^6) run for my system.
Then to extend the run to another 50 ns, I used the following method, :
tpbconv_dp -s equil_01.tpr -nsteps 5000 -o equil_02.tpr

Since I am doing a mutation study, I have multiple runs to analyze. What I
have noticed is, that some of the runs didn't complete, so to achieve
completion should I use the same step as above, but with new .tpr file
name, for eg:
tpbconv_dp -s equil_02.tpr -nsteps 5000 -o equil_03.tpr

Thanks in advance,
Shyno


-- 
Shyno Mathew
PhD student
Department of Chemical Engineering
Columbia University
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Re: [gmx-users] Gromacs installed , but no directory /bin under it

[Justin A. Lemkul]

On 5/23/12 10:06 PM, aiqunhu...@knights.ucf.edu wrote:

Hi Justin,

I am gonna reinstall Gromacs 4.5.5, and this time I am not gonna use LAM or MPI.
But can you explicitly tell me what inconsistencies are in my commands?


Please ignore that earlier remark.  I misread your directory structure when I 
mentioned that.


-Justin


because after I run 'make distclean' in all directories
(/home/Program/lam-7.1.4, /home/Program/fftw-3.3.1, /home/Program/gromacs-4.5)I
probably use these commands again except disabling MPI.

commands:
1) tar -zxvf fftw-3.3.1.tar.gz
tar –zxvf gromacs-4.5.tar.gz
tar -zxvf lam-7.1.4.tar.gz

(2) cd lam-7.1.3 ./configure --prefix=/home/Program/lam-7.1.4 --with-rsh="ssh-x"
make
sudo make install
(3)
export PATH=$PATH:/home/Program/lam-7.1.4/bin

(4)
cd fftw-3.3.1
&n! bsp; ./configure --enable-float --enable-mpi 
--prefix=/home/Program/fftw-3.3.1
make
make install
! (3)
export CPPFLAGS=-I/home/Program/fftw-3.3.1/include
export LDFLAGS=-L/home/Program/fftw-3.3.1/lib

(4) cd gromacs-4.5 ./configure --prefix=/home/Program/gromacs-4.5 --enable-mpi
--program-suffix=_mpi
make
sudo make install



 > Date: Wed, 23 May 2012 21:44:28 +0200
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] Gromacs installed , but no directory /bin under it
 >
 >
 >
 > On 5/23/12 9:37 PM, aiqunhu...@knights.ucf.edu wrote:
 > > Hi Justin, thanks a lot for replying.
 > > Regarding your question, in the beginning there were errors like this in
config.log:
 > >
 > > " cc: error: unrecognized option '-V'
 > > cc: fatal error: no in! put files
 > > compilation terminated.
 > > configure:4343: $? = 4
 > > configure:4332: cc -qversion >&5
 > > cc: error: unrecognized option '-qversion'
 > > cc: fatal error: no input files
 > > ...
 > > configure:6186: checking how to run the C preprocessor
 > > configure:6217: mpicc -E -I/home/Program/fftw-3.3.1/include conftest.c
 > > configure:6217: $? = 0
 > > configure:6231: mpicc -E -I/home/Program/fftw-3.3.1/include conftest.c
 > > conftest.c:21:28: fatal error: ac_nonexistent.h: No such file or directory
 > > compilation terminated.
 > > mpicc: No such file o! r directory
 > > configure:6231: $? = 1
 > > configure: failed program was:
 > > ...
 > >
 > > Thread model: posix
 > > gcc version 4.6.1 (Ubuntu/Linaro 4.6.1-9ubuntu3)
 > > configure:9684: $? = 0
 > > configure:9673: mpicc -V >! ;&5
 > > gcc: error: unrecognized option '-V'
 > > gcc: fatal error: no input files
 > > compilation terminated.
 > > configure:9684: $? = 4
 > > configure:9673: mpicc -qversion >&5
 > > gcc: error: unrecognized option '-qversion'
 > > gcc: fatal error: no input files
 > > compilation terminated
 > > .
 > >
 > > fatal error: libxml/parser.h: No such file or directory "
 > >
 > > I searched a little and found this page
 > > http://verahill.blogspot.com/2012/01/debian-testing-64-whee!
 > > zy-compiling_20.html
 > >

 to
 > > run this command
 > > /sudo apt-get install libxml2-dev /
 > > /and fixed the last fatal error: /libxml/parser.h: No such file or 
directory
 > > but I did't do anything about the other errors
 >! >
 >
 > libxml is an optional package.
 >
 > > In the first beginning I tried to install 4.5.5, but I didn't succeed. I 
got
 > > something like this"*** No rule to make target `../gmxlib/libgmx_mpi.la',
needed
 > > by `libmd_mpi.la'"
 > > I tried both enable shared and disable shared for cofiguring Gromacs4.5.5. 
It
 > > didn't succeed.
 > >
 >
 > This comes from the above error regarding mpicc not being found. I see you
 > installed lam previously. Don't use it. There are newer and better packages,
 > and likely you can easily install an Ubuntu package for a modern version of
 > OpenMPI that will be automatically configured for your environment.
 >
 > > Ok, since there are more threads, I won't use mpi. can I ask you that what 
do
 > > you mean by " not
 > > > install Gromacs within the source tree "? Can I create a new folder like
 > >! ; /home/program and install FFTW and Gromacs and everything needed in the
 > > /home/program?
 > >
 >
 > You can install programs wherever you like. What I was saying was to choose 
an
 > installation such that binaries are not installed as a subdirectory of the
 > source code. If you're not planning on doing any development, the source just
 > gunks up disk space, since all you're after is the executables.
 >
 > For instance, you may find it useful to install all your programs in some
 > subdirectory within $HOME. Just be careful to specify the locations 
correctly.
 > After sending my last message, I noticed a number of inconsistencies in your
 > commands that likely refer to nonexistent directories.
 >
 > -Justin
 >
 > --
 > 
 >
 > Justin A. Lemkul, Ph.D.
 > Research Scientist
 > Department of Biochemistry> Virginia Tech
 > Blacksburg, VA
 > jalemkul[at]vt.edu | (540) 231-9080
 > http:/

Re: [gmx-users] Restarting a run

[Justin A. Lemkul]

On 5/23/12 10:26 PM, Shyno Mathew wrote:

Dear Gromacs users,

I have question about restarts
First I did 50 ns (time step 2fs, total steps 25*10^6) run for my system. Then
to extend the run to another 50 ns, I used the following method, :
tpbconv_dp -s equil_01.tpr -nsteps 5000 -o equil_02.tpr

Since I am doing a mutation study, I have multiple runs to analyze. What I have
noticed is, that some of the runs didn't complete, so to achieve completion
should I use the same step as above, but with new .tpr file name, for eg:
tpbconv_dp -s equil_02.tpr -nsteps 5000 -o equil_03.tpr



If a run stops prematurely, you do not need to re-invoke tpbconv, simply pick up 
from the previous checkpoint with mdrun -cpi -append.


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

-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] Regarding error.

[Seera Suryanarayana]

Dear all gromacs users,
   while running the command "grompp -c
1UZ9_em.gro -p 1UZ9.top -o 1UZ9_b4pr.tpr -f pr.mdp" i am getting the
following error.

  File input/output error:
  pr.mdp

  Please tell me how to over come this error


Suryanarayana Seera,
PhD student,
Hyderabad,
India.
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[gmx-users] Regarding gromacs manual.

[Seera Suryanarayana]

Dear all gromacs users,

  I am new for MD and in particular using
gromacs software.I would like to learn basics of gromacs.Please tell me the
name of the  manual which one is suitable for me.

Suryanarayana Seera,
PhD student,
Hyderabad,
India.
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Re: [gmx-users] Justin umbrella sampling tutorial......

[rama david]

Thank you justin..
I solve script problem..

 I have another query ..
 As mention in tutorial , In step six , we have to do brief NPT
equilibration
 npt_umbrella.mdp link is
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/npt_umbrella.mdp
 After these we have to run MD ...mdp file link is

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_umbrella.mdp


1.  In both case define is same..
 In general When we are doing NPT we are position restrain whole
protein backbone ,
 But in these case we are only restrain chain B...Please explain in
detail ...

2.  The difference in mdp file is at gen_vel, and  run time 100 ps for  npt
, 10 ns for  md
  If both mdp file is same Then why to do separate npt and md

 ( Is the only reason is to generate velocity in npt simulation ???
Why we are not using velocity from
 pull *(step five)*   )

3 . If we are using the gen_vel = yes
  continuation= yes

  If continuation is yes, then why gen_vel is yes 

Please shade some light on meaning of continuation and gen_vel


Thank you in advance


With Best Wishes,
Rama David
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Re: [gmx-users] Regarding gromacs manual.

[Chandan Choudhury]

On Thu, May 24, 2012 at 10:39 AM, Seera Suryanarayana
wrote:

> Dear all gromacs users,
>
>   I am new for MD and in particular using
> gromacs software.I would like to learn basics of gromacs.Please tell me the
> name of the  manual which one is suitable for me.


http://www.gromacs.org/@api/deki/files/152/=manual-4.5.4.pdf

Chandan

>
>
> Suryanarayana Seera,
> PhD student,
> Hyderabad,
> India.
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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Re: [gmx-users] Regarding error.

[rama david]

On Thu, May 24, 2012 at 10:20 AM, Seera Suryanarayana
wrote:

> Dear all gromacs users,
>while running the command "grompp -c
> 1UZ9_em.gro -p 1UZ9.top -o 1UZ9_b4pr.tpr -f pr.mdp" i am getting the
> following error.
>
>   File input/output error:
>   pr.mdp
>
>   Please tell me how to over come this
> error
>

Hi Seera ,
 the error is self explainable,

 you dont  have pr.mdp in your working directory.
 Make pr.mdp as mention in tutorial

With Best Wishes,
Rama David

>
>
>
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Re: [gmx-users] Justin umbrella sampling tutorial......

[Justin A. Lemkul]

On 5/24/12 7:11 AM, rama david wrote:

Thank you justin..
I solve script problem..

  I have another query ..
  As mention in tutorial , In step six , we have to do brief NPT equilibration
  npt_umbrella.mdp link is
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/npt_umbrella.mdp
  After these we have to run MD ...mdp file link is
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_umbrella.mdp


1.  In both case define is same..
  In general When we are doing NPT we are position restrain whole protein
backbone ,
  But in these case we are only restrain chain B...Please explain in detail 
...



Please read the paper we published using this system.  It explains the 
conceptual details.



2.  The difference in mdp file is at gen_vel, and  run time 100 ps for  npt , 10
ns for  md
   If both mdp file is same Then why to do separate npt and md

  ( Is the only reason is to generate velocity in npt simulation ???  Why we
are not using velocity from
  pull /(step five)/   )

3 . If we are using the gen_vel = yes
   continuation= yes

   If continuation is yes, then why gen_vel is yes 

Please shade some light on meaning of continuation and gen_vel


At this point, you're basically starting a new simulation in the absence of a 
net pull force.  You're using the umbrella potential as a restraint, not to bias 
the motion, so you're re-equilibrating.  The use of "continuation = yes" simply 
implies that the starting configuration has already been constrained and thus 
the constraints should not be reset.  In this context, the difference between 
"yes" and "no" is likely not particularly relevant.


-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] g_rms -bm

[Kowsar Bagherzadeh]

Dear Users, 
I am trying to analyze a ligand-protein simulation results. I read in the 
manual that using g_rms command with –bm option produces a matrix of average 
bond angle deviations. And only bonds between atoms in the comparison groups 
are considered.  Does it mean that it is for the bonds and their angles that 
are already in existence? (Not the ones that may be formed throughout 
simulation, I mean the ligand may for example interact with residues through 
H-bonds) .I have made a group in my index file named Active site (including 
only the active site residues), and I have a LIG group as well. If I choose 
these two groups for g_rms with this command:
g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx
Does it show me how the ligand affects the active site residues bond angles?
And one more question, how can I study the ligand orientation in the active 
site?
Sogol-- 
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Re: [gmx-users] g_rms -bm

[Justin A. Lemkul]

On 5/24/12 7:24 AM, Kowsar Bagherzadeh wrote:



Dear Users,
I am trying to analyze a ligand-protein simulation results. I read in the manual
that using g_rms command with –bm option produces a matrix of average bond angle
deviations. And only bonds between atoms in the comparison groups are
considered. Does it mean that it is for the bonds and their angles that are
already in existence? (Not the ones that may be formed throughout simulation, I
mean the ligand may for example interact with residues through H-bonds) .I have


In this context, a "bond" means an actual chemical bond.  A hydrogen bond is a 
nonbonded interaction.



made a group in my index file named Active site (including only the active site
residues), and I have a LIG group as well. If I choose these two groups for
g_rms with this command:
/g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx**/
Does it show me how the ligand affects the active site residues bond angles?


Potentially.


And one more question, how can I study the ligand orientation in the active 
site?


That depends on how you define orientation - internal metrics like dihedrals or 
angles between planes of groups in the ligand, relative measurements like its 
position with respect to protein residues, etc.  All analysis tools are listed 
in the manual, Chapter 8 and Appendix D.  It's quite a lot to read, but you'll 
be able to identify all the various things you can analyze and how the 
information might be connected across different analysis routines.


-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] Justin umbrella sampling tutorial......

[rama david]

Hi Justin,

Thank you for your Reply

Before start tutorial I read your paper, It help me
a lot to understand the concept of umbrella sampling...

But truly I not understand the part in six step
 why to use define -DPOSRES_B  and not -DPOSRES,
I think I miss it ...


I will be a very greatfull to you, if you shade
some light on these 

Sorry for trouble

Thank you in advance

With best wishes,
Rama David



Thank you in advance

With Best Wishes,

Rama David
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Re: [gmx-users] Justin umbrella sampling tutorial......

[Justin A. Lemkul]

On 5/24/12 7:40 AM, rama david wrote:


Hi Justin,

Thank you for your Reply

Before start tutorial I read your paper, It help me
a lot to understand the concept of umbrella sampling...

But truly I not understand the part in six step
  why to use define -DPOSRES_B  and not -DPOSRES,
I think I miss it ...


I will be a very greatfull to you, if you shade
some light on these 



Using -DPOSRES_B restrains only one chain of the protein, thus mimicking the 
stability of a larger macromolecular assembly.  Using -DPOSRES restrains all 
protein chains, which accomplishes nothing when trying to do umbrella sampling. 
 The chain to which the umbrella potential is applied would not be able to move 
at all, thus rendering the pull force measurements ineffectual.


-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] ptn ptn interaction

[rethina malliga]

Hi,

I tried protein protein simulation in gromacs.

I prepared one ptn and kept seperately with its .top, .itp, .gro files.

Then I prepared another protein and I build the complex of pasting the .gro
file of first processed protein in the .gro file of second processed ptn.

In the topol.top  of second protein I included the molecule type at the
bottom and inserted

  ;Include ligand topology
  #include "posre.itp"

And i run succeccfully the newbox generation, solvent adding commands.

But with the ions adding command it shows fatal error that the atoms in
topol.top and solv.gro is different.

`Fatal error:
number of coordinates in coordinate file (solv.gro, 231262)
 does not match topology (topol.top, 237548)

on analysing the difference between two files i come to know that it is
taking the atoms of first protein for the second protein though i named
first and second proteins different.

I changed the residue information in .gro of first file to 1LIG and change
everything regarding second molecules name as 1LIG

and after retrying the ions adding command it says no such molecule type
found.

`Fatal error:
No such moleculetype 1LIG
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


kindly help me to trace where I m doing the mistake and to run ptn ptn
simulation.



-- 
Regards,
Rethina.

Rethina Malliga Gunasekaran,
Department Of BioInformatics,
Science Block,
Alagappa University,
Karaikudi – 630 003, India.
http://alagappauniversity.academia.edu/RethinamalligaGunasekaran/

**
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[gmx-users] Tabulated potential 1-4 interactions

[mohan maruthi sena]

Hi all,
   I am using tabulated potential option  for non bonded
interactions. The system that i am using contains on CA(alpha) CB(beta)
,atoms connected, If i use option
 energygrps = CA CB
 energytable = CA CA CB CB  it caluclates potential
between CA CA and CB CB , CA CB. I also want to use tabulated potential for
1,4 atoms  but this option does not take care of that, so how can i mention
that option in mdp file so that it uses tabulated potential for 1,4
interaction also.

Thanks in advance,


Regards,
Mohan
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Re: [gmx-users] ptn ptn interaction

[Justin A. Lemkul]

On 5/24/12 7:43 AM, rethina malliga wrote:

Hi,

I tried protein protein simulation in gromacs.

I prepared one ptn and kept seperately with its .top, .itp, .gro files.

Then I prepared another protein and I build the complex of pasting the .gro file
of first processed protein in the .gro file of second processed ptn.

In the topol.top  of second protein I included the molecule type at the bottom
and inserted
   ;Include ligand topology
   #include "posre.itp"



Be careful about name clashes here - the first protein (by default) will have a 
file named "posre.itp" that will be applied to it.  If you use the same name for 
different files, you'll probably get other errors.  I find it useful to call 
everything based on specific names, like "posre_proteinA.itp" or something similar.



And i run succeccfully the newbox generation, solvent adding commands.

But with the ions adding command it shows fatal error that the atoms in
topol.top and solv.gro is different.

`Fatal error:
number of coordinates in coordinate file (solv.gro, 231262)
  does not match topology (topol.top, 237548)

on analysing the difference between two files i come to know that it is taking
the atoms of first protein for the second protein though i named first and
second proteins different.



After you added the second protein, did you correctly update the [molecules] 
section of the topology?



I changed the residue information in .gro of first file to 1LIG and change
everything regarding second molecules name as 1LIG



Unless your protein residues are all called LIG, then this is not appropriate.


and after retrying the ions adding command it says no such molecule type found.

`Fatal error:
No such moleculetype 1LIG
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



This comes from incorrect naming.  Updating [molecules] correctly with the name 
of your second protein [moleculetype] will solve it.  Make sure you make changes 
to both the coordinate file and topology at all steps - they should always match.


-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] Justin umbrella sampling tutorial......

[rama david]

Thank you for your reply,

I am asking you again same question, EXTREMELY SORRY for my stupidity,

In step six , I unable to differentiate npt and production run by
mdp file as usualy we find difference by define term,

I think I get meaning upto reason why to use -DPOSRES_B,
but I want to know if we are using same mdp file in both condition
means the npt equilibriation is as same as md production ,

Then why to do npt, just run production md  with  DPOSRES_B


With my  best Wishes ,
Rama David
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[gmx-users] Re: Regarding error.

[vivek sharma]

Dear Suryanarayana,

This error itself tells you that the particular residue 'DAL' is not
available in the residue topology database of the force field you are using
for your simulation. You can check that by yourself in the *.rtp file of
corresponding force field.
The way out of this situation is to build a topology file(*.top/*.itp) for
particular residue/molecule 'DAL' by yourself (you can use topology
generators like topolbuild, PRODRG server etc for the same) and include it
with your molecule topology file.

You can find more details about the error at
"
http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database
".

Also, put your queries in gromacs mailing list which will help other users
and increase the chances of getting better solutions.

Good luck with the simulation,
~Vivek

On 24 May 2012 11:55, Seera Suryanarayana  wrote:

> Dear Vivek,
>  While running gromacs software i am getting following
> error.
>
> Fatal error:
> Residue 'DAL' not found in residue topology database.
>
> I am new for MD and in particular using of gromacs. Kindly tell me how to
> over come error which is i mentioned above.
>
>
> Suryanarayana Seera,
> PhD student,
> Hyderabad,
> India.
>
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