Re: [gmx-users] about g_sas analysis

[Tsjerk Wassenaar]

Hi,

Recently there was a relatively extensive discussion on the list
regarding g_sas. Check the archives.

Cheers,

Tsjerk

On Thu, Mar 18, 2010 at 9:07 AM, Milan Melichercik
 wrote:
> supti mukherjee wrote:
>>
>> Dear gromacs users,
>> I have some doubts regarding the options to be selected in g_sas program.
>> g_sas asks for two groups, first one for calculation and second one for
>> output. As I have understood from the manual that first group should contain
>> all non solvent groups and second one the whole or part of these groups. Now
>> my doubt is that in a system of protein+ligand, when I am selecting both the
>> protein and ligand in option 1 ( in the calculation group) it automatically
>> is sending the second selected group to second option ( that is in the
>> output group). Is the solvent accessible area  given in terms of the output
>> group in the xvg file?
>>  I want to calculate solvent accessibility of the ligand which is
>> surrounded by the protein. Selecting what option can mimic that situation
>> most closely?
>> Regards
>> Supti
>> NIMHANS, BANGALORE
>>
>>
>>
> You need to create new group which contains atoms from both protein and
> ligand (make_ndx or by hand) and input number of this new group - the most
> of the programs reads only one group per input (the rest write something
> about selecting two groups...). Therefore the second number is read for the
> second input (as the group for output).
> About the rest of you question - I don't feel fully qualified to answer it
> and I hope, somebody will.
> Best.
>
> Milan
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Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
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Re: [gmx-users] MD localized in the active site

[Tsjerk Wassenaar]

Hi,

You also have to spend a sufficient amount of thought on the question
whether an approach like that will give you what you're after. It's
not going to sample a relevant ensemble and you're disabling the long
range correlations that may be of influence on ligand binding.

Cheers,

Tsjerk

On Wed, Mar 17, 2010 at 9:01 PM, Justin A. Lemkul  wrote:
>
>
> Anna Marabotti wrote:
>>
>> Dear gmx-users,
>> I'd like to perform a molecular dynamics simulation on a protein-ligand
>> complex, in such a way that only residues belonging to the active site can
>> move, whereas the rest of the protein is kept fixed. I searched for some
>> information about how to do it with GROMACS, but I didn't find anything.
>> Could anybody give me some suggestions about this subject, please?
>
> You could create a custom posre.itp (using genrestr) to restrain whatever
> atoms you choose, but it won't speed up your calculations in any way, if
> that's what you're after.  You could also specify freezegrps in the .mdp
> file, which requires a custom index group; it may be more difficult to use
> this setup based on the types of exclusions that would be necessary within
> whatever is frozen.
>
> -Justin
>
>> Many thanks in advance and regards.
>> Anna
>> __
>> Anna Marabotti, Ph.D.
>> Laboratory of Bioinformatics and Computational Biology
>> Institute of Food Science - CNR
>> Via Roma, 64
>> 83100 Avellino
>> Phone: +39 0825 299651
>> Fax: +39 0825 781585
>> E-mail: amarabo...@isa.cnr.it 
>> Skype account: annam1972
>> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
>>  "If you think you're too small to make a change, try sleeping with a
>> mosquito"
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Medicinal Chemist
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Re: [gmx-users] cross-correlations as a function of interatomic distance

[Tsjerk Wassenaar]

Hi,

Well, since interatomic distances are properties of single
conformations and fluctuation covariances/correlations are properties
of sets of conformations, it is simply impossible. You might plot the
covariances/correlations against the mean distances, if you feel you
must. Be sure to use the atomic fluctuations and not the
per-coordinate fluctuations.

Cheers,

Tsjerk

On Tue, Mar 16, 2010 at 7:34 AM, Mark Abraham  wrote:
> On 16/03/2010 5:16 PM, shahab shariati wrote:
>>
>> Hi gromacs users
>>
>> After using g_covar for obtaining dynamic cross correlation map, how is
>> obtained cross-correlations as a function of interatomic distance?
>>
>> Thank you so much for any help!
>
> I'm not even sure whether "cross-correlations as a function of interatomic
> distance" makes sense. Perhaps you need to explain further what you mean.
> Writing out the maths of it may make it clear to you what it is you need to
> do with the output from g_covar.
>
> Mark
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Re: [gmx-users] rmsf question

[Tsjerk Wassenaar]

Hi Andrei,

> If I correctly uderstand the RMSF computed on C-alpha in PDB NMR
> structure, is a measure of the uncertanty in resolving the structure.

No, that's not what I said. You're saying that there's one structure
(the structure), but there is uncertainty in resolving it. That's not
the case. There is a distribution of structures that gives rise to a
set of signals, from which time and ensemble averaged distances
between certain pairs of atoms can be deduced. But this set of
distances is typically leaves a number of degrees of freedom, and on
top of that the time averaging may actually yield restraints that
cannot be satisfied simultaneously. So, structures have to be fit to
the set of distances, which is typically repeated a large number of
times using simulated annealing with different starting conditions.
>From the resulting set the ones best fitting the data are selected and
put forward as a representative set of structures. The least defined
regions, in terms of (distance) restraints are likely to show most
variation. But the structures are not weighted according to their
probabilities and therefore neither the average nor the fluctuations
can be expected to coincide with the moments of the Boltzmann
distribution.

> Compared to this the RMSF of C-alpha computed from a MD trajectory
> reflects the geometric fluctuations of the backbone in the Boltzmann
> distribution of states in the generated ensemble.

Assuming you have sampled long enough and not just trying to explain
drift as fluctuation :)

> The uncertanty in the NMR structure can be influenced by the thermal
> fluctuations in the backbone geometry.

Well, that's part of it, but the way the models are derived contributes a lot.

> Only in this respect the comparison of the two makes sense.
> Is this correct?

Comparisons can be made, but you have to formulate and justify your assumptions.

Cheers,

Tsjerk


-- 
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Re: [gmx-users] rmsf question

[Tsjerk Wassenaar]

Hi Andrei,

You can do it this way. But do mind that the ensemble from NMR is not
meant to reflect the Boltzmann distribution. Rather it is meant to
provide a number of plausible solutions given the (positive)
restraints from the experiments and the force field used for the
refinement. This means that the moments of the distribution (mean and
fluctuation) need not be comparable quantitatively. A more direct
comparison between experiments and simulations could be obtained by
comparing backbone order parameters.

Cheers,

Tsjerk

On Mon, Mar 15, 2010 at 8:45 AM, Andrei Neamtu  wrote:
> Dear Mark,
>
> Thank you very much for your response.
>
> What I meant was to obtain a RMSF plot form PDB mediated on each
> residue and to compare with a RMSF plot mediated on each residue
> obtained from a MD trajectory.
> I do not compare a frame from PDB with a frame from MD trajectory.
> So, in the PDB file each 'frame' (MODEL) in the NMR file has the same
> order and number of atoms.
> This is also true for the MD trajectory.
>
> In the end i compare the two plots to see if the residues along the
> chain have comparable 'flexibility'
>
> Is necessary in this case to have a correspondence between the order
> of atoms in PDb and in MD trajectory?
> In this sense the comparison makes sense? (I mean if I do the residue 
> mediation)
>
> (The PDB is a NMR structure and so it has the hydorgen added and no
> missing side chains. And, it has the same number of atoms as the gro
> file generated with pdb2gmx. And also the same number of atoms in the
> corresponding residues.)
>
>
>
> Many thanks,
> Andrei
>
>
>
> On Sun, Mar 14, 2010 at 3:16 PM, Mark Abraham  wrote:
>> On 14/03/2010 7:47 PM, Andrei Neamtu wrote:
>>>
>>> Hi,
>>>
>>> is there a rapid way to compute RMSF on an NMR ensemble from a PDB file?
>>
>> Yes, but that's not your problem, it seems :-)
>>
>>> g_rmsf needs a .tpr file.
>>
>> Not true. Inspect the lines in g_rmsf -h describing the file types suitable
>> for -f and -s. This is a fairly general GROMACS phenomenon.
>>
>>> This is OK with the MD trajectories but if I
>>> want to compare MD ensemble one with the NMR RMSF ensemble
>>> fluctuations from the original PDB this is not possible.
>>
>> That can be a trickier proposition. You need at least the atom order to
>> correspond to make such a comparison.
>>
>> If the original atom names are suitable for defining the default groups,
>> then you might be in business. Otherwise, you'll need to construct suitable
>> input for -s (and maybe -n), and see if it matters whether different atom
>> names in -f matter.
>>
>> Mark
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Re: [gmx-users] Regarding defining termini in new rtp entry

[Tsjerk Wassenaar]

Hi Ilya,

If it is an amino acid, albeit modified, you can make pdb2gmx
recognize it as such by adding it to the file 'aminoacids.dat'. This
file is in the installation directory. You can also copy it to your
working directory and change it there, as it will then take precedence
over the other one. Do mind to increment the number at the top of the
file for every amino acid you add.

Hope it helps,

Tsjerk

On Fri, Mar 12, 2010 at 3:56 PM, Joe Joe  wrote:
> How do I tell pdb2gmx what the termini are in my molecule. I added a non
> standard amino acid to the ffoplsaa.rtp database but pdb2gmx says "No N- or
> C-terminus found: this chain appears to contain no protein".
> thanks,
> Ilya
>
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Re: [gmx-users] g_rms warning

[Tsjerk Wassenaar]

Hi Carla,

You'll have to use index groups to extract a trajectory and reference
that correspond. If you have those you can get on with the RMSD.

Cheers,

Tsjerk

On Mon, Mar 8, 2010 at 11:44 AM, Carla Jamous  wrote:
> Hi everyone, please I just need a precision:
>
> I need to calculate the RMSD of a trajectory by comparing it to a reference
> structure that doesn't have the same number of atoms.
> Gromacs is calculating the RMSD, but meanwhile it generates this
> warning:"topology has 4839 atoms, whereas trajectory has 4834"
>
> Does it really affect the result of my RMSD or can I ignore it?
>
> Thanks
> Carla
>
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Re: [gmx-users] g_mindist periodic boundary condition

[Tsjerk Wassenaar]

Hi Dian,

Now why didn't I guess that you were trying on data obtained from
Amber?! Maybe because you didn't explicitly mentioned it. It always
helps to give a full account of what you were trying.

Anyway, I don't know the format of the top of my head, so you'll have
to look in another pdb file and copy/edit the line (I think it's
angles and then lengths, all %8.3f, but I'm not sure), or you have to
check the pdb format at www.rcsb.org/pdb

Hope it helps,

Tsjerk

On Thu, Mar 4, 2010 at 6:04 PM, Dian Jiao  wrote:
> Hi Tsjerk,
>
> My gromacs is 4.0.4.
>
> As it turns out, I do not have a CRYST1 keyword in my pdb file, so I guess
> the box is not defined yet. The pdb was taken from the trajectory of AMBER
> simulation, so it starts with the keyword "REMARK". How do I include box
> dimensions in pdb file then? Just add "CRYST1 24 24 24" in the first line?
> By the way is it CRYST1 or CRYSTL?
>
> And the command I was running was "g_mindist -f 1001.pdb -n 1001.ndx -od
> 1001_C".
>
> Dian
>
> On Thu, Mar 4, 2010 at 12:38 AM, Tsjerk Wassenaar  wrote:
>>
>> Hi Dian,
>>
>> Which version of gromacs are you using? Can you assert that the pdb
>> file has the correct box? It should have a line starting with CRYST1
>> (grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2  I think)
>> didn't write the CRYST1 record, and thus disallow PBC related
>> operations.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiao  wrote:
>> > The box is 24X24X24 (Angstrom). The dummy atom I added at the end is
>> > about
>> > 31 A away from the closest water in the box. But if it is periodic,
>> > shouldn't there be waters near the dummy too?
>> >
>> > On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham 
>> > wrote:
>> >>
>> >> On 4/03/2010 11:30 AM, Dian Jiao wrote:
>> >>>
>> >>> Hi Gromacs users,
>> >>>
>> >>> I was trying to compute minimum distance between groups in a cubic
>> >>> water
>> >>> box with g_mindist using periodic boundary condition. In order to test
>> >>> this, I added one more "atom" which is far away from any of the other
>> >>> atoms in the pdb file. The mindist between that atom and all the
>> >>> waters
>> >>> were computed. The output of g_mindist is 3.089281e+00. (the unit is
>> >>> nm,
>> >>> right?)
>> >>
>> >> You haven't said how big your box is, or how far "far away" is, so we
>> >> can't tell whether you think 3nm is too big, too small, etc.
>> >>
>> >>> The manual shows that pbc is one of the option of g_mindist, but isn't
>> >>> the default "yes"? I even tried with "-pbc" in the command, still did
>> >>> not work. Can anyone tell me how to turn on PBC in g_mindist?
>> >>
>> >> See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off.
>> >>
>> >> Mark
>> >> --
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>> >
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>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> Computational Chemist
>> Medicinal Chemist
>> Neuropharmacologist
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Re: [gmx-users] g_mindist periodic boundary condition

[Tsjerk Wassenaar]

Hi Dian,

Which version of gromacs are you using? Can you assert that the pdb
file has the correct box? It should have a line starting with CRYST1
(grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2  I think)
didn't write the CRYST1 record, and thus disallow PBC related
operations.

Cheers,

Tsjerk

On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiao  wrote:
> The box is 24X24X24 (Angstrom). The dummy atom I added at the end is about
> 31 A away from the closest water in the box. But if it is periodic,
> shouldn't there be waters near the dummy too?
>
> On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham 
> wrote:
>>
>> On 4/03/2010 11:30 AM, Dian Jiao wrote:
>>>
>>> Hi Gromacs users,
>>>
>>> I was trying to compute minimum distance between groups in a cubic water
>>> box with g_mindist using periodic boundary condition. In order to test
>>> this, I added one more "atom" which is far away from any of the other
>>> atoms in the pdb file. The mindist between that atom and all the waters
>>> were computed. The output of g_mindist is 3.089281e+00. (the unit is nm,
>>> right?)
>>
>> You haven't said how big your box is, or how far "far away" is, so we
>> can't tell whether you think 3nm is too big, too small, etc.
>>
>>> The manual shows that pbc is one of the option of g_mindist, but isn't
>>> the default "yes"? I even tried with "-pbc" in the command, still did
>>> not work. Can anyone tell me how to turn on PBC in g_mindist?
>>
>> See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off.
>>
>> Mark
>> --
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>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] gromacs memory usage

[Tsjerk Wassenaar]

Hi Amit,

I think the presentation gives right what you want: a rough estimate.
Now as Berk pointed out, to allocate more than 2GB of memory, you need
to compile in 64bit. Then, if you want to have a real feel for the
memory usage, there's no other way than trying. But fortunately, the
memory requirements of a (very) long simulation are equal to that of a
very short one, so it doesn't need to cost much time.

Cheers,

Tsjerk

On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey  wrote:
> Hi Mark,
>
> Yes thats one way to go about it. But it would have been great if i could
> get a rough estimation.
>
> Thank you.
>
> amit
>
>
> On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham 
> wrote:
>>
>> On 3/03/2010 12:53 PM, Amit Choubey wrote:
>>>
>>>    Hi Mark,
>>>
>>>    I quoted the memory usage requirements from a presentation by Berk
>>>    Hess, Following is the link to it
>>>
>>>
>>>
>>> http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf
>>>
>>>    l. In that presentation on pg 27,28 Berk does talk about memory
>>>    usage but then I am not sure if he referred to any other specific
>>> thing.
>>>
>>>    My system only contains SPC water. I want Berendsen T coupling and
>>>    Coulomb interaction with Reaction Field.
>>>
>>>    I just want a rough estimate of how big of a system of water can be
>>>    simulated on our super computers.
>>
>> Try increasingly large systems until it runs out of memory. There's your
>> answer.
>>
>> Mark
>>
>>> On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham >> > wrote:
>>>
>>>    - Original Message -
>>>    From: Amit Choubey mailto:kgp.a...@gmail.com>>
>>>    Date: Saturday, February 27, 2010 10:17
>>>    Subject: Re: [gmx-users] gromacs memory usage
>>>    To: Discussion list for GROMACS users >>    >
>>>
>>>     > Hi Mark,
>>>     > We have few nodes with 64 GB memory and many other with 16 GB of
>>>    memory. I am attempting a simulation of around 100 M atoms.>
>>>
>>>    Well, try some smaller systems and work upwards to see if you have a
>>>    limit in practice. 50K atoms can be run in less than 32GB over 64
>>>    processors. You didn't say whether your simulation system can run on
>>>    1 processor... if it does, then you can be sure the problem really
>>>    is related to parallelism.
>>>
>>>     > I did find some document which says one need (50bytes)*NATOMS on
>>>    master node, also one needs
>>>     >  (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute
>>>    nodes. Is this true?>
>>>
>>>    In general, no. It will vary with the simulation algorithm you're
>>>    using. Quoting such without attributing the source or describing the
>>>    context is next to useless. You also dropped a parenthesis.
>>>
>>>    Mark
>>>    --
>>>    gmx-users mailing list gmx-users@gromacs.org
>>>    
>>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>
>>>
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Re: [gmx-users] Continuous trajectory from trjconv?

[Tsjerk Wassenaar]

Hi Pablo,

You want to mutually exclusive things. That is by definition impossible.

Sorry,

Tsjerk

On Mon, Mar 1, 2010 at 11:02 AM, Pablo Englebienne  wrote:
> Hi, I made an NpT MD simulation of 10 copies of the same small molecule in
> CHCl3 (dodecahedron unit cell) for 20 ns. I want to visualize the evolution
> of the system and the distance between the molecules. I tried to visualize
> the system, but I can't get a continuous trajectory (i.e., without jumps)
> without the solutes diffusing out of the simulation box. The same thing
> happens for the inter-molecule distance, it oscillates wildly between a
> reasonable value (say, 0.5 nm) and 1/2 the size of the periodic cell.
>
> When I use trjconv with the "-pbc nojump -ur compact" options, the molecules
> diffuse out of the box, in a continuous trajectory, until they are way
> further apart than the size of the cell. When visualizing it in VMD,
> however, it turns out that not all molecules are isolated, but instead some
> are interacting with the periodic image of another molecule. I used "pbc
> wrap" from the PBCTools module within VMD and that brings all the molecules
> into a single cell, but then the trajectory is not continuous, with
> compounds jumping around the edges of the unit cell. It is then not
> straightforward to see the interaction among different molecules, as in some
> cases they are in opposite edges of the cell.
>
> If I use the "-pbc mol -ur compact" option, all molecules stay within a
> single unit cell, but there are jumps across the border of the unit cell as
> in the above case.
>
> I tried also using the "-center", "-fit rot+trans" and "-fit progressive"
> options (with groups containing either all molecules or a single residue)
> but this ultimately gave the same results.
>
> Would there be something else I could try to visualize the simulation so
> that the central unit cell would contain all residues in a continuous way?
>
> Thanks in advance for reading, and more for replying!
>
> Take care,
> Pablo
>
> --
> Pablo Englebienne, PhD
> Institute of Complex Molecular Systems (ICMS)
> Eindhoven University of Technology, TU/e
> PO Box 513, HG -1.26
> 5600 MB Eindhoven, The Netherlands
> Tel +31 40 247 5349
>
> --
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Re: [gmx-users] g_sas

[Tsjerk Wassenaar]

Hi Pawan,

The legends are contained in the .xvg file. Try viewing the file.

Cheers,

Tsjerk

On Mon, Mar 1, 2010 at 8:29 AM, pawan raghav  wrote:
> I executed the following command.
>
> g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg
>
> xmgrace -nxy mdrun.xvg
>
> I get two sets of values: one is bigger (black) than the other (red).
> I have checked the manual and other sources, but I could not find an
> answer about the black and red line.  If it was written in fine print and I
> missed it, I am sorry
> about that. So I want to know is the red lower value, the standard error or
> standard deviation or
> something else? What does red and black line shows also link the reference.
> --
> Pawan
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Re: [gmx-users] Energy minimisation of solvated protein - Tutorial

[Tsjerk Wassenaar]

Hi Anna,

You should mention the version of Gromacs you're using. One of the
versions did not write the box correctly to pdb files, which I think
happened in your case. If you take as the solvation step

genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro

instead of writing output to 1qlz-water.pdb, I think you should be fine.

The reason for writing a .pdb file is the easier visualization with a
multitude of programs.

Thanks for your interest in the tutorial.

Cheers,

Tsjerk

On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan
 wrote:
> Hi,
>
> I've been trying to go through the 'Introduction to Molecular Dynamics
> Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the
> tutorials listed on the GROMACS website.
>
> I've got to the stage where I am performing energy minimisation on my
> solvated protein but when I use grompp to create the .tpr file for mdrun, I
> get the error message:
>
> One of the box lengths is smaller than twice the cut-off length. Increase
> the box size or decrease rlist
>
>
> I am using the protein with pdb ID 1QLZ, one of the suggested structures for
> the tutorial and have so far carried out the following commands:
>
> % pdb2gmx -f 1qlz.pdb -o 1qlz.gro -p 1qlz.top -ignh
> % grompp -f minim.mdp -c 1qlz.gro -p 1qlz.top -o 1qlz-EM-vacuum.tpr
> % mdrun -v -deffnm 1qlz-EM-vacuum.tpr -c 1qlz-EM-vacuum.pdb
> % editconf -f 1qlz-EM-vacuum.pdb -o 1qlz-PBC.gro -bt dodecahedron -d 1.0
> % genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.pdb
> % grompp -v -f minim.mdp -c 1qlz-water.pdb -p 1qlz.top -o 1qlz-water.tpr
> % genion -s 1qlz-water.tpr -o 1qlz-solvated.pdb -conc 0.15 -neutral -pname
> NA+ -nname CL-
> % grompp -v -f minim_pbc.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o
> 1qlz-EM-solvated.tpr
>
> after which I receive the error message.
>
> The minim_pbd.mdp file I use in the last grompp command is the same as
> minim.mdp used in previous grompp commands (the latter file I downloaded as
> part of the tutorial) except that the line 'pbc = no' has been replaced by
> 'pbc = xyz'.
>
> I have tried increasing the value of 'd' in the editconf command, to 2,3 and
> even 8 but this doesn't make any difference.  (I have read that it is not a
> good idea to tamper with the cut-off values so have avoided doing that)  The
> box vector lengths when d = 1.0 are all 7.10051, and rvdw, rcoulomb = 1.0 in
> mimim.mdp and minim_pbd.mdp, so I don't understand what is going wrong...
>
> Anna
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[gmx-users] Re: tautology (Normal Mode Analysis)

[Tsjerk Wassenaar]

Hi Ken,

To stay close to tautology, although not being strictly tautological,
I think the answer to

"I want to do normal mode analysis, could you tell me how"

should be

"If you don't know how to do normal mode analysis, then you shouldn't
be doing normal mode analysis."

(Bounced to the user list for archiving; fun if someone searches the
exact string "how to do normal mode analysis".)

Cheers,

Tsjerk


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Re: [gmx-users] Re: Protein carbohydrate interaction simulation

[Tsjerk Wassenaar]

Ooh, this is just too funny :)

>> Its me, Pawan.

Hi Pawan!

>> Dont post questions like these in the forum.
>> Say to people that u did any ground work for what u want to study in.
>> Like what all ppaers u got, what exactly u want to work in and what is ur
>> control study and all that.
>> If u will ask generally then u will hardly get any proper suggestions from
>> the gromacs biggies.

So, can you disclose your list of biggies? Everybody's interested to
see whether he made it or not, except for Justin who already knows.
Oh, and adding to your advice, it also helps to write clear and close
to correct english, like using  you and you're in stead of u and ur.

>> There is this guy in Gromacs list called as Justin Lemkul. Try mailing him
>> for details.

This is really like talking to somebody about somebody in abstract,
with the person standing next to you! You wouldn't think that Justin
or any of the other biggies (hey, is there a hint of jealousy? :p)
wasn't reading these mails, would you?

> Please do not advertise me as a help service.  I am usually willing to help
> out with public posts to the forum, but will not respond to private emails
> unless it is directly related to my work.

But then there is a serious note to it all. It is close to sin to
write gromacs related questions that are not specific to a person's
work to someone in person. First, none of the people on this list is a
helpdesk or personal teacher, and second, by keeping discussions from
the list, you keep them from being archived, disallowing others to
learn from your questions.

If you want really good advice on how to get people to answer your
mails, better read:

http://catb.org/~esr/faqs/smart-questions.html

Cheers,

Tsjerk

-- 
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Re: [gmx-users] Normal Mode analysis

[Tsjerk Wassenaar]

> Aside from that, search the literature; published papers should have
> reproducible methodology :)

And.., methodology in published papers has proven to be publishable.

:)

Tsjerk

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Re: [gmx-users] (no subject)

[Tsjerk Wassenaar]

Hi E R Azhagiya singam,

You first have to ask yourself whether you're up to it. This is considered
an advanded topic. In particular for groups like these. To start with, do
you know the protonation state of the Zn(Cys)4 group in your case?

Cheers,

Tsjerk

On Fri, Feb 19, 2010 at 9:14 AM, babu gokul  wrote:

> Dear all
> I would like to simulate the molecule which consist of a zn atom
> coordinated to four CYS residue.  I would like to know how to insert the
> parameters for zn coordination. As I am new to Gromacs I would like to have
> detailed description.I would like to use OPLS force field.
> Thanking you
> E R Azhagiya singam
>
> --
> The INTERNET now has a personality. YOURS! See your Yahoo! 
> Homepage
> .
>
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Re: [gmx-users] Help with Segmentation fault!!!

[Tsjerk Wassenaar]

Hi Deisy,

> define   = -DFLEXIBLE
> integrator   = md

Well, probably you'd be better off with 'integrator = steep'. If
you're doing MD, better not define -DFLEXIBLE. But for the rest, you
give little account of what you're doing. What about the workflow,
where in your scheme are we? What are you trying to do? How about some
tutorial material?

Cheers,

Tsjerk

--
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Re: [gmx-users] pbc whole

[Tsjerk Wassenaar]

Hi Carla,

> I checked with genconf & now I'm certain that my ATP molecule is still with
> the protein

That's good to know :)

>>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol
>>> (centering on "Protein")

So what did come out of this then? It should have given you a compact
representation of your system with the protein in the center. But if
the protein's in the center and everything is put as close to that
center as possible, which is what "compact" does, then the ATP should
be there too. Can you make an image of the last frame and send a link
to it? Alternatively, I have a patched version of trjconv that you can
use to do the trick. I can send it if you want.

Cheers,

Tsjerk


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Re: [gmx-users] pbc whole

[Tsjerk Wassenaar]

Hi Carla,

What g_rmsf does is calculate the first (average) and second
(fluctuation) central moments. For that, it is required that the
conformational space is defined, which is done by fitting each frame
to the reference structure. The reference is only used for that. The
fluctuation is calculated about the mean position. It doesn't make
sense to most people to calculate a non-central second moment, so be
assured that that's not what g_rmsf does (for the few people
interested, it can be  done with g_covar :p).

g_rmsf does what you want.

Cheers,

Tsjerk

On Wed, Feb 17, 2010 at 3:06 PM, Carla Jamous  wrote:
> Thank you Tsjerk,
> but one more question:
> if I do the following: g_rmsf -f a.xtc -s b.tpr -o rmsf.xvg -ox average.pdb
> -n c.ndx
>
> does gromacs claculate the rmsf after fitting to b.tpr or to average.pdb?
> & if I want it to calculatefluctuations between the position of
> particle i and the time-averaged position of the same particle i, do I have
> to do:
>
> g_rmsf -f a.xtc -s average.pdb -o rmsf.xvg?
>
> Thank you & sorry to bother. I'm just trying to understand what g_rmsf
> really does, to help me analyze my results.
>
> Carla
>
> On Wed, Feb 17, 2010 at 10:25 AM, Tsjerk Wassenaar 
> wrote:
>>
>> Hi Carla,
>>
>> Justin's recipe should've worked. As he suggested, maybe the ligand is
>> not with the protein. You can check by multiplying your system with
>> genconf:
>>
>> genconf -f in.pdb -o out.pdb -nbox 2 2 2
>>
>> If the ligand is with the protein, one copy will be located in one of
>> the copies of the protein.
>>
>> g_rmsf does write the average structure, if requested. Use the option -ox
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Wed, Feb 17, 2010 at 10:08 AM, Carla Jamous 
>> wrote:
>> > Hi Justin,
>> > I'm still trying to figure out what happened with my ligand.
>> > Meanwhile, I have another question: I can't figure out how to calculate
>> > an
>> > average structure in gromacs.
>> > And does g_rmsf calculate the average structure automatically?
>> >
>> > Thanks again
>> > Carla
>> >
>> > On Tue, Feb 16, 2010 at 5:44 PM, Justin A. Lemkul 
>> > wrote:
>> >>
>> >>
>> >> Carla Jamous wrote:
>> >>>
>> >>> Hi Justin,
>> >>> Thank you for your answer but I'm still not getting my ligand to stay
>> >>> in
>> >>> the box.
>> >>>
>> >>> I tried the following(after taking a look at the mailing list
>> >>> archive):
>> >>>
>> >>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol
>> >>> (centering on "Protein")
>> >>> trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans
>> >>>
>> >>> So please do you have another advise to give me?
>> >>>
>> >>
>> >> If that's not working, then I wonder if your ligand is still actually
>> >> bound to your protein :)  The above sequence always works for me, as
>> >> long as
>> >> there actually is a complex.  You can also try -pbc cluster, but I know
>> >> that
>> >> algorithm can hang.
>> >>
>> >> -Justin
>> >>
>> >>> Thanks
>> >>> Carla
>> >>>
>> >>> On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul > >>> <mailto:jalem...@vt.edu>> wrote:
>> >>>
>> >>>
>> >>>
>> >>>    Carla Jamous wrote:
>> >>>
>> >>>        Hi everyone,
>> >>>        I'm using this command to extract my protein and my ligand from
>> >>>        the trajectory.
>> >>>
>> >>>        trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc
>> >>>        whole -n prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj
>> >>>
>> >>>        Before, I had a problem with residues of my protein showing at
>> >>>        the other end of the box, when I display my .xtc with VMD.
>> >>>        the "-pbc whole" fixed it.
>> >>>
>> >>>        However, now I have another issue: my ligand is at the other
>> >>> end
>> >>>        of the box. So please can anyone tell me what can I do to fix
>> >>>        that and get a reasonable RMSD value?
>> >>>

Re: [gmx-users] pbc whole

[Tsjerk Wassenaar]

Hi Carla,

Justin's recipe should've worked. As he suggested, maybe the ligand is
not with the protein. You can check by multiplying your system with
genconf:

genconf -f in.pdb -o out.pdb -nbox 2 2 2

If the ligand is with the protein, one copy will be located in one of
the copies of the protein.

g_rmsf does write the average structure, if requested. Use the option -ox

Cheers,

Tsjerk

On Wed, Feb 17, 2010 at 10:08 AM, Carla Jamous  wrote:
> Hi Justin,
> I'm still trying to figure out what happened with my ligand.
> Meanwhile, I have another question: I can't figure out how to calculate an
> average structure in gromacs.
> And does g_rmsf calculate the average structure automatically?
>
> Thanks again
> Carla
>
> On Tue, Feb 16, 2010 at 5:44 PM, Justin A. Lemkul  wrote:
>>
>>
>> Carla Jamous wrote:
>>>
>>> Hi Justin,
>>> Thank you for your answer but I'm still not getting my ligand to stay in
>>> the box.
>>>
>>> I tried the following(after taking a look at the mailing list archive):
>>>
>>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol
>>> (centering on "Protein")
>>> trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans
>>>
>>> So please do you have another advise to give me?
>>>
>>
>> If that's not working, then I wonder if your ligand is still actually
>> bound to your protein :)  The above sequence always works for me, as long as
>> there actually is a complex.  You can also try -pbc cluster, but I know that
>> algorithm can hang.
>>
>> -Justin
>>
>>> Thanks
>>> Carla
>>>
>>> On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul >> > wrote:
>>>
>>>
>>>
>>>    Carla Jamous wrote:
>>>
>>>        Hi everyone,
>>>        I'm using this command to extract my protein and my ligand from
>>>        the trajectory.
>>>
>>>        trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc
>>>        whole -n prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj
>>>
>>>        Before, I had a problem with residues of my protein showing at
>>>        the other end of the box, when I display my .xtc with VMD.
>>>        the "-pbc whole" fixed it.
>>>
>>>        However, now I have another issue: my ligand is at the other end
>>>        of the box. So please can anyone tell me what can I do to fix
>>>        that and get a reasonable RMSD value?
>>>
>>>
>>>    You may need several more iterations of trjconv (one rarely does the
>>>    trick), employing -pbc nojump, -pbc cluster, and/or -center.  For
>>>    protein-ligand complexes, I have often found that the combination of:
>>>
>>>    trjconv -pbc mol -ur compact -center
>>>
>>>    (centering on "Protein")
>>>
>>>    does the trick.  And it makes molecules whole, as well :)  I think
>>>    there are also some breakdowns (documented somewhere in the list
>>>    archive) when applying -fit and -pbc in the same step.  I believe it
>>>    is recommended to fix PBC first, then applying any sort of fitting
>>>    in a separate, subsequent step.
>>>
>>>    -Justin
>>>
>>>        Thank you
>>>        Carla
>>>
>>>
>>>    --    
>>>
>>>    Justin A. Lemkul
>>>    Ph.D. Candidate
>>>    ICTAS Doctoral Scholar
>>>    MILES-IGERT Trainee
>>>    Department of Biochemistry
>>>    Virginia Tech
>>>    Blacksburg, VA
>>>    jalemkul[at]vt.edu  | (540) 231-9080
>>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>>    
>>>    --    gmx-users mailing list    gmx-us...@gromacs.org
>>>    
>>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>    .
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>>>
>>>
>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
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Re: [gmx-users] Same starting structure but different trajectories

[Tsjerk Wassenaar]

Hi Emanuel,

Anything small can cause trajectories to diverge, it's chaos. The
machine on which is run can make the difference. This is also covered
in the list archives.

> ;Temperature coupling
> tcoupl           = nose-hoover
> tc-grps          = protein NA+ CFP SOL
> tau_t             = 0.1  0.1 0.1   0.1
> ref_t             = 300 300 300 300

This is bad practice. Where did you get that from? Not from any _good_
tutorial, surely. Check
http://www.gromacs.org/Documentation/Terminology/Thermostats to learn
more.

Cheers,

Tsjerk


-- 
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Re: [gmx-users] Problem - can't set dodecahedrons box

[Tsjerk Wassenaar]

Hi,

> You can post-process your trajectory using "trjconv -pbc mol -ur compact" to 
>see the real
> representation.

The real representation is the infinite periodic system; there is no
box shape there. For representation of a single unit cell you can take
any cut that is consistent with the lattice, all being equally real.

Cheers,

Tsjerk

-- 
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Re: [gmx-users] best interval for saving configurations ?

[Tsjerk Wassenaar]

It also strongly depends on what analysis you try to do. For
autocorrelation you should sample frequently enough, for other
configurational analysis, you don't need so many points, for
covariance analysis you should aim for a number of frames three times
the number of atoms you want to analyze.

Cheers,

Tsjerk

On Mon, Feb 8, 2010 at 11:07 AM, Baofu Qiao  wrote:
> Hi,
>
> it depends. Firstly how strong are the configurations related over time.
> Then the maximum of your harddisk. Generally it is in the order of
> magnitude of ps.
>
> shahab shariati wrote:
>> Hi all
>>
>>
>>
>> What is the best interval for saving configurations in full md step?  (every
>> what ps?)
>>
>>
>
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Re: [gmx-users] last line in .gro file

[Tsjerk Wassenaar]

Hi Vishal,

Here is  a python function that generates a triclinic representation
given a definition with lengths and angles. The argument L is a tuple
or list containing the lengths and angles.

def triclinic(L):
B = [[0,0,0],[0,0,0],[0,0,0]]

x, y, z, a, b, c = L[:6]

B[0][0] = x
if a == 90 and b == 90 and c == 90:
B[1][1] = y
B[2][2] = z
else:
a = a*pi/180
b = b*pi/180
c = c*pi/180
B[1][0] = y*cos(c)
B[1][1] = y*sin(c)
B[2][0] = z*cos(b)
B[2][1] = z*(cos(a)-cos(b)*cos(c))/sin(c)
B[2][2] = sqrt(z*z-B[2][0]**2-B[2][1]**2)

return B

Hope it helps,

Tsjerk

On Tue, Feb 2, 2010 at 9:23 PM, Erik Marklund  wrote:
> Hi,
>
> Since any unit cell can be formulated as a triclinic cell, the monoclinic
> cell is indeed supported. By definition it has two 90 degree angles and one
> that is not 90 degrees.  The box vectors can be of different lengths. You'll
> have to do the math and reading yourself to find out how this translates to
> a .gro box. The manual is your friend here.
>
> Good luck,
>
> Erik
>
> Vishal Agarwal skrev:
>>
>> Dear Justin,
>>
>> Thanks for replying. The table mentions only a few unit cell type. I am
>> using a monclinic unit cell. Do you know how these box vectors have been
>> derived.
>>
>> thanks
>> vishal
>>
>> On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul > > wrote:
>>
>>
>>
>>    Vishal Agarwal wrote:
>>
>>        Dear gmx-users,
>>
>>        I am new to GROMACS. Can anyone tell me what does the last
>>        line in .gro file stands for ?
>>
>>        The manual mentions
>>        "box[X][X],box[Y][Y],box[Z][Z],
>>        box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"
>>
>>        Can anyone explain what each of these mean in terms of cell
>>        parameters ?
>>
>>
>>    The last line contains the box vectors.  Specifics in terms of
>>    unit cell geometry are given in the manual, Table 3.1 and section
>>    3.2.1.
>>
>>    -Justin
>>
>>        Thanks,
>>        vishal
>>
>>
>>    --    
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu  | (540) 231-9080
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    
>>    --    gmx-users mailing list    gmx-us...@gromacs.org
>>    
>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>    .
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>>
>>
>>
>>
>> --
>> Regards
>>
>> ***
>> Vishal Agarwal
>> Research Scholar
>> University of Massachusetts, Amherst
>> ***
>> 'Your only obligation in any lifetime is to be true to yourself."
>>            ---Richard Bach
>
>
> --
> ---
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> er...@xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
>
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Re: [gmx-users] Re: Step 6 of lysozyme tutorial

[Tsjerk Wassenaar]

Hi Bharat,

Besides the notes of Justin, which lysozyme tutorial?
And for which GMX version was that tutorial written?

Tsjerk

On Sat, Jan 30, 2010 at 12:53 PM, Justin A. Lemkul  wrote:
>
>
> bharat gupta wrote:
>>
>> Hi
>>
>> I am getting the follwing error while running the mdrun command given
>> in the step six of the lysozyme tutorial :-
>>
>>
>> Program mdrun, VERSION 4.0.7
>> Source code file: gmxfio.c, line: 737
>>
>> Can not open file:
>> topol.tpr
>> ---
>>
>> "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)
>>
>>
>>
>> Can anybody tell me where i will find this topol.tpr file ???
>
> You don't find it anywhere - you were surely supposed to create it with
> grompp in the prior step.  If some previous step failed then this input
> wouldn't have been generated.  Read all messages printed to the screen
> carefully.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] Re: including a custom itp file in topology

[Tsjerk Wassenaar]

Hi,

rtp stands for 'Residue ToPology' and is used exclusively for building
block definitions, which are only used by pdb2gmx.
itp stands for 'Include ToPology' and can contain any part of a
topological description of a system, atom types, bond types,
moleculetypes, definitions, to be #included at the right point in the
master topology file. It is often used to separate out moleculetype
definitions, but also the top level force field parameters are
contained in a .itp file (ffoplsaa.itp for example).

For non standard residues, the residue has to be defined as a building
block and put in to a .rtp file in order to allow pdb2gmx to process
it. Non-bonded ligands need not be processed by pdb2gmx. With a proper
description in terms of coordinates and [ moleculetype ] (.itp file),
they can be easily merged with coordinates, c.q. topology as produced
by pdb2gmx.

Hope it helps,

Tsjerk

On Fri, Jan 29, 2010 at 1:45 PM, Jack Shultz  
wrote:
> I confess I don't know the difference between rtp and itp. What I was hoping
> was an easier way to generate topologies for complexes that have
> non-standard residue names like LIG. Alan's acpypi works. You just have to
> do some extra scripting. But it seems like pdb2gmx should have a way to load
> the files describing the non-standard residue names directly.
>
> On Fri, Jan 29, 2010 at 6:24 AM, Alan  wrote:
>>
>> Dear Berk,
>> I beg your pardon, but I have to assume that what you wrote below is not
>> correct so, right?
>> Should it be 'ligand.rtp' instead of 'ligand.itp'?
>> Once I have my hands on this new pdb2gmx, I believe I can tweak acpypi to
>> generate rtp files as well (but hdb and else probably not).
>> Cheers,
>> Alan
>>
>> On Fri, Jan 29, 2010 at 11:00,  wrote:
>>>
>>> > of them. So you can just put, e.g., a file called ligand.itp in your
>>> > force
>>> > field or current dir and pdb2gmx
>>> > will read it.
>>
>>
>>
>> --
>> Alan Wilter Sousa da Silva, D.Sc.
>> PDBe group, PiMS project http://www.pims-lims.org/
>> EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
>> +44 (0)1223 492 583 (office)
>>
>> --
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>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
>
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Re: [gmx-users] grompp gives "no molecules were defined in the system"

[Tsjerk Wassenaar]

Hi Marysa,

The error is about the definition of mulecules, which suggests that
there are no [ moleculetype ] directives. Did you #include the proper
.itp file(s) with the necessary moleculetype definitions? If not,
you'll have to provide more information, probably posting the topology
file itself.

Cheers,

Tsjerk

On Thu, Jan 28, 2010 at 12:27 PM, Marysa van den Berg
 wrote:
> Hi,
>
> I have a problem with Gromacs. I want to do MD simulations with my proteïn
> in a DPPC-membrane.
> Therefore I followed Justin Lemkul's tutorial on membrane proteïn
> simulation. I just used a bigger
> membrane (256 lipids instead of 128). I managed to correctly embed the
> proteïn in the bilayer,
> I solvated it with genbox and then I want to add ions. But when I use grompp
> to get a .tpr
> file for genion, Gromacs fives the following error:
>
> Program grompp, VERSION 4.0.7
> Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320
> Fatal error:
> No molecules were defined in the system
>
> I did update my topology in the [ molecules ] section and checked it twice
> to see if it fits with
> the .gro file. It is correct, so I don't know what the problem is. Before
> the solvation there was
> no problem with grompp, so it must have something to do with the solvation?
> I hope someone
> can help me.
>
> Thanks,
>
> Marysa van den Berg
>
> 
> Minder SPAM in de verbeterde Windows Live Hotmail
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Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

[Tsjerk Wassenaar]

Hi Vivek,

Either

1. Use the original ligand coordinates with the PRODRG topology

or

2. Fit the structure obtained from PRODRG to the original structure

Cheers,

Tsjerk

On Wed, Jan 27, 2010 at 5:58 AM, vivek sharma
 wrote:
> Hi Dallas,
> I am trying to run MD simulation over a docked complex (protein+ligand), to
> confirm their dynamic stability in water media.
> For the same I am using PRODRG server to generate topologies for ligand
> molecule as gromacs can generate topology for 20 standard residues. As
> mentioned in tutorial for drug-enzyme complex, I am editing the .top and
> .gro files to include the PRODRG generated files (DRGGMX.ITP in .top and
> DRGAPH.GRO in .gro file).
> I observe that their are changes in co-ordinate of ligand after processing
> them through PRODRG server. So these new co-ordinates for ligand are placing
> ligand away from the protein while the ligand molecule was in protein pocket
> in original docked complex.
>
> I hope it gives what I am trying to do, and where I am getting stuck.
>
> I am looking for some suggestions and more insight of the problem to solve
> it.
> Earlier I have done same procedure successfully for a different docked
> complex.
>
> Regards,
> Vivek
>
> 2010/1/27 Dallas B. Warren 
>>
>> So, what EXACTLY are you doing?
>>
>>
>>
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3010
>> dallas.war...@pharm.monash.edu.au
>> +61 3 9903 9167
>> -
>> When the only tool you own is a hammer, every problem begins to resemble a
>> nail.
>>
>>
>>
>> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
>> On Behalf Of vivek sharma
>> Sent: Monday, 25 January 2010 7:38 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Ligand coming out while trying Drug-enzyme
>> tutorial
>>
>>
>>
>> HI Tsjerk,
>>
>> Thanks for your reply. But, I can't see if it is going suddenly or
>> gradually.
>> What i can see is the ligand is away from the molecule after editing the
>> gro file with PRODRG output.
>>
>> It seems liek PRODRG has modified the co-ordinates that places ligand away
>> from the protein.
>>
>> ~Vivek
>>
>> 2010/1/25 Tsjerk Wassenaar 
>>
>> Hi Vivek,
>>
>> > Now when I am processing the modified .gro file to generate box, the
>> > ligand
>> > and cofactor are going away from the protein molecule and I am not able
>> > to
>> > analyze the complex.
>>
>> Gradually going away, or suddenly jumping?
>>
>> In the latter case, read up on periodic boundary conditions.
>>
>> Tsjerk
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> Computational Chemist
>> Medicinal Chemist
>> Neuropharmacologist
>> --
>>
>> gmx-users mailing list    gmx-us...@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>>
>>
>> --
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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] running unrestrained MD for tutorial

[Tsjerk Wassenaar]

Hi David,

Always check which version a tutorial is written for. And also always
mention which version you're running when posting a question/issue to
the list. Now, with this error, I know you're running the (broken) GMX
3.3.2. The tutorial was written for 3.3.1, but will also work with
3.3.3.

Cheers,

Tsjerk

On Mon, Jan 25, 2010 at 6:41 PM,   wrote:
> Dear Users,
>                      Re tutorial 
> http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/
>
>
>
> After running comand:
>
> grompp -v -f pr.mdp -c 1LW9-EM-solvated.gro -p 1LW9.top -o 1LW9-PR.tpr
>
> and
>
> mdrun -v -deffnm 1LW9-PR   (gave message Routine should not have been called:
>                                                                               
>                            gmx_sumi)
> also failed to produce 1LW9-PR.gro
>
> to proceed to next stage:
> grompp -v -f nvt.mdp -c 1LW9-PR.gro -p 1LW9.top -o 1LW9-NVT.tpr
>
> Can anyone help,
>
> Many Thanks,
>
> David.
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> 
>
>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] Re: about beta port of C27 FF to gromacs

[Tsjerk Wassenaar]

Hi Pär,

I actually refered to the .rtp file. I think that the edit was there.

Cheers,

Tsjerk

On Mon, Jan 25, 2010 at 12:24 PM, Pär Bjelkmar  wrote:
> Hi,
 ---
 Program pdb2gmx, VERSION 4.0.7
 Source code file: resall.c, line: 344

 Fatal error:
 in .rtp file in residue cmap at line:
       -C      N       CA      C       +N
 :q!
 ---
>>
>> Did somebody use vi to edit this file and accidently inserted rather than 
>> quit?
> Sharp eye! Nop I didn't change anything, this is how it looked in the 
> original message.
>
> /Pär--
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] Re: about beta port of C27 FF to gromacs

[Tsjerk Wassenaar]

Hi,
>> ---
>> Program pdb2gmx, VERSION 4.0.7
>> Source code file: resall.c, line: 344
>>
>> Fatal error:
>> in .rtp file in residue cmap at line:
>>       -C      N       CA      C       +N
>> :q!
>> ---

Did somebody use vi to edit this file and accidently inserted rather than quit?

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
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Re: [gmx-users] GMXRC Problem

[Tsjerk Wassenaar]

Hi Pawan,

Check which shell you're actually running (probably bash), and source
the shell specific GMXRC file (GMXRC.bash).

Cheers,

Tsjerk

On Mon, Jan 25, 2010 at 8:19 AM, pawan raghav  wrote:
> Dear Justin,
>
> I have some problem regarding GMXRC execution, I got an error while using
> gromacs-4.0.7 on windows vista using cygwin i.e.
>
> /usr/local/bin/GMXRC: line 35: return: can only  'return' from a function or
> sourced script.
> /usr/local/bin/GMXRC: line 44:CSH::command not found
> /cygdrive/c/Gromacs/bin/GMXRC.csh:line 8: syntax error near expected token
> 'setenv'
> /cygdrive/c/Gromacs/bin/GMXRC.csh: line 8: 'if Setenv
> LD_LIBRARY_PATH "" '
>
> So please tell how to setenv to execute GMXRC.
>
> --
> Pawan Kumar Raghav
> Bioinformatician
> Stem Cell and Gene Therapy Research Group
> Division of Radiation Biosciences
> INMAS, DRDO
> Timarpur Delhi-110054
>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

[Tsjerk Wassenaar]

Hi Vivek,

> Now when I am processing the modified .gro file to generate box, the ligand
> and cofactor are going away from the protein molecule and I am not able to
> analyze the complex.

Gradually going away, or suddenly jumping?

In the latter case, read up on periodic boundary conditions.

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] Lipid parameters for GROMOS96 force fields

[Tsjerk Wassenaar]

Hi,

Well, we have compared the G53a5/6 force field with the 43a2 one and
found consistently larger radii of gyration and higher RMSDs,
suggesting decreased stability. There's a thorough account of it in my
thesis 
(http://dissertations.ub.rug.nl/FILES/faculties/science/2006/t.a.wassenaar/04emb_c4.pdf)
and it's been published in JPCB in 2007 (DOI: 10.1021/jp068580v).

Cheers,

Tsjerk

On Thu, Jan 21, 2010 at 2:24 PM, XAvier Periole  wrote:
>
> The instability of helices with the G53a6 force field is definitely real
> and unfortunately not documented. Some people are working on it ...
>
> I would advise to be very carefull in interpreting results with this FF.
>
> XAvier.
>
> On Jan 21, 2010, at 2:13 PM, Justin A. Lemkul wrote:
>
>>
>>
>> Krzysztof Mlynarczyk wrote:
>>>
>>> 2010/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>>   Krzysztof Mlynarczyk wrote:
>>>       2. If not, is there any way to derive the proper parameters for
>>>       the force field of my choice using the lipid parameters from
>>>       Peter Tieleman's website or e.g. the parameters published by
>>>       Andreas Kukol for G53a6?
>>>   I don't see why you need to do such reverse engineering.  The Kukol
>>>   parameters for lipids under 53a6 can be directly combined with a
>>>   G53a6 protein without any issues; I believe that was the purpose of
>>>   the whole new derivation :)
>>> I received a message that G53a6 is beta-sheet biased and alpha helices do
>>> not perform as well as they should. My protein contains 7 transmembrane
>>> helices, that's why I'm worried.
>>
>> Is this published somewhere?  That would be important information.
>>  Perhaps this is the case for model peptides or short fragments, but I have
>> certainly done a number of simulations using 53a6 with well-folded globular
>> proteins and I do not see any such instability (i.e., alpha->beta conversion
>> or unwinding of alpha-helices).  I do believe it is possible in certain
>> scenarios, but I don't know that a large 7TM protein like yours would suffer
>> adversely.
>>
>>> I know that there are changes between parameter sets both in non-bonded
>>> and bonded terms and one rtp entry will probably not work well when pasted
>>> into a different force field from the same family. G96 family uses symbols
>>> like gd_5 that are substituted by appropriate parameters later through the
>>> use of preprocessor. While it is possible to find that gd_5 is the same as
>>> gd_15 in another version of G96 and substitute those symbols in topologies,
>>> the changes in non bonded parameters still can spoil what was working well
>>> elsewhere. That's why I was also asking for some checked and ready-to-use
>>> topologies for a particular force field.
>>
>> Many of the bonded parameters carry over between force fields, but
>> certainly new entries were created between 43a2 and 53a6, so yes, some
>> re-working would likely be necessary.  There is a lipid 43a2 parameter set
>> on the User Contribution site, like I said before, I just don't know if
>> there is a reference for it.
>>
>>>   As an aside, you are quite right that multiple force fields within
>>>   the same simulation is incorrect.  However, the Berger lipid
>>>   parameters may be an exception to this rule, since they are really a
>>>   hybridized version of OPLS-UA and Gromos87 parameters (some of which
>>>   were modified anyway), so they really don't belong to any one
>>>   particular force field.  The Berger/G87 combination is widely used,
>>>   but essentially amounts to the following: lipid interactions are
>>>   Berger-Berger or OPLS-OPLS interactions, while protein-lipid
>>>   interations are Berger-G87, and protein-protein interactions are
>>>   G87-G87.  You can see quite quickly why things become complicated!
>>>   Based on a discussion I had with Dr. Tieleman, it seems to be
>>>   reasonable to use the G96 parameter set of your choice in
>>>   conjunction with lipid.itp (Berger lipids), although other
>>>   approaches may be more rigorously correct (pure G96 parameters such
>>>   as those by Kukol, pure OPLS recently derived by Ulmschneider, or
>>>   the modifications to the Berger parameters from the Tieleman group,
>>>   to name a few).  If you want to use a G96-lipid.itp combination, I
>>>   created a tutorial that teaches you how to build the system and
>>>   properly prepare the topology.  It is linked from the Tutorials page
>>>   of the Gromacs site.
>>> I found this tutorial earlier and was also in doubt if this approach was
>>> correct. But if it works, perhaps I should give it a try.
>>> I gotta make a _good_ decision in the end...
>>
>> As do we all :)  My work with G53a6+Berger has thus far been quite
>> reliable, from everything I can measure, but that certainly does not
>> preclude the possibility (even likelihood) that there are better procedures
>> out there, like those I quoted above, and certainly others (CHARMM is also
>> popular for membrane proteins, but Gromacs will only *officially* support

Re: [gmx-users] how to analysis crystal structure and 2D projections by PCA?

[Tsjerk Wassenaar]

Xi Zhao,

Find some elementary text on PCA and read it thoroughly.

Tsjerk

On Wed, Jan 20, 2010 at 2:40 PM, xi zhao  wrote:

>
> Dear users:
> I want to analyse a crystal structure by PCA, and want to show its 2D
> projection, but I meet errors" segment fault"
> my procedure:
> g_covar_d -f crystal strucutre.pdb -s crystal strucutre.pdb  -o eig.xvg -v
> eig.trr
> g_anaeig_d -f  crystal strucutre.pdb -eig eig.xvg -v eig.trr -2d 2d.xvg
> -first 1 -last 2
> but produce errors.
> Please help me!
> thank you!
> [image: 
> 4]
>
> --
> 好玩贺卡等你发，邮箱贺卡全新上线！
> --
> gmx-users mailing listgmx-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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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] occupancy

[Tsjerk Wassenaar]

Hi Carla,

You can do lots of things. You can edit the occupancy field by hand,
or do it with a tool like sed. You can also neglect the warning,
provided that you're pretty sure the structure is okay. Partial
occupancies occur when atoms can not be exclusively assigned to a
single position. In those cases pdb2gmx takes the first location
listed. Occupancies of 0 occur when an atom position is completely
guessed or modeled in. Check the PDB file format to learn more.

Cheers,

Tsjerk

On Tue, Jan 19, 2010 at 4:56 PM, Carla Jamous  wrote:
> Hi,
> I'm encountering a problem with pdb2gmx & occupancy. I searched the mailing
> list & followed this advice: "do NOT throw away crystallographic water
> molecules before you run genbox". I kept my pdb's water mlolecules & ran
> pdb2gmx.
>
> But still I get this warning:
> " there were 0 atoms with zero occupancy and 1 atoms with occupancy unequal
> to one (out of 2658 atoms). Check your pdb file."
>
> What can I do to stop having this warning?
>
> Thanks
>
> Carla
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] dynamic cross correlation map (DCCM)

[Tsjerk Wassenaar]

Hi,

Well I'd say that 'DCCM' refers to the matrix (map) of correlations
and not to that of covariances. More specifically, it refers to
correlations of positional fluctuations. PCA, on the other hand,
refers to the extraction of components or axes which better describe
the data than the original axes do, not specifying what kind of data,
nor whether correlations or covariances be used for their
determination. That's quite a distinction.
g_covar gives the covariance matrix, not the correlation matrix. I
believe there was a modified version in the contributions section
which was able to compute correlations.

Cheers,

Tsjerk


On Tue, Jan 19, 2010 at 12:50 PM, Justin A. Lemkul  wrote:
>
>
> leila karami wrote:
>>
>> Hi
>>  I want to obtain dynamic cross correlation map (DCCM). I used following
>> command for obtaining covariance matrix.
>>  g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l
>> covar.log -xpm covar.xpm.
>>  my system consists protein of 70 aminoacids. I want survey correlated and
>> anti-correlated motion between residues.
>>  Is my manner true? If so, which of output files in above give me dynamic
>> cross correlation map (DCCM)? otherwise, please guide me.
>>
>
> No one has ever been able to explain to me the difference between DCCM and
> PCA, so I'd say you're correct at least in obtaining the covariance matrix,
> which will give you information about correlated and anticorrelated motion.
>  "DCCM" seems to be a popular term with the AMBER crowd, but I don't know
> that their manual even gives the equations used for such an analysis to
> potentially differentiate it from PCA.  I believe there are some tips in
> their mail reflector, however.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] The size of the domain decomposition grid (1) does not match the number of nodes (8).

[Tsjerk Wassenaar]

Hi Chris,

Don't have an answer too this one, but noticed the argument to the -np option

> -np $(wc -l $PBS_NODEFILE | gawk '{print $1}')

Maybe it's a bit easier on the eye to use:

-np $(sed -n $= $PBS_NODEFILE)

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] Missing Residues are list ind pdb file

[Tsjerk Wassenaar]

Hi Jack,

On Fri, Jan 15, 2010 at 8:05 PM, Jack Shultz  
wrote:
> I'm trying to prep Fe-Hydrogenase again (1YQW). I took out all the
> non-standard residues. Re-named n-terminal and c-terminal residues. Took out
> connects because that worked last time though I'm uncertain if connect
> really maters.

Thank god you didn't went up a hill to dance under the full moon. You
might have thought that that was also part of solving your error and
would only be preparing structures once a month then!

> Another issue with preping a protein. Its says I a missing H and HA for this
> residue, but have those atoms listed there. Why does it say CYSH instead of
> CYS2 on residue 15 ???

Well, the closest other CYS-SG is 0.287 nm:

 CYS2414 SG18376   0.287   1.574   2.660   2.205   1.101   2.402   1.361

That is well beyond the cut-off used for assigning SS bonds, so it
must be a stand-alone, protonated cysteine (CYSH).

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

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Re: [gmx-users] Unstable Minimizations

[Tsjerk Wassenaar]

Hi,

Okay, they're read in some cases. But not in pdb2gmx related to
building a topology as far as I can see. I should've written:

pdb2gmx doesn't distinguish between ATOM and HETATM entries.
pdb2gmx does not read CONECT records.
Now the 'TER' recoord... That makes a difference.

Cheers,

Tsjerk

On Thu, Jan 14, 2010 at 9:23 PM, Erik Marklund  wrote:
> Tsjerk Wassenaar skrev:
>>
>> Hi Jack,
>>
>> On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz > <mailto:j...@drugdiscoveryathome.com>> wrote:
>>
>>    Problem Solved.
>>        I replaced HETATM with ATOM, I fixed BOTH N-terminal and
>>    C-terminal. I kept TER and END. Removed all CONECT. Renamed the
>>    CYS to CYS2. No other non-AminoAcid residues were present. Most of
>>    this is described by the FFAmber site
>>    http://chemistry.csulb.edu/ffamber/
>>
>>
>> Gromacs doesn't distinguish between ATOM and HETATM entries.
>> Gromacs does not read CONECT records.
>> Now the 'TER' recoord... That makes a difference.
>
> I may be wrong, but I think Gromacs reads CONNECT records nowadays.
>
> /Erik
>>
>> Cheers,
>>
>> Tsjerk
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> Computational Chemist
>> Medicinal Chemist
>> Neuropharmacologist
>>
>
>
> --
> ---
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> er...@xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
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Medicinal Chemist
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Re: [gmx-users] Unstable Minimizations

[Tsjerk Wassenaar]

Hi Jack,

On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz 
wrote:

> Problem Solved.
>
> I replaced HETATM with ATOM, I fixed BOTH N-terminal and C-terminal. I kept
> TER and END. Removed all CONECT. Renamed the CYS to CYS2. No other
> non-AminoAcid residues were present. Most of this is described by the
> FFAmber site
> http://chemistry.csulb.edu/ffamber/
>
>

Gromacs doesn't distinguish between ATOM and HETATM entries.
Gromacs does not read CONECT records.
Now the 'TER' recoord... That makes a difference.

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

[Tsjerk Wassenaar]

Now try hard to resist running on multiple processors...

Tsjerk

On Mon, Jan 11, 2010 at 8:11 PM, Chih-Ying Lin  wrote:
>
>
>
> Today's Topics:
>
>   1. 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken
>      (Chih-Ying Lin)
>   2. 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken     (output
>      file) (Chih-Ying Lin)
>
>
> --
> 
>
> Message: 1
> Date: Sun, 10 Jan 2010 10:11:17 +0800
> From: Chih-Ying Lin 
> Subject: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation
>        Broken
> To: gmx-users@gromacs.org
> Message-ID:
>        <5777f3841001091811l41fbe079ida9822609fc8e...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi
> 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the
> simulation on Gromacs.
> System = 6LYZ.pdb + CL- + water molecules
>
> Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all.
> Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step
> Position restrained MD.
>
> The commands are as follows.
> minim.mdp and pr.mdp are as follows.
> And outputs are as follows.
>
> Any thing wrong?
> Thank you
> Lin
>
>
> 1. Energy minimization of the structure (vacuum)
> pbc=no
> grompp_mpi -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr
> mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-vacuum
>
>
> 2. Periodic boundary conditions
> editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -box 6.0 6.0
> 6.0
>
>
> 3. Solvent addition
> genbox_mpi -cp 6LYZ-PBC.gro -cs spc216.gro -p 6LYZ.top -o 6LYZ-water.gro
>
>
> 4. Addition of ions: counter charge and concentration
> grompp_mpi -v -f minim.mdp -c 6LYZ-water.gro -p 6LYZ.top -o 6LYZ-water.tpr
> genion_mpi -s 6LYZ-water.tpr -o 6LYZ-solvated.gro -nn 8 -nname CL-
>
>
> 5 Energy minimization of the solvated system   => Potential Energy went to
> the very negative number
> pbc =xyz (minim.mdp)
> grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o
> 6LYZ-EM-solvated
> mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-solvated
>
>
> 6 Relaxation of solvent and hydrogen atom positions: Position restrained
> MD   => Simulation Broke
> grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr
> mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR
>
>
> =
> minim.mdp
>
> ; LINES STARTING WITH ';' ARE COMMENTS
> title           = Minimization of Lysozyme (1LW9.pdb)   ; Title of run
> ; The following lines tell the program the standard locations where to
> find certain files
> cpp             = /lib/cpp      ; Preprocessor
> ; Definea can be used to control processes
> define          = -DFLEXIBLE
> ; Parameters describing what to do, when to stop and what to save
> integrator      = steep         ; Algorithm (steep = steepest descent
> minimization)
> emtol           = 1.0           ; Stop minimization when the maximum force <
> 1.0 kJ/mol
> nsteps          = 5         ; Maximum number of (minimization) steps
> to perform
> nstenergy       = 1             ; Write energies to disk every nstenergy
> steps
> energygrps      = System        ; Which energy group(s) to write to disk
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist         = 5             ; Frequency to update the neighbor list
> and long range forces
> ns_type         = simple        ; Method to determine neighbor list
> (simple, grid)
> rlist           = 1.0           ; Cut-off for making neighbor list (short
> range forces)
> coulombtype     = cut-off       ; Treatment of long range electrostatic
> interactions
> rcoulomb        = 1.0           ; long range electrostatic cut-off
> rvdw            = 1.0           ; long range Van der Waals cut-off
> constraints     = none          ; Bond types to replace by constraints
> pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
>
> =
> pr.mdp
>
> ; VARIOUS PREPROCESSING OPTIONS
> title                    =
> cpp                      = /lib/cpp
> include                  =
> define                   = -DPOSRES
> ; RUN CONTROL PARAMETERS
> integrator               = md
> tinit                    = 0
> dt                       = 0.001
> nsteps                   = 5000
> nstcomm                  = 0
> ; OUTPUT CONTROL OPTIONS
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> nstlog                   = 10
> nstenergy                = 1
> nstxtcout                = 0
> xtc_precision            = 1000
> xtc-grps                 = System
> energygrps               = Protein Non-Protein
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist                  = 5
> ns-type                  = Grid
> pbc                      = xyz
> rlist                

Re: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broke

[Tsjerk Wassenaar]

Hi Chih-Ying,

Like Mark said, start from scratch and trace your steps carefully.
There's nothing special about that lysozyme structure. In fact, the
protocols I use for the tutorials work flawlessly with it! I think
you'd best step through the tutorial again, using 6LYZ.pdb. I know
that at some points the tutorial deviates from what you need/want. In
these cases, make notes of what happens with the tutorial way of doing
it and see how your way of doing deviates from that. I'd say it's best
to change the protocol starting from the end, like changing the .mdp
options first and see whether it still goes. One of the differences
between your protocol and the one in the tutorial is likely to be the
cause of your problem. It's up to you to track it.

Cheers,

Tsjerk

On Mon, Jan 11, 2010 at 10:19 AM, Mark Abraham  wrote:
> Chih-Ying Lin wrote:
>>
>> Hi
>>>
>>> From Tsjerk,
>>
>> "Previously you had an issue with the addition of ions to your .top
>> file. In your protocol, it's not mentioned. Have you made sure that
>> issue is cleared?"   => Yes, I did.
>>
>>
>>
>> I encountered two cases that my simulation broke.
>> Case I => 6LYZ + ligands + water molecules + CL-
>>           => Gromacs 3.3.3
>>           => error from the addition of ions to my .top file
>>           => The problem is solved and the simulation runs successfully.
>>
>>
>> Case II => 6LYZ + water molecules + CL-
>>            => Gromacs 4.0.5
>>            => Have tried the correct addition of ions to my .top file
>>            => The potential energy goes very negative after EM
>>            => the PR step broke.
>
> Almost certainly, you've done it wrong. I've lost track of how many times
> you've posted this little detail about what you've done. We're not at all
> interested in seeing just a broad description of what you've done. The
> details all have to be right, and since you have a problem with a relatively
> simple stage of doing MD, you're getting at least one detail wrong.
> Accordingly, we're not much interested in anything that's been filtered
> through your head, because we all know our heads are imperfect and computers
> are literal.
>
> Start from a clean working directory and produce an actual list of commands
> you've used, by copying and pasting from your terminal. I've given you that
> kind of advice at least three times now. If you want people to help, please
> look like you're trying to follow their advice. We don't owe it to you. If
> you want help, you need to make it easy for us to help you.
>
> Mark
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] Unstable Minimizations

[Tsjerk Wassenaar]

Hi Jack, Justin,

Is this related to last weeks post? I suggested that you might have
seen long bond warnings, which in this case certainly show up. Lots of
them. But one stands out: there's a break in the chain of 3.3 nm!
During minimization an attempt is made to bring these ends together,
which causes failure. Probably pdb2gmx missed that there should be two
chains rather than one.

When designing a workflow, or adapting one for a new situation, you
have to start stepwise. Well, trying an existing workflow is okay, but
if it fails, you'll have to trace steps and check for anything that is
out of the ordinary. You're stop is the step with pdb2gmx. Something
is not working there. Make sure to get to know what pdb2gmx requires
in order to process a structure and make sure that you make the input
comply with these requirements. The main requirements are:

1. every chain needs to have a unique chain identifier
2. there should be no missing atoms (other than hydrogens)
3. there should be no missing residues , except possibly at the termini.
4. there should be no residues (ligands) that are not in the building
block database for the force field you're using
5. atom names in the coordinate file should be consistent with those
in the building block database
6. there should be no atoms in residues that are not listed in the
building block entry, except possibly for hydrogen atoms, which can be
stripped using the -ignh flag

Like I replied last week, your problem probably relates to 1. Some
programs (CNS/X-PLOR) use the segment identifier field at the end of
the line, rather than the chain identifier more in the middle. You can
fix that with sed or python (the latter being more readable ;)):

sed -e '{/^\(ATOM  \|HETATM\)/
s/^\(.\{21\}\).\(.\{50\}\)\(.\)/\1\3\2\3/}' in.pdb > out.pdb

python -c "for i in [ l for l in open('in.pdb') if
l.startswith('ATOM') ]: print i[:21]+i[71]+i[22:]," > out.pdb

I'm not exactly sure that 71 (72) in the python line is the right
field for the segid; you'd better check the PDB specification for
that. The sed line should be correct as is.

Cheers,

Tsjerk
Cheers,

Tsjerk
On Mon, Jan 11, 2010 at 3:58 AM, Justin A. Lemkul  wrote:
>
>
> On 1/10/10 9:47 PM, Jack Shultz wrote:
>>
>> Thanks Justin,
>> I went back to the original pdb files. These were conformations of the
>> same protein derived from molecular dynamics simulations performed by
>> Andrey.
>> What I intially attempted was preping the structures using tleap, hoping
>> to paint in missing atoms for residues. Then use this to replace
>
> Well, it seems that you may be hoping for too much :)  Your log file shows a
> whole bunch of failures that look to be related to some early processing of
> your structure, and other warnings about close contacts detected in tleap.
>
> I think you may need to start with an actual intact structure, or else coax
> your preparation steps to make this happen.  I am not too familiar with
> tleap and sleap, do they magically fix missing atoms?
>
> -Justin
>
>> non-standard residues
>> sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g fzd2_md7-8_c6_cc.pdb | sed s/PRO\ B\
>> \ \ 1/NPROB\ \ \ 1/g | sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\
>> \ 99/CPHEB\ \ 99/g | sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\
>> CPHE/OC2\ CPHE/g | sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed
>> s/CYS\ /CYN\ /g > protein2.pdb
>> Then fixed the nterminal residue name. Finally replaced all CYS to CYS2
>> I went back and did the same thing except for tleap. It pdb2gmx seems to
>> process these files without needing the tleap step.
>> Still I see some of the same lincs errors.
>> rms 10.669050, max 173.182678 (between atoms 1857 and 1859)
>> rms 10.669803, max 173.177811 (between atoms 1857 and 1859)
>> rms 10.670179, max 173.175400 (between atoms 1857 and 1859)
>> rms 10.670368, max 173.174149 (between atoms 1857 and 1859)
>> rms 10.670460, max 173.173553 (between atoms 1857 and 1859)
>> rms 10.670508, max 173.173141 (between atoms 1857 and 1859)
>> rms 10.670531, max 173.173035 (between atoms 1857 and 1859)
>> rms 10.670543, max 173.172958 (between atoms 1857 and 1859)
>> rms 10.670549, max 173.172928 (between atoms 1857 and 1859)
>> rms 10.670552, max 173.172913 (between atoms 1857 and 1859)
>> rms 10.670554, max 173.172913 (between atoms 1857 and 1859)
>> rms 10.670554, max 173.172913 (between atoms 1857 and 1859)
>> ATOM   1857  CA  HIE   120      43.362  28.084  25.727  1.00  0.00
>> ATOM   1858  HA  HIE   120      43.677  27.135  25.748  1.00  0.00
>> ATOM   1859  CB  HIE   120      42.112  28.226  24.788  1.00  0.00
>> also this atom consistently has a very high Fmax
>> Step=    3, Dmax= 1.4e-02 nm, Epot=  1.45860e+10 Fmax= 2.82224e+12,
>> atom= 19392
>> Step=    4, Dmax= 7.2e-03 nm, Epot=  1.45396e+10 Fmax= 2.82207e+12,
>> atom= 19392
>> Step=    5, Dmax= 3.6e-03 nm, Epot=  1.45106e+10 Fmax= 2.82194e+12,
>> atom= 19392
>> Step=    6, Dmax= 1.8e-03 nm, Epot=  1.44953e+10 Fmax= 2.82181e+12,
>> atom= 19392
>> Step=    7, Dmax= 9.0

Re: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

[Tsjerk Wassenaar]

Hi Lin,

First of all, I would suggest sticking to a single processor until you
have a protocol that works.
Previously you had an issue with the addition of ions to your .top
file. In your protocol, it's not mentioned. Have you made sure that
issue is cleared?

Cheers,

Tsjerk

On Sun, Jan 10, 2010 at 5:25 AM, Justin A. Lemkul  wrote:
>
>
> On 1/9/10 10:42 PM, Chih-Ying Lin wrote:
>>
>> Hi
>> I did the EM and the potential energy went to the very negative number.
>> But the simulaiton broke in the PR step.
>> Thank you
>> Lin
>>
>
> Saying the system broke is useless.  There will certainly be some
> information in the .log file (LINCS warnings, etc).  If that is the case,
> then you need to follow the standard advice that is always given in such
> cases:
>
> http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> If you want more detailed advice, provide real output - information from how
> well the EM converged, messages in the .log file (unless it's just LINCS
> stuff, see the above links).  Also realize that EM does not always remove
> all potentially problematic contacts.  Your system may require a bit more
> finesse.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
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Re: [gmx-users] Opening .o files

[Tsjerk Wassenaar]

Lum,

There is none. These are binary object files resulting from
compilation of the source code. Why do you think you would need to
read those?

Tsjerk

On Fri, Jan 8, 2010 at 7:06 PM, Lum Nforbi  wrote:
> Dear all,
>
>    I am having problems opening the g_energy.o file in the gromacs-4.0.5
> folder. Can someone tell me how to open this file? What is the general way
> of opening .o files?
>
> Thank you,
> Lum
>
> --
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Energy units

[Tsjerk Wassenaar]

Hi,

I think that the best interpretation is that the energy is given as kJ
per mole of simulation systems :)

Cheers,

Tsjerk

On Thu, Jan 7, 2010 at 8:42 AM, Mark Abraham  wrote:
> Cheong Wee Loong, Daniel wrote:
>>
>> Thanks Mark for your reply.
>>
>> So if I understand you correctly, it's not really a mole of anything in
>> particular, it's just an energy value divided by Avogadro's number, and this
>> happens to be consistent with the forcefield parameters as well.  So if you
>> have just a single molecule, that energy value is still divided by
>> Avogadro's number.
>>
>> So if I were to take an interaction energy per unit area to estimate an
>> interfacial energy, and I want to relate this to an experimental value given
>> in dynes/cm, I would just need to multiply by Avogadro's number, in addition
>> to all the other unit conversions (kJ/nm2 to dynes/cm), for the units to be
>> consistent.  Am I correct in my understanding?
>
> I think so. Whether such a quantity can be measured with an MM force field
> might be another matter!
>
> Mark
>
>> -Original Message-
>> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
>> On Behalf Of Mark Abraham
>> Sent: Thursday, January 07, 2010 3:03 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Energy units
>>
>> Cheong Wee Loong, Daniel wrote:
>>>
>>> Hi all,
>>>
>>>
>>>
>>> This may be a silly and trivial question, but the energy unit given in
>>> Gromacs is kJ/mol.  What I don't quite understand is, the energy is per
>>> mole of what exactly?
>>
>> In a very real sense, it doesn't matter. It's just a label for a
>> convenient bucket of energy for chemistry.
>>
>> The energy of an isolated water molecule has a certain value, which we
>> might measure in joules relative to some defined zero. Two such
>> molecules at infinite separation would have twice that energy, etc. Once
>> we start approaching Avogadro's number, we would prefer to express that
>> energy as kJ/mol just for our numerical convenience.
>>
>> Equally, we could take a water molecule and a methane molecule at
>> infinite separation, and add their energy... and add lots more... and
>> get irritated at the size of the number, and just divide by Avogadro for
>> convenience. The system is no longer homogeneous, but so long as we
>> compare energies formed in the same way, our conclusions will be valid.
>>
>> MD force fields are typically parameterized against things like
>> experimental or computational enthalpies of formation, normally measured
>> in kJ/mol (unless you're a unlucky enough to be American!). So the
>> parameters that get derived are conveniently measured in units derived
>> from kJ/mol. We could convert them to "absolute" joules, but the numbers
>> would all be stupid. There's a reason quantum chemists work in Hartrees!
>> Were we to work in absolute joules, the numbers we'd produce then would
>> still relate to the numbers we actually produce in kJ/mol - by Avogadro.
>>
>> Mark
>>
>>> The energy is system size dependent, so if I double the number of
>>> molecules, the energy will double accordingly.  But then the unit kJ/mol
>>> seems to imply that it is size-independent.  So how do I reconcile this?
>>>
>>>
>>>
>>> Also, let's say I have a protein molecule surrounded by water
>>> molecules.  Again in this case, I don't quite understand what "per mole"
>>> means in this case.
>>>
>>>
>>>
>>> Thanks in advance for any insights you can teach me.
>>>
>>>
>>>
>>> Daniel
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> 
>>> This email is confidential and may be privileged. If you are not the
>>> intended recipient, please delete it and notify us immediately. Please
>>> do not copy or use it for any purpose, or disclose its contents to any
>>> other person. Thank you.
>>>
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Re: [gmx-users] trouble minimizing structure with mdrun

[Tsjerk Wassenaar]

Hi Jack,

> On Mon, Jan 4, 2010 at 2:44 AM, Tsjerk Wassenaar  wrote:
>> Hi Jack,
>>



>> After preparation with (V|NA)MD, did pdb2gmx correctly assign chains,
>> or did it tie chains together? In the latter case it would have issued
>> a number of "Long Bond Warnings". Did anything else odd show up in
>> the output of any of those steps? Did you actually read through it?

Post pdb2gmx/grompp output to help us help you.

Cheers,

Tsjerk

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Re: [gmx-users] trouble minimizing structure with mdrun

[Tsjerk Wassenaar]

Hi Jack,

Can you be more specific? A quick glance at 1YQW shows that there's
quite a bit of exotic stuff, including several times the infamous
Fe4S4 center. How did you deal with that? At first instance, what
protocol did you used, and what error did you get (and at which
point)?
After preparation with (V|NA)MD, did pdb2gmx correctly assign chains,
or did it tie chains together? In the latter case it would have issued
a number of "Long Bond Warnings". Did everything else odd show up in
the output of any of those steps? Did you actually read through it?

Cheers,

Tsjerk

On Mon, Jan 4, 2010 at 1:38 AM, Jack Shultz  
wrote:
> I've been having trouble minimizing a structure using gromacs so I
> decided to try using another MD app and see if I can generate a more
> relaxed structure.
> Using VMD & NAMD I was able to minimize and run MD for this structure
> from RCSB.ORG 1YQW.pdb. It was solvated and ionized.
>
> I then took the last frame from a 10,000 step trajectory and exported
> it into a pdb file. I preped it so it was compatible with amber99sb
> port for gromacs
> read it into tleap using amebr99sb and wrote a pdb file from that
> Then fixed residues so it it was compatible with gromac
>
> pdb2gmx -ff amber99sb -f protein2.pdb -water spce -ignh
> editconf -bt triclinic -f conf.gro -d 1.0
> genbox -cp out.gro -cs ffamber_tip3p.gro
> grompp -f em.mdp
> echo 13 |genion -s topol.tpr -neutral -conc 0.15 -p topol.top
> grompp -f em.mdp -c out.gro
> mdrun -s topol.tpr -v
>
> Back Off! I just backed up md.log to ./#md.log.2#
> Getting Loaded...
> Reading file topol.tpr, VERSION 4.0.5 (single precision)
> Loaded with Money
>
>
> Back Off! I just backed up traj.trr to ./#traj.trr.2#
>
> Back Off! I just backed up ener.edr to ./#ener.edr.2#
> Polak-Ribiere Conjugate Gradients:
>   Tolerance (Fmax)   =  2.0e+02
>   Number of steps    =        1
>   F-max             =  2.97876e+06 on atom 16106
>   F-Norm            =  2.59700e+04
>
> Step 0, Epot=4.125301e+07, Fnorm=2.399e+04, Fmax=2.975e+06 (atom 16106)
> Step 1, Epot=4.111934e+07, Fnorm=2.285e+04, Fmax=2.969e+06 (atom 16106)
> Step 2, Epot=4.092903e+07, Fnorm=2.216e+04, Fmax=2.959e+06 (atom 16106)
>
> 
>
> Step 127, Epot=7.765358e+06, Fnorm=1.020e+05, Fmax=2.836e+07 (atom 28298)
> Step 128, Epot=1.606771e+08, Fnorm=6.739e+07, Fmax=1.876e+10 (atom 10310)
> Step 129, Epot=5.454451e+09, Fnorm=4.339e+09, Fmax=1.179e+12 (atom 36500)
> There were 2 inconsistent shifts. Check your topology
>
>
>
>
> em.mdp parameters
> define = -DFLEXIBLE
> integrator = cg
> nsteps = 1
> constraints = none
> emtol = 200.0
> nstcgsteep = 10 ; do a steep every 10 steps of cg
> emstep = 0.01 ; used with steep
> nstcomm = 1
> coulombtype = PME
> ns_type = grid
> rlist = 1.0
> rcoulomb = 1.0
> rvdw = 1.4
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
> nstxout = 0 ; write coords every # step
> optimize_fft = yes
> table-extension = 100
> ld_seed = -1
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
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Re: [gmx-users] Simulation Box break into 16 domains => .tpr file is wrong (Gromacs 3.3.3)

[Tsjerk Wassenaar]

Hi,

> Tsjerk gave me suggestion to check the .tpr file created by the command
> grompp.

I also suggested to try and find out why the water molecules got garbled.

Between adding solvent and energy minimization, you also added
chloride to counter the net positive charge. I assume you used genion
for that, which is the most sensible way to do so. Genion typically
adds the ions at the end of the topology. I further assume that you
manually updated the topology by adding a line 'CL-   26' under [
system ]. But if you inserted that line _before_ the line specifying
the number of solvent molecules, whereas in your .gro the chloride
ions were at the end of it, then you had a discrepancy between the
two. In such cases, grompp uses the topology information in stead of
the coordinate file information, but does issue a set of warnings. If
my assumptions are correct, then if you had sent the grompp output at
first instance, we would have been immediately able to pinpoint your
error. Besides, if you had looked at the output from grompp yourself,
you would (should) have noticed that something was wrong there.

Cheers,

Tsjerk


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Re: [gmx-users] About gromacs run...

[Tsjerk Wassenaar]

Hi Henry,

Doing so will give you a loss of precision and you won't have continuity for
the thermo/barostat. You would be better off using tpbconv -extend or
tpbconv -until, with the .tpr, .edr, and .trr as input. That will also save
editing files.

Hope it helps,

Tsjerk



On Sat, Jan 2, 2010 at 10:37 AM, Henry Yang  wrote:

> Dear users,
> Happy new yera to all.
>
> I have just a very simple query..
> I am running a simulation for 100 ns. I have decided to run it by 10 ns
> step of each. In every run, the gromacs generated confout.gro file, the
> traj.trr, traj.xtc, md.log , ener.edr file, state.cpt etc. The next time
> when i run the simulation for the next 10 ns , I have edited the em.mdp file
> and just change the tinit to the last time that i was run and the nsteps to
> 500 for 10 ns.. And the command i used for grompp is ...
>
> grompp -f em.mdp -c confout.gro -p topol.top -o topol.tpr
>
> And then it will generate the topol.tpr file. and the command is then
>
> mdrun
>
> My question is is that oaky ... or I have to use any more file in the
> grompp command like that traj.trr or state.cpt for tracking velocity??
>
> Thnx...
>
> /Henry
> Biochemistry.
>
>
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Re: [gmx-users] Simulation Break => Due to bad domain decomposition ? (MPI) => Gromacs Version 3.3.3

[Tsjerk Wassenaar]

Hi Lin,

> I used Gromacs version 3.3.3.

There is no domain decomposition in gromacs 3.3.3.

Furthermore, you again give no account of what you're doing in terms
of command lines and don't show the grompp output. This is pointless.

Tsjerk

> My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7
> )
> MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64   => 16 nodes in total
> After doing the energy minimization, => the potential energy is extremely
> high ( say, ten to the 9th order )
> I visualized the " Simulation-System-EM-solvated.gro " after the energy
> minimization.
> Then, I found that the Simulation Sysmtem is devided into 16 domains very
> clearly and the molecules (protein, ligand, and water) break into atoms in
> the boundaries.
> I have checked that the 20 ligands are not overlapped each other and are not
> overlapped with protein from the beginning.
>
>
>
> More, i have created 10 alike system and each is with "one protein + 20
> ligand + water molecules"
> Two of them get the "minus potential energy" after energy minimization and I
> can continue running the MD simulation successfully.
> Others of them get the "extreme high positive potential energy" and the
> system is devided into 16 domains after energy minimization and the
> simulation broke afterall.
>
>
>
> With one protein + 10 ligand + water molecules, ( 6 x 6 x 6 )
> There is no problems like that.
>
>
> Please give me your ideas to solve the problem.
>
> Thank you
> Lin
>
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Re: [gmx-users] get 3 roation angles over time

[Tsjerk Wassenaar]

Hi Marc,

Which rotation angles? I suppose you mean the Euler angles, but then,
XYZ, XYX, ZYZ? I may be able to help. Contact me off list if you're
interested.

Cheers,

Tsjerk

On Fri, Jan 1, 2010 at 9:02 AM,   wrote:
> Dear Gromacs users,
>
> my system consists of two rigid bodies "a" and "b". The body "a" has no 
> rotation or translation over time. Body "b" rotates and translates over time.
> For my system I got the initial structure as PDB file and a XTC trajectory.
> How do I get in any easy way from the XTC trajectory the three rotation 
> angles of the rigid body "b" over time (someting like a 3 column output file) 
> ?
>
> I already searched the gromacs mailinglist and I locked at the commands 
> "g_rms", "g_rdf", "g_sorient", "g_chi", "g_confrms", "g_bundle" and "g_rmsf".
> But it seems that non of the commands really does what I want :( .
>
> Any help is welcome, thanks and a happy new year
> Marc
>
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Re: [gmx-users] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?

[Tsjerk Wassenaar]

Hi,

So many posts and replies on a single issue, and still no exact
command lines, nor grompp output, nor gromacs version. Lin, please be
aware that such errors only make sense in the context of what you did.
You'll have to provide all information that might be related to it.
I'm pretty sure that your command lines will reveal the problem, and
otherwise the grompp output will.

If I have to make a guess, which is all one can do with the
information provided, I'd say the PBC is incorrect. Maybe you
converted to .pdb format at an intermediary step which is known to
remove the PBC in some gromacs versions.

Cheers,

Tsjerk

On Thu, Dec 31, 2009 at 2:47 AM, Mark Abraham  wrote:
> Chih-Ying Lin wrote:
>>
>>  Hi
>> what does the max max 597108032.00 (between atoms 366 and 368) mean?
>> is it the max force or max length of the system?
>> where is the max force listed?
>
> Don't know.
>
>> max 597108032.00 (between atoms 366 and 368) rms 26394490.00
>> bonds that rotated more than 30 degrees:
>> what does previous, current mean?
>> is it previous length and current length?
>
> Yeah probably. You need to understand what LINCS does to make some sense of
> this output.
>
> It doesn't really matter though. A well-behaved simulation will have none of
> these warnings. Atoms 366 and 368 are connected by a constraint and unhappy
> at the start of the simulation. In the output you quote, their distance has
> gone from under 1nm to a ridiculous number. Look at the region of those
> atoms in the starting configuration, and work out why. The most likely
> hypothesis is that some other atom is so close to them that they experienced
> a massive force, and had massive LJ.
>
> Mark
>
>> Thank you
>> Lin
>>    Step 0, time 0 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> max 597108032.00 (between atoms 366 and 368) rms 26394490.00
>> bonds that rotated more than 30 degrees:
>>  *atom 1 atom 2  angle  previous, current, constraint length
>> *     26     39   52.0    0.1530   0.1699      0.1530     39     40   69.4
>>    0.1230   0.1423      0.1230       39     41   40.7    0.1330   0.1502
>>  0.1330     75     76   36.0    0.1250   0.1252      0.1250        133
>>  134   69.5    0.1530   0.1937      0.1530
>>    134    135   89.8    0.1470   0.2036      0.1470
>>    344    346   42.4    0.1470   0.2090      0.1470
>>    346    347   42.2    0.1530   0.2141      0.1530
>>    346    359   63.9    0.1530 26006.0332      0.1530
>>    359    360   56.9    0.1230 26006.0469      0.1230
>>    359    361   83.2    0.1330 82898.5859      0.1330
>>    361    362   77.5    0.1000 82845.7109      0.1000
>>    361    363   83.8    0.1470 398710.1875      0.1470
>>    363    364   89.3    0.1530 1909291.8750      0.1530
>>    363    369   85.2    0.1530 393002.8125      0.1530
>>    364    365   90.0    0.1508 31146174.      0.1530
>>    365    366   90.2    0.1544 66925512.      0.1530
>>    366    367   92.7    0.1301 73689816.      0.1250
>>    366    368   87.0    0.1305 74638504.      0.1250
>>    369    370   72.1    0.1230 65978.3203      0.1230
>>    369    371   72.6    0.1330 66864.2812      0.1330
>>    371    372   85.7    0.1000 10685.0596      0.1000
>>    371    373   61.0    0.1470 10685.1035      0.1470      373    374
>> 33.3    0.1530   0.1896      0.1530
>>    373    377   33.5    0.1530   0.1933      0.1530
>>    547    548   90.1    0.1089   0.1358      0.1090
>>    898    900   89.9    0.1530   0.4741      0.1530
>>
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Re: [gmx-users] fix a group in truncated octahedron

[Tsjerk Wassenaar]

Wende,

This is the third time you post this exact message. Apparently, nobody
felt equipped to reply to your post, either because nobody knows the
answer, or your message and intent were not clear enough. In either
case, reposting your message over and over is completely useless and
annoying.

Please read http://catb.org/~esr/faqs/smart-questions.html

Tsjerk

On Tue, Dec 29, 2009 at 9:07 AM, lammps lammps  wrote:
> Hi GMX users,
>
> I want to fix a group in a truncate octahedron. How can I dealt with the
> question below,
> There is One spherical rigid body consists of  face-center cubic lattices
> fixed in the center of the box. I do not want to calculate the force and
> energy between the paritcles of this rigid body, so that no matter how large
> force between them shoud not blow up the rigid body.   How can I do this?
>
> Thanks in advance.
> --
> wende
>
> --
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-- 
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Medicinal Chemist
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Re: [gmx-users] convert B-factor

[Tsjerk Wassenaar]

Hi Antonio,

You can do something like:

grep -v "^#@" rmsf1.xvg > rmsf1.dat
grep -v "^#@" rmsf2.xvg > rmsf2.dat
paste rmsf1.dat rmsf2.dat | awk '{print $4-$2}' > difference.dat

That will give you a file with the rmsf difference. You can use
editconf to read such data into the b-factor field, although you may
need to modify the file a bit. Check editconf -h for that.

Hope it helps,

Tsjerk



On Mon, Dec 28, 2009 at 7:52 AM, AntonioLeung  wrote:
> I know how to calculate, and have calculated the RMSF of  two trajectories
> (of the same molecule), and I want to compare the two RMSFs. I want convert
> their
>
> discrepancy into B-factors. Can you tell me more detailed?
>
>
>
> -- Original --
> From:  "Mark Abraham";
> Date:  Mon, Dec 28, 2009 11:04 AM
> To:  "Discussion list for GROMACS users";
> Subject:  Re: [gmx-users] convert B-factor
>
> AntonioLeung wrote:
>> Dear all,
>> I want to convert the difference of two rmsf data sets into B-factor of
>> a coordinate (to illustrate their difference by coloring the structure
>> by B-factor), can anyone tell me how to do it?
>
> g_rmsf -h
>
> Mark
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-- 
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Computational Chemist
Medicinal Chemist
Neuropharmacologist
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[gmx-users] Re: Help with Gromacs

[Tsjerk Wassenaar]

Hi Pavan,

Please, I'm not a user list. This is in no way attached to the
tutorials of mine.

But your problem arises because you're mixing things up. You're using
a new run input (.tpr) file, and a checkpoint (.cpt) file. Either you
continue runs using checkpoint files (preferred) or you generate a new
.tpr file and use that, leaving the checkpoint file. This could for
instance be done because you want to change the output frequency for
some block.
The .part***. addition is added because you don't give the option
-append, that would otherwise cause the subsequent trajectory/energy
stuff be appended to already existing files. Without that option,
gromacs adds a part identifier to avoid overwriting existing files.

Cheers,

Tsjerk


On Wed, Dec 23, 2009 at 10:14 PM, Pavan Ghatty  wrote:
> Restarts are still a cause of heart-burn Tsjerk.
> I have these files at the moment:
> 1ea5.grompp4.cpt
> 1ea5.grompp4.edr
> 1ea5.grompp4.gro
> 1ea5.grompp4.log
> 1ea5.grompp4.tpr
> 1ea5.grompp4.trr
> md.mdp --> http://compbio.ornl.gov/~pkc/md.txt
> The aim for now is to generate a bunch of 5ps trajectory files that look
> like 1ea5.grompp[4-100].trr .I will then use trjcat to concatenate all the
> .trr files. From my understanding mdrun needs .tpr (only topology is read)
> and .cpt files to extend a simulation.
>
> tpbconv -s ./1ea5.grompp4.tpr -f ./1ea5.grompp4.trr -e ./1ea5.grompp4.edr -o
> ./1ea5.grompp5.tpr
>
> This gave ./1ea5.grompp5.tpr with
> nsteps   = 5000
> and such.
>
> Then,
> mdrun -v -s ./1ea5.grompp5.tpr -cpi ./1ea5.grompp4.cpt -deffnm
> ./1ea5.grompp5
> gave me,
> 1ea5.grompp5.tpr
> 1ea5.grompp5.part0002.xtc
> 1ea5.grompp5.part0002.trr
> 1ea5.grompp5.part0002.log
> 1ea5.grompp5.part0002.gro
> 1ea5.grompp5.part0002.edr
> 1ea5.grompp5.cpt
>
> I don't understand why the output of xtc/trr/log is not
> 1ea5.grompp5.(xtc/trr/log). This creates a problem with the next script
> which looks like:
> tpbconv -s ./1ea5.grompp5.tpr -f ./1ea5.grompp5.trr -e ./1ea5.grompp5.edr -o
> ./1ea5.grompp6.tpr -extend 5
> and so on. Just to see what happens I did
> tpbconv -s 1ea5.grompp5.tpr -f ./1ea5.grompp5.part002.trr -e
> ./1ea5.grompp5.part0002.edr -o ./1ea5.grompp6.tpr -extend 5
> and ran
> mdrun -v -s ./1ea5.grompp6.tpr -cpi ./1ea5.grompp5.cpt -deffnm
> ./1ea5.grompp6
>
> This gave
> 1ea5.grompp6.part0003.xtc
> 1ea5.grompp6.part0003.trr
> 1ea5.grompp6.part0003.log
> 1ea5.grompp6.part0003.gro
> 1ea5.grompp6.part0003.edr
>
> What am I doing wrong?
> g_energy -f 1ea5.grompp5.part0002.edr -o temp.xvg  [total energy] gave
>     2.00
> -834920.625000
>     3.00  -831025.187500
>     4.00  -829585.187500
>     5.00  -828792.437500
> g_energy -f 1ea5.grompp6.part0003.edr -o temp.xvg  [total energy] gave
>     5.00  -828792.50
>     6.00  -828115.00
>     7.00  -828224.312500
>     8.00  -827586.187500
>     9.00  -828065.50
>    10.00  -828509.125000
> Since the energies at step 5.000 are (almost) the same from grompp5.trr  and
> grompp6.trr, can I assume that the simulation is reliably moving forward?
> The trajectories at this time are too small to notice any jumps.
>
> Pavan
>
> On Tue, Dec 22, 2009 at 9:05 AM, Tsjerk Wassenaar  wrote:
>>
>> Hi Pavan,
>>
>> The first thing is to formulate your research question. Second you
>> have to determine which tools are best suited to investigate and
>> answer that question. Third, you have to determine how to use these
>> tools optimally to answer the question.
>> In your study you also have to consider how others have addressed the
>> same or similar issues previously and reflect on the correctness of
>> their approach.
>> That is about as specific as I can answer your question, as you
>> haven't given a formulation of your question. Aside from that, note
>> that your best option is likely to consist of several approaches
>> combined, and reflect on commonalities and differences between these.
>> In your case that would come down to performing simulations with both
>> 43a1/43a2 and 45a3. That will allow you to put the results from the
>> earlier study in scope.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Mon, Dec 21, 2009 at 3:56 PM, Pavan Ghatty 
>> wrote:
>> > Sorry I hit the send button by mistake.
>> >>
>> >> Hi Tsjerk,
>> >> I managed to run the simulation over the weekend. But the question of
>> >> forcefield kept bothering me. Especially the attached paper. The aim of
>> >> my
>> >> simulation is to see the flexibility of the aromatic residues (chi_1
&g

Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

[Tsjerk Wassenaar]

Xi Zhao,

I have no script either. It's not my homework, and I'm not on your payroll.
If I need a script like that and write it, I'll be happy to share it with
you. But that's not going to be soon. At present, I don't even have a data
set to use to develop something like it. On the other hand, if you put
effort in writing a script for it (you may want to try and learn a bit of
python), and get stuck, I'll be happy to reflect on your code, as will
others that are on this list. That is how things work here.

Cheers,

Tsjerk

On Wed, Dec 23, 2009 at 2:07 AM, xi zhao  wrote:

>
>
> Dear Mr Tsjerk Wassenaar :
> Thank you for your help!
> I only study on conformation transfromation (transformation) of protein,
> and need point to corresponding conformation in 2d projection or free energy
> landscape! I have no any script, please help me!
> Best regards!
>
> [image: 
> 4]<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>
> --- *09年12月22日，周二, Tsjerk Wassenaar * 写道：
>
>
> 发件人: Tsjerk Wassenaar 
> 主题: Re: [gmx-users] how to obtain corresponding conformation for each point
> in the 2-D projection
> 收件人: "Discussion list for GROMACS users" 
> 日期: 2009年12月22日,周二,下午7:43
>
>
> Ni hao Xi Zhao,
>
> Please note again that you're working with projections. There is not
> necessarily a single conformation that corresponds to the energy minimum
> from your projection space.
> You can obtain the minimum from the 2D projection and then find the
> conformation that yields the projection closest to that point, by taking the
> Euclidean distance between the projection and the minimum. You'll have to do
> a bit of scripting there.
>
> Cheers,
>
>
> Tsjerk
>
> On Mon, Dec 21, 2009 at 2:51 PM, xi zhao 
> http://cn.mc151.mail.yahoo.com/mc/compose?to=zhaoxiitc2...@yahoo.com.cn>
> > wrote:
>
>>   Dear Mr *Tsjerk Wassenaar ：*
>> *Thank you for your help! *
>> *what you said is reasonal, but how to *implement them, or detial
>> procedure? The 2d projections can convert to a free energy landscape, and
>> how to obtain conformation in the  minimum of energy surface?
>> best regards!
>>
>>
>> [image: 
>> 4]<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>>
>> --- *09年12月21日，周一, Tsjerk Wassenaar 
>> http://cn.mc151.mail.yahoo.com/mc/compose?to=tsje...@gmail.com>
>> >* 写道：
>>
>>
>> 发件人: Tsjerk Wassenaar 
>> http://cn.mc151.mail.yahoo.com/mc/compose?to=tsje...@gmail.com>
>> >
>> 主题: Re: [gmx-users] how to obtain corresponding conformation for each
>> point in the 2-D projection
>> 收件人: "Discussion list for GROMACS users" 
>> http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
>> >
>> 日期: 2009年12月21日,周一,下午7:57
>>
>>
>> Ni hao,
>>
>> Since it's a projection, there is not (in general) a single conformation
>> for each point in the 2D plane. On the other hand, the points you obtained
>> are derived from distinct (ordered) conformations, so it is trivial to
>> retrieve them. Each conformation (time) yields one point: find the time for
>> which the point corresponds with the one your interested in, and extract the
>> conformation from the trajectory.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> 2009/12/20 xi zhao 
>> http://cn.mc151.mail.yahoo.com/mc/compose?to=zhaoxiitc2...@yahoo.com.cn>
>> >
>>
>>>   Dear users for gromacs:
>>> We know that observing the sampled conformations in the subspace spanned
>>> by the eigenvectors is a so-called two-dimensional projection(2D
>>> projection), in 2-D projection, each point represents a snapshot from
>>> the simulation, and the distribution shows the sampled region along the
>>> first two eigenvectors during the simulation. But I feel confounded,
>>> because I do not know to how to obtain corresponding conformation for
>>> each point in the 2-D projection.Please help me!
>>> best regards!
>>> thank you!
>>>
>>>
>>> [image: 
>>> 4]<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>>> --
>>> 好玩贺卡等你发，邮箱贺卡全新上线！<http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>
>>> --
>>> gmx-users mailing list
>>> gmx-users@gromacs.org<http://cn.mc151.mail.yahoo.c

Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

[Tsjerk Wassenaar]

Ni hao Xi Zhao,

Please note again that you're working with projections. There is not
necessarily a single conformation that corresponds to the energy minimum
from your projection space.
You can obtain the minimum from the 2D projection and then find the
conformation that yields the projection closest to that point, by taking the
Euclidean distance between the projection and the minimum. You'll have to do
a bit of scripting there.

Cheers,


Tsjerk

On Mon, Dec 21, 2009 at 2:51 PM, xi zhao  wrote:

> Dear Mr *Tsjerk Wassenaar ：*
> *Thank you for your help! *
> *what you said is reasonal, but how to *implement them, or detial
> procedure? The 2d projections can convert to a free energy landscape, and
> how to obtain conformation in the  minimum of energy surface?
> best regards!
>
>
> [image: 
> 4]<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>
> --- *09年12月21日，周一, Tsjerk Wassenaar * 写道：
>
>
> 发件人: Tsjerk Wassenaar 
> 主题: Re: [gmx-users] how to obtain corresponding conformation for each point
> in the 2-D projection
> 收件人: "Discussion list for GROMACS users" 
> 日期: 2009年12月21日,周一,下午7:57
>
>
> Ni hao,
>
> Since it's a projection, there is not (in general) a single conformation
> for each point in the 2D plane. On the other hand, the points you obtained
> are derived from distinct (ordered) conformations, so it is trivial to
> retrieve them. Each conformation (time) yields one point: find the time for
> which the point corresponds with the one your interested in, and extract the
> conformation from the trajectory.
>
> Cheers,
>
> Tsjerk
>
> 2009/12/20 xi zhao 
> http://cn.mc151.mail.yahoo.com/mc/compose?to=zhaoxiitc2...@yahoo.com.cn>
> >
>
>>   Dear users for gromacs:
>> We know that observing the sampled conformations in the subspace spanned
>> by the eigenvectors is a so-called two-dimensional projection(2D
>> projection), in 2-D projection, each point represents a snapshot from
>> the simulation, and the distribution shows the sampled region along the
>> first two eigenvectors during the simulation. But I feel confounded,
>> because I do not know to how to obtain corresponding conformation for
>> each point in the 2-D projection.Please help me!
>> best regards!
>> thank you!
>>
>>
>> [image: 
>> 4]<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>> --
>> 好玩贺卡等你发，邮箱贺卡全新上线！<http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>
>> --
>> gmx-users mailing list
>> gmx-users@gromacs.org<http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/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<http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>
>> .
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
>
>
> -下面为附件内容-
>
> --
> gmx-users mailing list
> gmx-users@gromacs.org<http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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<http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>
> .
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> 好玩贺卡等你发，邮箱贺卡全新上线！<http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>
> --
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

[Tsjerk Wassenaar]

Ni hao,

Since it's a projection, there is not (in general) a single conformation for
each point in the 2D plane. On the other hand, the points you obtained are
derived from distinct (ordered) conformations, so it is trivial to retrieve
them. Each conformation (time) yields one point: find the time for which the
point corresponds with the one your interested in, and extract the
conformation from the trajectory.

Cheers,

Tsjerk

2009/12/20 xi zhao 

> Dear users for gromacs:
> We know that observing the sampled conformations in the subspace spanned
> by the eigenvectors is a so-called two-dimensional projection(2D
> projection), in 2-D projection, each point represents a snapshot from
> the simulation, and the distribution shows the sampled region along the
> first two eigenvectors during the simulation. But I feel confounded,
> because I do not know to how to obtain corresponding conformation for
> each point in the 2-D projection.Please help me!
> best regards!
> thank you!
>
>
> [image: 
> 4]
> --
> 好玩贺卡等你发，邮箱贺卡全新上线！
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] trjcat error

[Tsjerk Wassenaar]

Hi Anirban,

Check each trajectory with gmxcheck to see whether they are okay.

Cheers,

Tsjerk

On Fri, Dec 18, 2009 at 7:32 AM, Anirban Ghosh
 wrote:
> Hi ALL,
>
> I have 3 5 nano-seconds trajectory files (.trr) of a protein+lipid+water
> simulation. I am using trjcat to join them into a single .trr file for
> analysis and getting the following error:
>
> ---
> Continue writing frames from PRO_10_NS.part0003.trr t=4604 ps,
> frame=2302
>  ->  frame   3990 time 7980.000 ps ->  frame   3910 time 7820.000 ps
> ---
> Program trjcat, VERSION 4.0.5
> Source code file: trnio.c, line: 66
>
> File input/output error:
> Can not determine precision of trn file
> 
>
> What should I do? Any suggestion is welcome.
>
>
> Regards,
>
> Anirban
>
>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] g_rms (rmsd vs residue no)

[Tsjerk Wassenaar]

Hi Leila,

There is no such option. This has been discussed on the list quite
recently. You can try to be creative with index groups to get what you
want.

Cheers,

Tsjerk


On Wed, Dec 9, 2009 at 9:56 AM, leila karami  wrote:
> Hi
>
> g_rms gives us a xvg file containing rmsd vs time.
>
> I want obtain rmsd vs residue number.
>
> what option should be used with g_rms?
>
> Any help will highly appreciated!
>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
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Re: [gmx-users] minimum residue distances

[Tsjerk Wassenaar]

Hi Carla,

Please be specific with your questions, regardless of your level of
expertise and field. Are you after a program to calculate minimal
distances, which would be a Gromacs specific question? In that case
have a look at g_mdmat, g_mindist, g_dist. Also be sure to get current
on the use of make_ndx to generate index groups for specific
calculations.
There is not a formula for calculating the minimal distance between
residues. There are algorithms, but are you really interested in
those? As for the distance itself, the square root of the sum of
squares of the differences is not specific to molecular dynamics.

Cheers,

Tsjerk

On Mon, Dec 7, 2009 at 11:18 AM, Carla Jamous  wrote:
> Hi everyone,
> since i'm in beginner in molecular dynamics, I still have some trouble with
> finding the adequate formulas. Now, I'm trying to find the formula to
> calculate the minimum residue distances. I didn't find it in Gromacs manual,
> so please does anyone have an idea?
>
> Thanks
>
> Carla
>
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-- 
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Computational Chemist
Medicinal Chemist
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Re: [gmx-users] g_mindist after trjconv -fit give different results

[Tsjerk Wassenaar]

Hi Elad,

You can't count on operations that involve PBC after fitting. In your
case, you can use

trjconv -fit translation

to remove translational degrees of freedom only, keeping the system
consistent with PBC.

Hope it helps,

Tsjerk

On Sun, Dec 6, 2009 at 8:50 PM,   wrote:
> Hi Tsjerk,
> thanks for the reply.
>
> Will the MSD of the molecule also be affected by the fitting.
> I'm trying to calculate the relative diffusion coefficient of an ion near a
> protein. For this I thought to first fix the system according to the protein
> and then calculate the msd of the ion.
> I noticed in the g_msd code that periodicity is taken into account (as
> expected). However, in g_msd the interest of the periodicity handling
> regards regards the atom position relative to itself in previous frames.
> Will this relative movement (of the atom in relation to itself in the
> previous frame) be kept after doing "trjconv -fit".
>
> Thanks.
>
>>
>> Hi Elad,
>>
>> This has been mentioned several times before, in a different context.
>> But fitting only affects coordinates, and not the PBC. So after
>> fitting the coordinates and the PBC don't match any more and any
>> analysis requiring PBC, such as calculating minimal distances, will
>> give garbled results. Always do such things on untransformed
>> trajectories.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Fri, Dec 4, 2009 at 7:43 PM,   wrote:
>>>
>>> Hi all,
>>>
>>> I have a system of protein+water+ions.
>>> I measured the minimum distance between one of the ions to the protein.
>>>
>>> Afterwards I fitted the trajectory using g_trjconv -fit rot+trans
>>>
>>> Did the same mindist again and the graphs are not always identical.
>>>
>>> Any suggestions?
>>>
>>> I use gromacs 4.0.5 with an octahedron box.
>>> same problem happens when I do trjconv -fit rot but does not happen when
>>> -fit trans.
>>>
>>> In VMD I do see a difference in the position of the ion relative to the
>>> protein.
>>>
>>> Thanks.
>>> Elad P.
>>>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] g_mindist after trjconv -fit give different results

[Tsjerk Wassenaar]

Hi Elad,

This has been mentioned several times before, in a different context.
But fitting only affects coordinates, and not the PBC. So after
fitting the coordinates and the PBC don't match any more and any
analysis requiring PBC, such as calculating minimal distances, will
give garbled results. Always do such things on untransformed
trajectories.

Cheers,

Tsjerk

On Fri, Dec 4, 2009 at 7:43 PM,   wrote:
> Hi all,
>
> I have a system of protein+water+ions.
> I measured the minimum distance between one of the ions to the protein.
>
> Afterwards I fitted the trajectory using g_trjconv -fit rot+trans
>
> Did the same mindist again and the graphs are not always identical.
>
> Any suggestions?
>
> I use gromacs 4.0.5 with an octahedron box.
> same problem happens when I do trjconv -fit rot but does not happen when
> -fit trans.
>
> In VMD I do see a difference in the position of the ion relative to the
> protein.
>
> Thanks.
> Elad P.
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] Reducing Standard Error output

[Tsjerk Wassenaar]

Hi Jack,

The option -v is for verbose output.
The LINCS warnings may indicate an issue regarding the stability of
your system. They usually precede crashes. Maybe you need to
equilibrate a bit further.

Hope it helps,

Tsjerk

On Thu, Dec 3, 2009 at 1:26 PM, Jack Shultz  
wrote:
> Our first run typically produces this output
>
> Getting Loaded...
> Reading file md.tpr, VERSION 4.0.5 (single precision)
> Loaded with Money
>
> starting mdrun 'Protein in water'
> 500 steps,      1.0 ps.
>
> step 0
> step 100, remaining runtime:    95 s          Fraction complete: 0.2
>
> step 200, remaining runtime:    70 s          Fraction complete: 0.4
>
> step 300, remaining runtime:    46 s          Fraction complete: 0.6
>
> step 400, remaining runtime:    23 s          Fraction complete: 0.8
>
> Writing final coordinates.
>
> step 500, remaining runtime:     0 s          Fraction complete: 1
>
>        Parallel run - timing based on wallclock.
>
>               NODE (s)   Real (s)      (%)
>       Time:    119.000    119.000    100.0
>                       1:59
>               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
> Performance:     55.372      3.138      0.728     32.990
>
> gcq#0: Thanx for Using GROMACS - Have a Nice Day
>
>
> For our project's workflow we are extending the simulations using
> these arguments,
> -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md
>
> but I notice there is much more standard error output than I was
> expecting, in addition to a LINCS WARNING. Should I be worried about
> that warning?
> Is there a way we can turn off these error reports for each timestep?
>
> Step 785, time 1.57 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.051275, max 3.234419 (between atoms 2396 and 2397)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   2396   2397  103.7    0.0973   0.4065      0.0960
>
> Step 786, time 1.572 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.31, max 0.001926 (between atoms 2396 and 2397)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   2396   2397   69.5    0.4065   0.0962      0.0960
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: SV: SV: SV: [gmx-users] g_saltbr

[Tsjerk Wassenaar]

Hi Sarah,

You may file the bug report. You can submit a small part of the
trajectory to reproduce the error :)

Cheers,

Tsjerk

On Wed, Dec 2, 2009 at 10:11 PM, Sarah Witzke  wrote:
> Hi Tsjerk and others,
>
> This is a very good explanation! Thank you. Did you mean I should file a bug 
> report or are you doing it since you understand the code?
>
> Thank you all!
> Sarah
>
> 
>
> Fra: gmx-users-boun...@gromacs.org på vegne af Tsjerk Wassenaar
> Sendt: on 02-12-2009 19:29
> Til: jalem...@vt.edu; Discussion list for GROMACS users
> Emne: Re: SV: SV: SV: [gmx-users] g_saltbr
>
>
>
> Hi,
>
> Of course the real answer is in the code...
>
>  if (bSep) {
>    snew(buf,256);
>    for(i=0; (i      for(j=i+1; (j        if (nWithin[i][j]) {
>          sprintf(buf,"sb-%s:%s.xvg",cg[i].label,cg[j].label);
>          fp=xvgropen(buf,buf,"Time (ps)","Distance (nm)");
> ...
>
> So, a file is opened for each combination of charge(d) groups for
> which the distance is lower than the cut-off, at least once in the
> trajectory. The label is a property of the charge group, and is set
> somewhere before:
>
>      sprintf(buf,"%s%d",*(atoms->resname[resnr]),resnr+1);
>      cg[ncg].label=strdup(buf);
>
> Althogether, this just means that you have multiple charge(d) groups
> per residue, which are assigned the same label. Let's see, a phosphate
> and a choline, two residues, 2*2=4 possible salt bridges between them.
> Seems to add up, doesn't it? Probably should be considered a bug
> though. Better file it...
>
> Cheers,
>
> Tsjerk
>
> On Wed, Dec 2, 2009 at 7:10 PM, Justin A. Lemkul  wrote:
>>
>>
>> Sarah Witzke wrote:
>>
>> 
>>
>>> In each of the files are a set of distances as a function of time - it
>>> does not seem that strange, that the size is equal then.
>>> When I plot for instance the four .xvg files mentioned above I get four
>>> different curves. Also "diff" lists that every line is different.
>>>
>>> I really don't understand what I'am doing wrong.
>>
>> I don't know that you are necessarily doing anything wrong, but it's hard to
>> diagnose the potential problems without actually seeing what might be in
>> those .xvg files.  Can you post short snippets of a few of them, just to
>> demonstrate what the difference is?  I am wondering if there is so much
>> memory required, that the calculation is dumping out the resulting data
>> prematurely and therefore over-writing incomplete output files.  Just a
>> guess, but worth considering.
>>
>> -Justin
>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
>> gmx-users mailing list    gmx-us...@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
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>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
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Re: SV: SV: SV: [gmx-users] g_saltbr

[Tsjerk Wassenaar]

Hi,

Of course the real answer is in the code...

  if (bSep) {
snew(buf,256);
for(i=0; (iresname[resnr]),resnr+1);
  cg[ncg].label=strdup(buf);

Althogether, this just means that you have multiple charge(d) groups
per residue, which are assigned the same label. Let's see, a phosphate
and a choline, two residues, 2*2=4 possible salt bridges between them.
Seems to add up, doesn't it? Probably should be considered a bug
though. Better file it...

Cheers,

Tsjerk

On Wed, Dec 2, 2009 at 7:10 PM, Justin A. Lemkul  wrote:
>
>
> Sarah Witzke wrote:
>
> 
>
>> In each of the files are a set of distances as a function of time - it
>> does not seem that strange, that the size is equal then.
>> When I plot for instance the four .xvg files mentioned above I get four
>> different curves. Also "diff" lists that every line is different.
>>
>> I really don't understand what I'am doing wrong.
>
> I don't know that you are necessarily doing anything wrong, but it's hard to
> diagnose the potential problems without actually seeing what might be in
> those .xvg files.  Can you post short snippets of a few of them, just to
> demonstrate what the difference is?  I am wondering if there is so much
> memory required, that the calculation is dumping out the resulting data
> prematurely and therefore over-writing incomplete output files.  Just a
> guess, but worth considering.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] g_mindist , trajectory only CA atoms, to small values?

[Tsjerk Wassenaar]

Hi Peter,

> Instead of the pairs with the shortest distance a much further pair is 
> selected. Although the output pair from "atm-pair.out" has a distance of more 
> then 100 Angstrom the value in  the file "mindist.xvg" is smaller then one 
> Angstrom.

Periodic Boundary Conditions?

You mention in another post that removing the header solves your
'bug'. The way you express yourself indicates you haven't got a clue
what you've removed. Dangerous... Bad idea. You've probably removed a
line which started with CRYST1, preceded by a line REMARK This is a
simulation box, or something along those lines. Sure, if you remove
PBC that way, no gromacs utility will ever see that things should be
close to each other. But you're the one that's mistaken, not the
program. Don't let yourself be mislead by visualization programs.

Hope it helps,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
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Re: [gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

[Tsjerk Wassenaar]

Hi Daniel,

The problem is likely that your vesicle is interacting with itself
over the periodic boundaries. There are regions where there is no
solvent inbetween. That means that lipids can go over from one image
to the other by diffusion, which will not be compensated by using -pbc
nojump. You seem to be out of luck there.
The solution to solve this problem would be to rebuild the vesicle by
minimizing the sum of squared deviations from the center using shifts
over the lattice. But that is not implemented.

Cheers,

Tsjerk


On Tue, Dec 1, 2009 at 2:55 PM, Daniel Parton
 wrote:
> Hi,
>
> I've tried using trjconv -pbc nojump with a .tpr created from the first
> frame of the trajectory (clustered so the vesicle should be whole). The
> output trajectory starts with a complete vesicle, but small numbers of lipid
> particles progressively move to places outside of the box. By the end of the
> trajectory there appear to be 8 groups of particles outside the box, which
> have the same overall spherical shape as the vesicle, but are comprised of
> only a few hundred particles. I have uploaded some pictures here:
> http://img109.imageshack.us/g/trajenddat.jpg/
>
> traj-start is the first frame of the unprocessed trajectory:
> http://img40.imageshack.us/img40/2181/trajstartdat.jpg
>
> traj-end is the last frame of the unprocessed trajectory:
> http://img109.imageshack.us/img109/8227/trajenddat.jpg
>
> nojump-start is the first frame of the trajectory following trjconv -pbc
> nojump, as described above. The vesicle starts whole:
> http://img138.imageshack.us/img138/4531/nojumpstartdat.jpg
>
> nojump-end is the last frame of the trajectory following trjconv -pbc
> nojump. Note that some particles have moved to being outside the box,
> seeming to take up space resembling 8 copies of the vesicle system.
> http://img689.imageshack.us/img689/2821/nojumpenddat.jpg
>
> 0ns-cluster is the first frame of the trajectory, clustered using trjconv
> -pbc cluster. The pbc option may have gone a bit wrong? Particles which
> should be very close to the box boundary seem to have been moved to other
> places in or outside the box. Other parts which lie some way inside or
> outside the box appear (correctly) as part of the vesicle:
> http://img222.imageshack.us/img222/4268/0nsclusterdat.jpg
>
> So I am wondering the problem lies with the 0ns-cluster system. As some
> particles are not part of the vesicle in this representation, this could
> explain why some particles are not being counted as part of the vesicle by
> trjconv -pbc nojump. Does this seem likely, and has anyone seen similar
> behaviour to that seen in 0ns-cluster, where trjconv -pbc cluster has been
> used with a rhombic dodecahedron box?
>
> Many thanks for all of your help so far,
>
> Daniel
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

[Tsjerk Wassenaar]

Hi,

> trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster

You might want to use -dump to extract a specific frame, rather than using -e:

trjconv -f a.xtc -o a_cluster.gro -pbc cluster -dump 0

Also, do mind that for a subsequent call to trjconv, using -pbc nojump
and the extracted frame as reference structure, the difference between
the dumped frame and the first in the trajectory should not be too
large. Otherwise -pbc nojump produces garbled results.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

[Tsjerk Wassenaar]

Hi Daniel,

If the structure is correct in the coordinate file you used as input
to generate the .tpr, you can use that structure as reference to
trjconv, using -pbc nojump.

Cheers,

Tsjerk

On Mon, Nov 30, 2009 at 6:17 PM, Daniel Parton
 wrote:
> Hi,
>
> Thanks for the suggestion to use trjconv -pbc nojump. Unfortunately, it has
> not worked, as the vesicle is still not whole in the trajectory. I have
> tried subsequently centering the trajectory, and representing the system
> with -ur compact, but still it does not work. I am wondering if the problem
> lies with the initial frame. I don't understand very well the geometrical
> theories for how it is possible to represent a rhombic dodecahedron as a
> triclinic box, so I'm relying only on what I see when viewing the system
> with VMD. But looking at the first frame, it appears to be impossible for
> the vesicle to be whole in the triclinic box. After converting with trjconv
> -ur compact, the system appears as expected - the vesicle is whole and
> centered, with a shell of water around it, extending to the edges of the
> rhombic dodecahedron box.
>
> So my feeling is that although the vesicle appears to be whole when viewed
> with the compact representation, it is impossible to make the vesicle whole
> in the triclinic representation, as certain dimensions of the box are too
> small. Just as further explanation, I think that if the box:vesicle size
> ratio was larger, then it should be possible to fit the whole vesicle in the
> triclinic box. Thus trjconv -pbc nojump does not help, as the vesicle is not
> whole in the first (or any) frame. Does this make sense, and would it seem
> likely to be the problem? And if so, could there be a way around this
> problem?
>
> Regards,
>
> Daniel
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Re: [gmx-users] Problem with output structures generated by energy minimization with GROMACS 4

[Tsjerk Wassenaar]

Ni Hao,

You don't give too much information here. What exactly are you doing?
What are the commands? What's the difference between the first and the
second pass of EM? One thing to check is whether the output/input file
has a correct box definition.

Cheers,

Tsjerk

2009/11/30 HAO JIANG :
> Hi,
>
> I got a problem with the output structure files (gro/trr/xtc) generated by
> the energy minimization with GROMACS 4. That is, when I used the generated
> structure as the input for further minimizations or MD simulations, I got
> very large potential energy and forces at step 0, as if the structure had
> not been optimized at all. On the other hand, there is no problem when
> the input structure is taken from a previous MD run, and I got the expected
> potential at step 0. There is no problem, too, if I use GROMACS 3 to do the
> minimization.
>
> Any help is greatly appreciated!
>
> Hao Jiang
>
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Re: [gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

[Tsjerk Wassenaar]

Hi Daniel,

This doesn't exactly answer your question, but if your vesicle is
whole at the start, can't you better keep it that way using -pbc
nojump? If necessary, you can also recenter afterwards.

Hope it helps,

Tsjerk

On Mon, Nov 30, 2009 at 12:24 PM, Daniel Parton
 wrote:
> Hi,
>
> I am running a coarse-grained simulation of a lipid vesicle (~70,000
> particles), using a rhombic dodecahedron box to limit the amount of solvent
> I require.  The vesicle (unsurprisingly) moves over the periodic boundaries
> during the simulation.  Various analyses I am conducting require the vesicle
> to be whole, so I have been trying to use trjconv with the -pbc cluster
> option, selecting the lipids as the group to be clustered.  I am only
> interested in the lipid behaviour, so I am using a trajectory with only the
> lipids included.  However, at certain frames, the program seems to enter an
> infinite loop, producing many lines of the following sort of information:
>
> ...
> COM:   12.445     5.934    15.354  iter = 2359
> COM:   12.675     6.135     3.094  iter = 2360
> COM:   12.455     5.934    15.368  iter = 2361
> COM:   12.686     6.131     3.116  iter = 2362
> COM:   12.454     5.945    15.396  iter = 2363
> COM:   12.720     6.168     3.176  iter = 2364
> COM:   12.461     5.947    15.435  iter = 2365
> COM:   12.731     6.174     3.221  iter = 2366
> COM:   12.468     5.945    15.475  iter = 2367
> COM:   12.723     6.172     3.247  iter = 2368
> ...
>
> This is using gromacs version 3.2.1, as with any later version I have tried
> (3.3.3, 4.0.4, 4.0.5), trjconv -pbc clust  won't work at all, even with
> cubic simulation boxes.  I have successfully used version 3.2.1 many times
> for this purpose when dealing with cubic simulation boxes.
>
> I have tried many different ways to get this to work, such as converting to
> the compact representation before clustering.  Also, the frame where the
> program is the first one where a lipid has moved over a periodic boundary,
> when the system is viewed as the compact representation.  The same behaviour
> occurs when that frame is dumped out as a .gro file and the program is run
> on that file only.
>
> Does anyone have any idea how to get this to work?  Any help would be much
> appreciated!  Please let me know if you need more information about my
> simulation set-up.
>
> Daniel Parton
>
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Re: [gmx-users] g_msd => The MSD and periodic boundary condition

[Tsjerk Wassenaar]

Hi,

> Removing periodicity from the trajectory can be done after simulation
> using g_traj with the "-nojump" option.

Actually,

trjconv -pbc nojump

Cheers,

Tsjerk

>
> Best,
> Lukasz
>
> --
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> http://cwiklik.wordpress.com
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Re: [gmx-users] Unexpected behavior of g_msd

[Tsjerk Wassenaar]

Hi Darrell,

You can check whether the output is identical to a trajectory of the
specified frames...
It may well be that the counting for the regression is done on  the frames read:
100 - 60 = 40 ps
Then 4 and 35.9 would correspond to 64 and 95.9. The answer is in the
code... But using a subtrajectory may give you good hint.

Hope it helps,

Tsjerk

On Wed, Nov 25, 2009 at 7:42 AM, Darrell Koskinen  wrote:
> Dear GROMACS-ites,
> I am a little confused by the behavior of g_msd. I have a trr file with data
> points from t=0 to t=100 ps and thought that the following command would
> perform a regression for the data points between t=60 ps and t=100 ps to
> determine the diffision constant of the ammonia gas in the simualtion:
>
> *g_msd -f mdtraj.trr -s mdtopol.tpr -type x -b 60 -e 100*
>
> However, the output:
> *
> /trn version: GMX_trn_file (single precision)
> Reading frame     900 time   90.000
>
> Used 4 restart points spaced 10 ps over 39.9 ps
>
> Fitting from 4 to 35.9 ps
>
> D[       NH3] 3625.5647 (+/- 2802.0500) 1e-5 cm^2/s
> /*
> seems to indicate that the regression was performed between t=4 ps and
> t=35.9 ps.
>
> Could you please explain to me what is happening?
>
> Thanks.
>
> Darrell
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Re: [gmx-users] covariance

[Tsjerk Wassenaar]

Hi Morteza,

To me, your initial question seemed to relate to scaling/constraining
the covariances. But I also take most any opportunity to warn people
not to think too ligthly about PCA :) You can use xpm2ps to combine
the matrices and recolorize according to the range of the combined
set.

Hope it helps,

Tsjerk

2009/11/19 Morteza Khabiri :
> Dear Tsjerk
>
> Thanks for your help and reply. I thing my question was not clear.
> I want to compare  2 covariance map. but in one map the red colour shows e.g
> 1 nm^2 fluctuation and in other map the red colour shows e.g 0.5 nm^2
> fluctuation. I wanted that both map be in the same scale of colour
> intensity. I mean in both red color max range be 1 nm^2 till the
> comparison of 2 map on a basis of colour intensity be easier. I hope I
> could make my question clear.
>
>
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Re: [gmx-users] covariance

[Tsjerk Wassenaar]

Hi Morteza,

Your question suggests a lack of understanding of the principles (not
principals) of covariance analysis. It is probably best to read a bit
more on the background of this technique, until you realize what it
is, what it can do, and what it can't. There are a number of
discussions archived on the matter. I also briefly touch the topic in
the tutorial at http://nmr.chem.uu.nl/~tsjerk/course/molmod/
(analysis). But the best references to get to understand the technique
are probably from statistics. Googling will yield plenty of documents.
If you feel that I'm off with this reply, then please give a more
detailed account of what you intend to do and how you think covariance
analysis will help you achieving your aim.

Hope it helps,

Tsjerk

2009/11/19 Morteza Khabiri :
> Dear gmxuser
>
> I want to compare a dimer covariance which was already run in 2 different
> situation. The problem is that the scale of produced covariance (which
> produced by -xpma) in 2 case is different e.g the scale for one of them
> start from -0.18 to 0.05 and other -0.15 to 0.052. Is there any
> possibility to calculate covarianse in the same scale?
>
> thanks
>
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Re: [gmx-users] segmentation fault in g_anaeig

[Tsjerk Wassenaar]

Hi Nilu,

Can you paste the exact commands you entered, and indicate the
selections you made? Oh, and can you check the archives to whether
this is the same problem that was reported a few weeks ago?

Cheers,

Tsjerk

On Tue, Nov 17, 2009 at 5:53 PM, Nilu Chakrabarti
 wrote:
> I am used to do PC analysis with g_covar followed by g_anaeig.
> But recently, I am getting segmentation fault with g_anaeig.
> The g_covar gives eigenval.xvg, eigenvec.trr and average.pdb.
>
> In the next step I use those 3 files to generate -
> (1) a projection of each individual vectors on the traj using -proj OR
> (2) a set of pdbs for each vector using -extr -nframes options.
> In each case I am receiving segmentation fault without any other message
> anywhere in a file. So i have no way of figuring out where the problem is.
> I am seeing this problem with gmx v 3.3.3  as well as with v 4.0.5.
>
> I will appreciate any help and suggestions. Thanks a bunch.
>
> --
> Nilu
>
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Re: [gmx-users] pdb2gmx : treat CL as C

[Tsjerk Wassenaar]

Oops, there's an .rtp entry. Shame on me :$
Maybe a good idea though to post the output of pdb2gmx.

Cheers,

Tsjerk

On Tue, Nov 17, 2009 at 3:44 PM, Tsjerk Wassenaar  wrote:
> Justin,
>
>> What is the problem?  It looks like you got everything to work, but the .pdb
>> file you've posted is misformatted on the CL lines:
>>
>> ATOM     14  C14 PCD     1      -2.372  -1.395   0.000  1.00  0.00
>> C
>> ATOM     15 CL1  PCD     1       5.070   1.618  -0.001  1.00  0.00
>>  CL
>>
>> Note how the atom name "CL1" is shifted relative to "C14" so pdb2gmx handled
>> it incorrectly.  Formatting is not merely a suggestion!
>
> This is correct formatting, according to the PDB file format! Of the
> four character positions denoting the atom name, the first two are
> used to indicate the element.
>
> But what is this talking about pdb2gmx if there's a hand written
> .top/.itp file in stead of an .rtp entry? Of course it will fail. And
> if that's not the problem, Nilesh is still not providing a proper
> description of what he's doing.
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
>



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Re: [gmx-users] pdb2gmx : treat CL as C

[Tsjerk Wassenaar]

Justin,

> What is the problem?  It looks like you got everything to work, but the .pdb
> file you've posted is misformatted on the CL lines:
>
> ATOM     14  C14 PCD     1      -2.372  -1.395   0.000  1.00  0.00
> C
> ATOM     15 CL1  PCD     1       5.070   1.618  -0.001  1.00  0.00
>  CL
>
> Note how the atom name "CL1" is shifted relative to "C14" so pdb2gmx handled
> it incorrectly.  Formatting is not merely a suggestion!

This is correct formatting, according to the PDB file format! Of the
four character positions denoting the atom name, the first two are
used to indicate the element.

But what is this talking about pdb2gmx if there's a hand written
.top/.itp file in stead of an .rtp entry? Of course it will fail. And
if that's not the problem, Nilesh is still not providing a proper
description of what he's doing.

Tsjerk

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Re: [gmx-users] Segfaults with trjconv and g_dist

[Tsjerk Wassenaar]

Hi Ondrej,

Please paste the exact series of commands you used. That will make it
easier to indicate where errors are being introduced.

Cheers,

Tsjerk

On Mon, Nov 16, 2009 at 6:53 PM, Ondrej Marsalek
 wrote:
> Hi Tsjerk,
>
> this is the kind of problem that I was expecting, but though that it
> could be resolved by providing a custom index file that uses numbering
> that corresponds to the reduced file. This, however, does not seem to
> work for me. Even when use pass (using -n) and index file (created
> based on the reduced file) that uses only indices within the range
> present in the reduced file, it still crashes. Using wrong index file
> (with indices from the full configuration) indeed fails, but with a
> nice error message.
>
> As a side note, it would be nice to avoid segfaults in general, even
> with wrong user input.
>
> Ondrej
>
>
> On Mon, Nov 16, 2009 at 18:38, Tsjerk Wassenaar  wrote:
>> Hi Ondrej,
>>
>> This is not a bug, but arises from the inconsistency of the .tpr file
>> and the .xtc file. g_dist uses an internal index group derived from
>> the .tpr file. But that file contains more atoms than the trajectory
>> file, and some index numbers for counterions are higher than the
>> highest entry in the frame from the trajectory. Hence, you get a
>> segmentation fault. If you create an index group yourself from the
>> .tpr file, you have the same issue. To avoid it, you can create a
>> coordinate file from the .tpr matching the atoms in the .xtc file.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Mon, Nov 16, 2009 at 6:22 PM, Ondrej Marsalek
>>  wrote:
>>> Dear all,
>>>
>>> as a quick check, before I dive deeper, I would like to ask the following.
>>>
>>> I have a simulation (protein in water and counterions) for which I
>>> have defined an xtc output group (protein and conunterions). If I try
>>> to run trjconv or g_dist over this xtc file (and a proper reduced
>>> index file), I get a segmentation fault. I also get this if I filter
>>> out water from the full trr file and try to process the rest. If I use
>>> the original trr file for g_dist or trjconv, it works just fine.
>>> Before I try to resolve this, I'd like to know if anyone has
>>> encountered anything like this. Tested on 4.0.4 and 4.0.5.
>>>
>>> In case this will need a bug report - are tpr files portable, is it OK
>>> to attach one to a bug report?
>>>
>>> Thanks,
>>> Ondrej
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>>>
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> Computational Chemist
>> Medicinal Chemist
>> Neuropharmacologist
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Re: [gmx-users] Segfaults with trjconv and g_dist

[Tsjerk Wassenaar]

Hi Ondrej,

This is not a bug, but arises from the inconsistency of the .tpr file
and the .xtc file. g_dist uses an internal index group derived from
the .tpr file. But that file contains more atoms than the trajectory
file, and some index numbers for counterions are higher than the
highest entry in the frame from the trajectory. Hence, you get a
segmentation fault. If you create an index group yourself from the
.tpr file, you have the same issue. To avoid it, you can create a
coordinate file from the .tpr matching the atoms in the .xtc file.

Hope it helps,

Tsjerk

On Mon, Nov 16, 2009 at 6:22 PM, Ondrej Marsalek
 wrote:
> Dear all,
>
> as a quick check, before I dive deeper, I would like to ask the following.
>
> I have a simulation (protein in water and counterions) for which I
> have defined an xtc output group (protein and conunterions). If I try
> to run trjconv or g_dist over this xtc file (and a proper reduced
> index file), I get a segmentation fault. I also get this if I filter
> out water from the full trr file and try to process the rest. If I use
> the original trr file for g_dist or trjconv, it works just fine.
> Before I try to resolve this, I'd like to know if anyone has
> encountered anything like this. Tested on 4.0.4 and 4.0.5.
>
> In case this will need a bug report - are tpr files portable, is it OK
> to attach one to a bug report?
>
> Thanks,
> Ondrej
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Medicinal Chemist
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Re: [gmx-users] Constraints & Restraints

[Tsjerk Wassenaar]

Hi Darrell,

Constraints and restraints also apply to relative positions. A bond
constraint fixes the bond to a certain distance. constraints =
all-bonds means that all bonds are to be converted to constraints,
rather than have them flexible, e.g. harmonic. Harmonic bonds are
actually more like restraints, penalizing deviations from the
equilibrium values. These equilibrium values and the 'penalty
function' are described in the force field.

Hope it helps,

Tsjerk

On Wed, Nov 11, 2009 at 9:32 PM,   wrote:
>
> Hi,
> I just have a quick question on contraints and restraints. My
> understanding is that "constraints" fix the position of an atom in
> space and "restraints" restrain the deviation of the atom's position
> from its equilibrium point. Is that correct? If so, then I am a little
> confused by the purpose of "constraints = all-bonds" or "constraints
> = none" in an mdp file, since by selection of a force field, which has
> bond/angle/dihedral stretching/bending/torsion constants, we are
> specifying the constraints applied to the simulation. So then what is
> the purpose of "constraints = all-bonds" and "constraints = none"?
>
> Thanks.
>
> Darrell
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Medicinal Chemist
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Re: [gmx-users] pdb2gmx -missing

[Tsjerk Wassenaar]

Hi,

Well, -ignh is not the right answer here. I recall that just a few
days ago someone posted the same problem. For Amber you need to tag
the first and last residue. For your GLY, it means you have to rename
it to NGLY.

Itamar,

The warning mentions an atom missing from the .pdb file. These have to
be built according to the rules in the .hdb file. The option -ignh is
to strip off hydrogen atoms that are present in the .pdb file, but are
not listed in the .rtp file and are thus not part of the residue
according to the force field. Please make sure that your replies are
to the point, because replies that are amiss may confuse the original
poster and bring them even further from solving their problems.

Cheers,

Tsjerk

On Wed, Nov 11, 2009 at 9:16 AM, Itamar Kass  wrote:
> Hi,
>
> Try to use -ignh.
>
> On Wed, Nov 11, 2009 at 7:09 PM, leila karami  wrote:
>> I do command pdb2gmx but follow warning and error is came up:
>>
>> WARNING: atom H is missing in residue GLY 1 in the pdb file
>>  You might need to add atom H to the hydrogen database of residue
>> GLY
>>  in the file ff???.hdb (see the manual)
>>
>> Fatal error:
>> There were 1 missing atoms in molecule Protein_A, if you want to use this
>> incomplete topology anyhow, use the option -missing
>>
>> my pdb file is:
>>
>> HETATM    1  N   GLY A   1  19.949  29.046  10.462
>> HETATM    2  CA  GLY A   1  19.485  28.078   9.486
>> HETATM    3  C   GLY A   1  20.152  28.247   8.136
>> HETATM    4  O   GLY A   1  19.859  29.193   7.405
>> HETATM    5 1H   GLY A   1  20.545  29.773  10.181
>> HETATM    6 2HA  GLY A   1  19.690  27.084   9.856
>> HETATM    7 2H   GLY A   1  20.356  28.562  11.250
>> HETATM    8 3H   GLY A   1  19.099  29.546  10.681
>> HETATM    9 1HA  GLY A   1  18.415  28.236   9.347
>>
>> and my ffamber03.hdb of gly is
>>
>> GLY 2
>> 1 1 H N -C CA
>> 2 6 HA CA N C
>>
>> NGLY 2
>> 3 4 H N CA C
>> 2 6 HA CA N C
>>
>> how I add H to hdb file?
>>
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-- 
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Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] energy minimization - not converge

[Tsjerk Wassenaar]

Hi Leila,

Where does it say that you encountered an error?
You also could've checked the wiki/mailing lists for this and found
that this is normal and sufficient for starting an MD simulation.

Cheers,

Tsjerk

On Wed, Nov 11, 2009 at 9:10 AM, leila karami  wrote:
> Hi
>
> I want to do energy minimization but follow subject is came up:
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up ooo.gro to ./#ooo.gro.5#
>
> Steepest Descents did not converge to Fmax < 2000 in 101 steps.
> Potential Energy  = -3.2421097e+05
> Maximum force =  1.4766100e+04 on atom 1441
> Norm of force =  2.5146213e+02
>
> my em.mdp file is:
>
> cpp =  /usr/bin/cpp
> define  =  -DFLEX_SPC
> constraints =  none
> integrator  =  cg
> nsteps  =  100
> ;
> ; Energy minimizing stuff
> ;
> emtol   =  2000
> emstep  =  0.01
>
> nstcomm =  1
> ns_type =  grid
> rlist   =  1
> rcoulomb    =  1.0
> rvdw    =  1.0
> Tcoupl  =  no
> Pcoupl  =  no
> gen_vel =  no
>
> I changed nsteps to 1000, 2000 and 1. also I changed emtol to 500 but
> same error came up again.
> please guide me
>
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-- 
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Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] Re: Installation on Windows

[Tsjerk Wassenaar]

Hi Pawan,

It may be unintentional, but your post is rather impolite. Do mind
that the people that answer questions here have no obligation to help
you. Nobody should put any effort in making something more user
friendly, unless it is part of their job, e.g. for classes. You can
ask if somebody would have the kindness to put such effort in.

Installing under windows is usually considered awkward. The best way,
as is indicated in the pages that Mark referred to - not his tutorial
by any means -, is to install it under a *nix emulator like Cygwin.
That brings in the need to know a bit about a *nix environment. Plenty
of tutorial material for that out there, but that has nothing to do
with Gromacs per se. That should be your effort. I can understand that
it raises frustration that you can't get it to work, but at this
point, that stands apart from Gromacs. There are other fora for help
on getting started with *nix, cygwin, etc.

Cheers,

Tsjerk

On Tue, Nov 10, 2009 at 9:03 AM, pawan raghav  wrote:
> Dear,
>
> Your tutorial for windows are lacking of proper guidence. You should post
> the steps to use it to make it more user friendly.
>
> As I have tried from last two months but after installing it I really don't
> know to execute commands on windows. If you can guide me then why don't you
> not tell me the steps for using it on windows.


-- 
Tsjerk A. Wassenaar, Ph.D.

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Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] topology file in .dat format

[Tsjerk Wassenaar]

Hi Subarna,

There is no .dat format for topologies. It may be named .dat, but the
inside (format) is what matters. If you're confident it is gromos96
format, you can #include it the same way as other molecule definition
topology files. Do mind that there's quite a difference between
GROMOS96 43a1, 43a2, 45a3, 53a5 and 53a6...

Cheers,

Tsjerk

On Tue, Nov 10, 2009 at 8:30 AM, subarna thakur
 wrote:
> Hello
> I have a gromos96 topology file for a ligand and it is in xx.dat format.How
> do I include this file in my gromacs version 4.0 simulation of a protein?
>
> Subarna
>
> 
> The INTERNET now has a personality. YOURS! See your Yahoo! Homepage.
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-- 
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Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] Re: NAN in g_anaeig -proj

[Tsjerk Wassenaar]

Hi Alex,

Unfortunately I don't have time to dig into that now. It might indeed
be a bug though and you might want to consider file a bugzilla report:
http://bugzilla.gromacs.org
That will put it on the table of the developers.

Cheers,

Tsjerk


2009/10/30 alexander yakovenko :
> Hi Tsjerk!
> That is where I encountered NANs problem (except it was 10 eigenvectos, but
> for 1 NANs appears as well). I used -over option to check eigenvectors only.
>
> Now it seems for me that it is a bug and not my stupid typing mistake. What
> can really help in this case (IMHO!) is my problem in your debugger - I
> found that the problem appears even if I try to project trajectory of single
> frame gro file:
> g_anaeig_d -v sss_1000_eigenvec.trr -f sss_after_mdsi_1000.gro -s
> sss_mdsi_1000.tpr -first 1 -last 1 -n sss.ndx -proj
> so I can send you gzipped problem.
> Regards,
> Alex.
>
>
>
> Message: 6
> Date: Fri, 30 Oct 2009 12:53:28 +0100
> From: Tsjerk Wassenaar 
> Subject: Re: [gmx-users] NAN in g_anaeig -proj
> To: Discussion list for GROMACS users 
> Message-ID:
> <8ff898150910300453n550a6358sf596cff4771c9...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Alex,
>
> Sorry for not replying earlier. Still haven't had time to do checks
> myself. But have you already tried to see what happens if you only
> request projections?:
>
> g_anaeig_d -v sss_1000_eigenvec.trr -f sss_mdsi_1000.trr -s
> sss_mdsi_1000.tpr -first 1 -last 1 -n sss.ndx -proj
>
> Cheers,
>
> Tsjerk
>
> 2009/10/29 alexander yakovenko :
>> Hi all!
>> I just wonder if anyone run (know solution) into a problem trying to
>> project
>> a trajectory on the eigenvector(s) (with g_anaeig -proj ) from covariace
>> matrix.
>> All projections I have calculated are nan. However, the eigenvalues are OK
>> and the g_anaeig -comp -v2 -eig2 -over options works OK so eigenvectors
>> seems are OK  (but g_anaeig -2d fails to nan too). I am using
>> gromacs-4.0.5
>> on x86-64 CentOS5 (compiled with gcc-34).
>> Regards,
>> Alex.
>> P.S. The sequence of commands that reveals the problem is attached bellow:
>>
>> g_covar_d -f sss_mdsi_1000.trr -s sss_mdsi_1000.tpr -n sss.ndx -o
>> sss_1000_eigenval.xvg -xpm sss_1000_covar.xpm -v sss_1000_eigenvec.trr
>> -mwa
>> -l
>> ...
>> Option Filename  Type Description
>> 
>>   -f sss_mdsi_1000.trr  Input    Trajectory: xtc trr trj gro g96 pdb
>> cpt
>>   -s sss_mdsi_1000.tpr  Input    Structure+mass(db): tpr tpb tpa gro
>> g96
>>    pdb
>>   -n    sss.ndx  Input, Opt!  Index file
>>   -o sss_1000_eigenval.xvg  Output   xvgr/xmgr file
>>   -v sss_1000_eigenvec.trr  Output   Full precision trajectory: trr
>> trj
>>    cpt
>>  -av    average.pdb  Output   Structure file: gro g96 pdb
>>   -l  covar.log  Output   Log file
>> -ascii    covar.dat  Output, Opt. Generic data file
>> -xpm sss_1000_covar.xpm  Output, Opt! X PixMap compatible matrix file
>> -xpma    covara.xpm  Output, Opt. X PixMap compatible matrix file
>>
>> Option   Type   Value   Description
>> --
>> -[no]h   bool   no  Print help info and quit
>> -nice    int    19  Set the nicelevel
>> -b   time   0   First frame (ps) to read from trajectory
>> -e   time   0   Last frame (ps) to read from trajectory
>> -dt  time   0   Only use frame when t MOD dt = first time (ps)
>> -tu  enum   ps  Time unit: ps, fs, ns, us, ms or s
>> -[no]xvgr    bool   yes Add specific codes (legends etc.) in the
>> output
>>     xvg files for the xmgrace program
>> -[no]fit bool   yes Fit to a reference structure
>> -[no]ref bool   no  Use the deviation from the conformation in the
>>     structure file instead of from the average
>> -[no]mwa bool   yes Mass-weighted covariance analysis
>> -last    int    -1  Last eigenvector to write away (-1 is till the
>>     last)
>> -[no]pbc bool   yes Apply corrections for periodic boundary
>> conditions
>>
>> Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)
>> Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)
>>
>> Choose a group for the least squares fit
>> Group 0 (  System) has 31748 elements
>> ...

Re: [gmx-users] NAN in g_anaeig -proj

[Tsjerk Wassenaar]

Hi Alex,

Sorry for not replying earlier. Still haven't had time to do checks
myself. But have you already tried to see what happens if you only
request projections?:

g_anaeig_d -v sss_1000_eigenvec.trr -f sss_mdsi_1000.trr -s
sss_mdsi_1000.tpr -first 1 -last 1 -n sss.ndx -proj

Cheers,

Tsjerk

2009/10/29 alexander yakovenko :
> Hi all!
> I just wonder if anyone run (know solution) into a problem trying to project
> a trajectory on the eigenvector(s) (with g_anaeig -proj ) from covariace
> matrix.
> All projections I have calculated are nan. However, the eigenvalues are OK
> and the g_anaeig -comp -v2 -eig2 -over options works OK so eigenvectors
> seems are OK  (but g_anaeig -2d fails to nan too). I am using gromacs-4.0.5
> on x86-64 CentOS5 (compiled with gcc-34).
> Regards,
> Alex.
> P.S. The sequence of commands that reveals the problem is attached bellow:
>
> g_covar_d -f sss_mdsi_1000.trr -s sss_mdsi_1000.tpr -n sss.ndx -o
> sss_1000_eigenval.xvg -xpm sss_1000_covar.xpm -v sss_1000_eigenvec.trr -mwa
> -l
> ...
> Option Filename  Type Description
> 
>   -f sss_mdsi_1000.trr  Input    Trajectory: xtc trr trj gro g96 pdb cpt
>   -s sss_mdsi_1000.tpr  Input    Structure+mass(db): tpr tpb tpa gro g96
>    pdb
>   -n    sss.ndx  Input, Opt!  Index file
>   -o sss_1000_eigenval.xvg  Output   xvgr/xmgr file
>   -v sss_1000_eigenvec.trr  Output   Full precision trajectory: trr trj
>    cpt
>  -av    average.pdb  Output   Structure file: gro g96 pdb
>   -l  covar.log  Output   Log file
> -ascii    covar.dat  Output, Opt. Generic data file
> -xpm sss_1000_covar.xpm  Output, Opt! X PixMap compatible matrix file
> -xpma    covara.xpm  Output, Opt. X PixMap compatible matrix file
>
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -nice    int    19  Set the nicelevel
> -b   time   0   First frame (ps) to read from trajectory
> -e   time   0   Last frame (ps) to read from trajectory
> -dt  time   0   Only use frame when t MOD dt = first time (ps)
> -tu  enum   ps  Time unit: ps, fs, ns, us, ms or s
> -[no]xvgr    bool   yes Add specific codes (legends etc.) in the output
>     xvg files for the xmgrace program
> -[no]fit bool   yes Fit to a reference structure
> -[no]ref bool   no  Use the deviation from the conformation in the
>     structure file instead of from the average
> -[no]mwa bool   yes Mass-weighted covariance analysis
> -last    int    -1  Last eigenvector to write away (-1 is till the
>     last)
> -[no]pbc bool   yes Apply corrections for periodic boundary
> conditions
>
> Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)
> Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)
>
> Choose a group for the least squares fit
> Group 0 (  System) has 31748 elements
> ...
> Group    20 ( active_site) has    54 elements
> Select a group: 20
> Selected 20: 'active_site'
>
> Choose a group for the covariance analysis
> Group 0 (  System) has 31748 elements
> ...
> Group    20 ( active_site) has    54 elements
> Select a group: 20
> Selected 20: 'active_site'
> Calculating the average structure ...
> trn version: GMX_trn_file (double precision)
> Last frame   2000 time 2000.000
>
> Constructing covariance matrix (162x162) ...
> Last frame   2000 time 2000.000
> Read 2001 frames
>
> Trace of the covariance matrix: 6.22756 (u nm^2)
>
> 100%
> Diagonalizing ...
>
> Sum of the eigenvalues: 6.22756 (u nm^2)
>
> Writing eigenvalues to sss_1000_eigenval.xvg
>
> Writing reference, average structure & eigenvectors 1--162 to
> sss_1000_eigenvec.trr
>
> Wrote the log to covar.log
>
> gcq#86: "Shake Barrels Of Whisky Down My Throat" (Throwing Muses)
>
>
>
> g_anaeig_d -v sss_1000_eigenvec.trr -eig sss_1000_eigenval.xvg -v2
> sss_1000_eigenvec.trr -eig2 sss_1000_eigenval.xvg -f sss_mdsi_1000.trr -s
> sss_mdsi_1000.tpr -first 1 -last 10 -n sss.ndx -proj -over
>
> ...
>
> Option Filename  Type Description
> 
>   -v sss_1000_eigenvec.trr  Input    Full precision trajectory: trr trj
>    cpt
>  -v2 sss_1000_eigenvec.trr  Input, Opt!  Full precision trajectory: trr trj
>    cpt
>   -f sss_mdsi_1000.trr  Input, Opt!  Trajectory: xtc trr trj gro g96 pdb cpt
>   -s sss_mdsi_1000.tpr  Input, Opt!  Structure+mass(db): tpr tpb tpa gro g96
>    pdb
>   -n    sss.ndx  Input, Opt!  Index file
> -eig sss_1000_eigenval.xvg  Input, Opt!  xvgr/xmgr file
> -eig2sss_1000_eigenval.x

Re: [gmx-users] nans in g_anaeig

[Tsjerk Wassenaar]

Hi Alex,

Can you paste the actual sequence of commands you used?

Cheers,

Tsjerk

2009/10/27 alexander yakovenko :
> Hi all!
> I run into a problem trying to project trajectory on the eigenvector(s)
> (with g_anaeig -proj ) from covariace matrix - all projections are nan. The
> eigenvalues are OK, the g_anaeig -comp -v2 -eig2 -over options works OK so
> eigenvectors seems are OK  (but g_anaeig -2d fails to nan too). I am using
> gromacs-4.0.5 on x86-64 CentOS5 (compiled with gcc-34).
> What can help me to project it properly?
> Regards,
> Alex.
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Re: how to calculate g_sdf and ionic conductivity

[Tsjerk Wassenaar]

Hi IMA,

Have you checked the g_sdf help? It provides information about the
purpose of the four groups, and how they should be related. What
you're trying to do here is nonsensical. Do you know what you want to
do (physicochemically)?

Cheers,

Tsjerk

On Wed, Oct 21, 2009 at 11:15 AM, naimah haron naimah
 wrote:
> Dear Mark
> Thanks for your suggestions.
> 1) Regarding to the g_sdf, the problem is I have 3 groups ( system, cation,
> anion) in my index file.
> But, before using g_sdf, I should have 4 groups. So, how about the last
> group?
> 2) When I used g_sdf command ( g_sdf -s topol.tpr -f trj.trr -n index.ndx
> -r), it mention to select the group for 4 times. My question is, how to
> select the group?
>
> THANKS
>  IMA
>
> 
> From: "gmx-users-requ...@gromacs.org" 
> To: gmx-users@gromacs.org
> Sent: Wed, October 21, 2009 3:22:12 PM
> Subject: gmx-users Digest, Vol 66, Issue 135
>
> Send gmx-users mailing list submissions to
> gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
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> or, via email, send a message with subject or body 'help' to
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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: Re: Chloroform (CHCl3) solvent box for G53a5 forcefield
>   (Justin A. Lemkul)
>   2. why are the values of the LJ interaction energynegative and
>   the values of the Coulomb interaction energypositive between two
>   group. (Jinyao Wang)
>   3. Re: why are the values of the LJ interactionenergynegative
>   and the values of the Coulomb interaction energypositive between
>   twogroup. (Mark Abraham)
>   4. Fatal error: 2 particles communicated to PME node 0 are more
>   than a cell length out of the domain decomposition cell of their
>   charge group (wuxiao)
>   5. Re: Fatal error: 2 particles communicated to PME node0 are
>   more than a cell length out of the domain decomposition cell of
>   their charge group (Mark Abraham)
>   6. g_rdf and number of atoms to include (Enemark Soeren)
>   7. how to calculate g_sdf and ionic conductivity
>   (naimah haron naimah)
>   8. Re: how to calculate g_sdf and ionic conductivity (Mark Abraham)
>
>
> --
>
> Message: 1
> Date: Tue, 20 Oct 2009 19:18:05 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5
> forcefield
> To: Discussion list for GROMACS users 
> Message-ID: <4ade452d.6090...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Pablo Englebienne wrote:
>
>> Thanks for confirming this, Justin.
>>
>> I decided not to use the user-contributed CHCl3 box because the topology
>> is not consistent with the GROMOS atom types: the CH is united atom
>> (although the mass is 12.01100, it should probably be 13.01900?), while
>> in G53a5 there are parameters for C, H and Cl. Has someone ever used
>> this box successfully?
>>
>> I was able to equilibrate the box in NVT (100-200ps gives a stable
>> simulation), although it exploded at constant pressure. After looking at
>> some references on the mailing lists (both GMX and AMBER), I tried
>> increasing tau_p from 2.0 to 5.0 and that yielded a stable 100 ps
>> simulation, although the system later (continuing for further ~150 ps)
>> started to oscillate wildly in temperature and pressure.
>>
>> What is the effect of increasing tau_p? Besides making the dynamics
>> stable, would changing its value affect the outcome of the simulation in
>> any other way?
>
> By increasing tau_p you are reducing the stringency of the pressure
> coupling,
> i.e. allowing the system to change a bit more between coordinate scaling.
> By
> decreasing the frequency of coordinate scaling in extremis, you would lose
> the
> benefit of pressure coupling and achieve an NVT ensemble, with the box
> dimensions being essentially static.  In the case of a tau_p of 2.0 vs. 5.0,
> you
> should not have this problem.
>
> If the provided box uses a united-atom CH, I would suspect it is not
> suitable
> for GROMOS96 parameters, as you have discovered.  In all G96 variants, the H
> is
> explicitly represented.  You might consider coming up with your own box.
> Start
> with a coordinate file for one molecule, use genconf to generate a box, and
> equilibrate.
>
> If you want any further information about diagnosing the current problem,
> posting the .mdp file would be helpful.
>
> -Justin
>
>>
>> Thanks again!
>> ___
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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at ht

Re: [gmx-users] Box vector error

[Tsjerk Wassenaar]

Hi Prem,

There is just something terribly wrong with your system if it goes
flat like that. But with only the information you give here, no one
can tell you more than that.

Cheers,

Tsjerk

On Wed, Oct 21, 2009 at 10:18 AM, Prem Singh Kaushal
 wrote:
> Dear All
>
>     I am using GROMCS 3.3.1 version. I had started the simulation of protein 
> in
> water with an octahedral box of dimension 9.76276   9.20449   7.97128   
> 0.0
>  0.0   3.25425   0.0  -3.25425  4.60225. However after 25ns the
> simulation aborts with the following error:
>
> Fatal error:
> One of the box vectors has become shorter than twice the cut-off length or one
> of the box diagonal elements has become smaller than the cut-off.
> The box size at this pint is
>
> At this time point box has changed drastically with vectors,   2.61137  
> 15.10480
>  18.99570   0.0   0.0   0.2   0.0   0.2   0.3.
>
> I tried to restart simulation, going back,  from the time point where there 
> was
> no substantial change in the dimensions of the box, but simulations aborts 
> again
> after some time with the same error. The time points at which simulation 
> aborts
> are random. Having simulated for 25ns now i do not want to change the box 
> shape
> and resimulate everything again.
>
> I shall appreciate you prompt suggestions regarding this.
>
> With regards
> Prem
>
>
>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Long Simulation Time

[Tsjerk Wassenaar]

Hi Lin,

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

Cheers,

Tsjerk

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

[Tsjerk Wassenaar]

Hi,

You have to use -pbc nojump with a _suitable_ reference.

Cheers,

Tsjerk

On Sun, Oct 18, 2009 at 11:59 AM, hazizian  wrote:
> Hi again
> I use -pbc mol -ur compact but the problem still exist.
>
>
> --
> Tehran University of Medical Sciences
> www.tums.ac.ir
>
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Example file for DNA

[Tsjerk Wassenaar]

Hi,

I stripped the following from a script of mine. The original script
did some additional things before, involving first a conversion from
PDB to CNS format and later to GMX format. I rearranged it without
testing. You can try it and if you find that it doesn't do a proper
job, you can send me the before and after file.

Hope it helps (hope it works ;))

Tsjerk

###

#!/bin/bash

# RENAME RESIDUES
DNA_PDB2GMX='s/\(^.\{17\}\)DG  /\1DGUA/; s/\(^.\{17\}\)DA  /\1DADE/;
s/\(^.\{17\}\)DC  /\1DCYT/; s/\(^.\{17\}\)DT  /\1DTHY/'
RNA_PDB2GMX='s/\(^.\{17\}\) G  /\1 GUA/; s/\(^.\{17\}\) A  /\1 ADE/;
s/\(^.\{17\}\) C  /\1 CYT/; s/\(^.\{17\}\) U  /\1 URA/'

# RENAME ATOMS AND DELETHE HYDROGENS
NUCL_DELHYD="/^.\{13\}H.'/d; /^.\{13\}H7..THY/d; /^.\{12\}H5''/d"
THY_C72C5M='s/\(^.\{13\}C\)7 .THY/\15M.THY/'
NUCL_PDBS2GMX="$NUCL_DELHYD; $THY_C72C5M; s/\(^.\{12\}...\)'/\1\*/"

sed -e "{ $NUCL_PDB2GMX; $DNA_PDB2GMX; $RNA_PDB2GMX }" $1



On Sat, Oct 17, 2009 at 3:08 AM, Justin A. Lemkul  wrote:
>
>
> David Crosby wrote:
>>
>> Hello fellow GROMACS users!
>>
>> I've been having a heck of a time with the reformatting of a DNA molecule
>> into a GROMACS-compatible format.  I know that residues (bases) must be
>> renamed to DTHR, etc., though it would be endlessly helpful if someone
>> could
>> please send me an example pdb or gmx file I can use as reference.  Better
>> yet, if anyone has a nifty program that will reformat a nucleic acid model
>> into the GROMACS format, that would answer my prayers!  The duplex I'm
>> working with is only 21nt, so it's not insane to have to modify the file
>> by
>> hand...
>>
>
> A simple Perl script can make substitutions, or you can use a text editor
> like vi or a command like sed.  In about 4 commands, the whole file can be
> re-named.  In vi, for example:
>
> :1,$s/DT  /DTHY/g
>
> ...and all of your thymines are re-named (note the spacing is important).
>
> -Justin
>
>> Thanks in advance!
>> Dave Crosby
>>
>> University of California, Irvine
>> Dept of Pathology and Laboratory Medicine
>>
>> ___
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>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution

[Tsjerk Wassenaar]

Hi Simone,

The temperature coupling might be a cause for an error like that to
occur. Try to understand that coupling ions separately may cause large
fluctuations in there velocities and hence cause sudden large
displacements that may put an ion on top of a solvent molecule that
can't be settled anymore due to that.

I assume you fixed that error, but think it's good to have a bit of
background (and please read some more) to help avoiding such mistakes
later on. If the problem persists while the T-coupling error is fixed,
then there's something else wrong :) Is it always the same water
molecule, or are they always in the neighbourhood, or does the error
occur at random water molecules? Is the water molecule close to the
edge of the box when the error occurs? Since you have all frames, you
can easily check the trajectory all the way :) You may also try
running with NVT to see whether that fixes the problem. Did you
actually equilibrate the temperature first, before putting the
pressure on? O, and you might want to show your md.mdp, as that's
where the simulation is breaking.

Hope it helps,

Tsjerk

On Fri, Oct 16, 2009 at 1:49 PM, Justin A. Lemkul  wrote:
>
>
> Simone Cirri wrote:
>>
>> Justin A. Lemkul wrote:
>>
>>    ; Berendsen temperature coupling is on in three groups
>>    Tcoupl              =  berendsen
>>
>>    tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+
>>
>>    ref_t               =  300      300     300
>>
>>    Never couple solvent and ions separately. Surely grompp warned you
>>    that you should be using "Protein Non-Protein"? See here:
>>
>>    http://www.gromacs.org/Documentation/Terminology/Thermostats
>>
>>
>> Hi Justin, thanks for the suggestion. Actually, it's an error I've always
>> been doing and I'm glad I've solved it.
>> However, I'm afraid it has nothing to do with the problem, because I just
>> tried to run the MD again (after modifying the md.mdp as you told me) and
>> the fatal error is still there.
>> I've noticed the the T-coupling mistake is also in pr.mdp. Do you think
>> that correcting it and re-running the PR simulation would fix the "water
>> molecule can not be settled" problem?
>
> It's probably worth a shot.  It's not appropriate to couple solvent and ions
> separately in any phase, equilibration or data collection.
>
> -Justin
>
>> Anyway here is the pr.mdp (as it was before):
>>
>> title               =  hsacyx
>> warnings            =  10
>> cpp                 =  /lib/cpp
>> define              =  -DPOSRES
>> constraints         =  all-bonds
>> integrator          =  md
>> dt                  =  0.002    ; ps !
>> nsteps              =  10    ; total 200.0 ps.
>> nstcomm             =  1
>> nstxout             =  250
>> nstvout             =  1000
>> nstfout             =  0
>> nstlog              =  10
>> nstenergy           =  10
>> nstlist             =  10
>> ns_type             =  grid
>> rlist               =  0.9
>> coulombtype        =  PME
>> rcoulomb            =  0.9
>> rvdw                =  0.9
>> fourierspacing        =  0.12
>> fourier_nx        =  0
>> fourier_ny        =  0
>> fourier_nz        =  0
>> pme_order        =  6
>> ewald_rtol        =  1e-5
>> optimize_fft        =  yes
>> ; Berendsen temperature coupling is on in four  groups
>> Tcoupl              =  berendsen
>> tau_t               =  0.1     0.1    0.1
>> tc-grps            =  Protein     SOL    NA+
>> ref_t               =  300     300    300
>> ; Pressure coupling is on
>> Pcoupl              =  berendsen
>> pcoupltype          =  isotropic
>> tau_p               =  0.5
>> compressibility     =  4.5e-5
>> ref_p               =  1.0
>> ; Generate velocites is on at 300 K.
>> gen_vel             =  yes
>> gen_temp            =  300.0
>> gen_seed            =  173529
>>
>> Thank you
>>
>> Simone Cirri
>>
>>
>> 
>>
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>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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> Can'

Re: [gmx-users] g_hbond and hydrogen bonds involving sulfur

[Tsjerk Wassenaar]

Hi Diana,

> Well, minorities should not be disregarded just because they are poorly
> represented...In some cases a rare event makes all the difference. I think
> it would be helpeful to have the possiblity to calculate S-H...X bonds or
> X-H...S bonds with g_hbond.

In many cases these tools come about on a per-need-implementation
basis. You or any of your colleagues is most welcome to provide a
modification of g_hbond that will calculate hydrogen bonds other than
O|N-H-O|N. You can't really expect somebody to just invest time to
make your life easy, without profit for him/herself.

> We found a simple, although, not very elegant way to get around the
> question. What we did was to create a topology, for hbond calculation
> purposes only, where SG in a given cysteine was replaced by an OG. Basicaly,
> we used a sulfur disguised of oxigen, what an atom has to do to be accepted
> as one of the guys :P

This assumes that the geometrical criteria for hydrogen bonds
involving sulfur are equal to those involving oxygen and/or nitrogen.
But is that true? Sulfur is much larger and has much more
delocalization of charge. This will alter the properties of hydrogen
bonds. For instance, the hydrogen bond is much weaker, ergo has a much
shallower potential well, and will thus have a broader distribution
that might be considered 'hydrogen bond'. On the other hand, the
weakness might actually call for a stricter definition. The angle will
definitely have a broader range, because of delocalization of
electrons over the atomic surface.

It's not that easy...

But that's just my two cents.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Re: Re: Pyroglutamic Acid - Topology (pdb2gmx)

[Tsjerk Wassenaar]

Hey,

> The problem comes from the special linkage between PGL and whatever the
> subsequent amino acid is - the amide is formed through the side chain.  As
> such, you will need to specify a special bond in specbond.dat before this
> connectivity will be recognized.  If this is successful, then the PHE should
> no longer be recognized as a terminal residue and thus will not receive any
> additional protonation.

That's not correct. Pyroglutamic acid is basically a proline with an
oxy group due to formation of an intra-residue ester bond. There's no
bond between the side chain and the next amino acid.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
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