Re: [gmx-users] changing protonation state of a residue during a simulation

[Justin Lemkul]

On 5/15/13 7:14 PM, Payman Pirzadeh wrote:

Hello,
I am simulating a protein using side chain pKa values estimated from
PROPKA based on crystal structure of the protein. I re-estimated the pKa
of side chains after running 10 independent replica of 50ns (500ns in
total) of NPT simulations. It turned out that the average pKa of a
surface Glu was overestimated in the crystal structure (protonated), and
needs to be reconsidered (not protonated). I was wondering how I can
re-assign the protonation state of this single residue without going
through pdb2gmx (or may be I have to) to keep the current conformation
of the protein and currently equilibrated solvent molecules? Is there a
way to continue the current simulations I have and only change the
charge of this single surface Glu?


No, because doing so (1) isn't possible and (2) doesn't make sense.  You're not 
just changing charges, you're deleting an atom.  You have to generate a new 
topology with pdb2gmx, simple as that.  You can easily just run the whole system 
through pdb2gmx to preserve the configuration (provided you don't have any other 
weird molecules involved that pdb2gmx won't like, but you can also work around 
that easily).  Preserving the coordinates is relatively insignificant compared 
to the fact that there is no way to preserve the previous ensemble.  You can't 
change the topology and then try to continue from a previous state (i.e., 
checkpoint file), so you have to re-equilibrate anyway.


-Justin

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Department of Biochemistry
Virginia Tech
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Re: [gmx-users] g_dist problem in Implicit solvent

[Justin Lemkul]

On 5/15/13 7:15 PM, Tong Li wrote:

Hi Justin,

I really appreciate your reply! I finally solved the problem: change the 
machine…

I have no idea why this happens, the machine I run simulation on is HP Z600,
Ubuntu. The package is directly installed from the ‘Ubuntu software center’.
This system is installed one month ago, it is Ubuntu 12.10. The simulation runs
perfectly on the machine. However, after the simulation, my post processing got
the aforementioned problem. I checked a whole day but didn’t get any clue,
totally lost myself. When I was about to leave my office yesterday, I did my
last try on the HPC server from our university. It finished, without any 
problem.

I guess it is due to the automatically installation of Gromacs on my HP Z600.
Anyway, the problem is solved, even though I still have no idea why that bug
happened.

Thank you so much for your help and sorry about the annoying question I 
proposed.



It's not annoying.  On the contrary, it's very useful to know that there might 
be broken packages out there in case someone else runs into it.  For what it's 
worth, I have had problems with Ubuntu packages in the past, though my issues 
were related to pdb2gmx.  It is for this reason that, to this day, I always 
install Gromacs myself from source.


-Justin

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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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Re: [Spam:*****] [gmx-users] REMD analysis

[bharat gupta]

The plots that I showed in my last mail were for all replicas. I tried
plotting the first 500 ps of replica_index and replica_time files. I think
the plots look fine, and there could be problem with the plotting tool .
Here the link for both files ,
https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp
https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp

Now regarding the high acceptance ratio which is 0.5 , I came across a
paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have
mentioned that their average acceptance ratio ranged between 30 to 80%. I
have a question here, how did they calculate the range for the average
acceptance ratio or is it average ratio for each replica . Actually, this
is the reference I am following. I am also interested in peptide folding
simulation, similar to this article.

I want to know, whether the average acceptance ratio that I have got for my
trial simulation is correct , together with the replica_temp and
replica_remd plots. Can I proceed for large production runs to complete my
experiment ??




On Tue, May 14, 2013 at 6:34 PM, XAvier Periole  wrote:

>
> The interval between the exchange trial affect the efficiency of REMD but
> not the the exchange ratio (at least in principle).
>
> In you case I am not sure what the plot are showing! Are these showing all
> the replicas? what are the units?
>
> On May 14, 2013, at 5:07 AM, bharat gupta 
> wrote:
>
> > Dear Sir,
> >
> > Here's the result for the REMD trial with large temperature gaps.
> >
> > Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9
> 424.4
> > 447.1 471.0 496.1 522.6 550.5 579.9 610.8
> >
> > Out of md16.log :
> >
> > Replica exchange statistics
> > Repl  249 attempts, 125 odd, 124 even
> > Repl  average probabilities:
> > Repl 0123456789   10   11   12
> > 13   14   15
> > Repl  .40  .34  .38  .43  .43  .36  .45  .40  .37  .48  .47  .45  .47
> > .44  .46
> >
> > Repl  number of exchanges:
> > Repl 0123456789   10   11   12
> > 13   14   15
> > Repl   50   42   46   52   57   40   58   49   42   53   61   63   56
> > 57   58
> >
> > Repl  average number of exchanges:
> > Repl 0123456789   10   11   12
> > 13   14   15
> > Repl  .40  .34  .37  .42  .46  .32  .46  .40  .34  .43  .49  .51  .45
> > .46  .46
> > Average acceptance ratio : 0.46
> >
> > But, the repli_index.xvg and replica_temp.xvg files still shows that the
> > replicas does not exchange equally well .
> >
> > https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png
> > https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png
> >
> > what could be wrong in this case?? Is it the mdp file settings or
> implicit
> > solvent setting. Does the time to replica to exhange also affects their
> > swapping ??
> >
> >
> >
> > On Tue, May 14, 2013 at 12:24 AM, XAvier Periole 
> wrote:
> >
> >>
> >> You need to increase the temperature gaps indeed if you want acceptance
> >> ratio ~0.2/0.3. But again this won't work with the water …
> >>
> >> It is not clear what happens in your index file but probably a problem
> >> from grace to plot so many points … you can try to increase the "Max
> >> drawing path length" in the preference menu of grace.
> >>
> >> On May 13, 2013, at 4:22 PM, bharat gupta 
> >> wrote:
> >>
> >>> Dear Sir,
> >>>
> >>> I repeated the simulation again for 25 replicas with the following
> temp.
> >>> distribution .
> >>>
> >>> 280
> >>> 289.1
> >>> 298.5
> >>> 308.2
> >>> 318.2
> >>> 328.6
> >>> 339.3
> >>> 350.3
> >>> 361.7
> >>> 373.5
> >>> 385.6
> >>> 398.1
> >>> 411.1
> >>> 424.4
> >>> 438.3
> >>> 452.5
> >>> 467.2
> >>> 482.4
> >>> 498.1
> >>> 514.3
> >>> 531.0
> >>> 548.3
> >>> 566.1
> >>> 584.5
> >>> 603.5
> >>> 623.2
> >>>
> >>> The output of md.log file is :-
> >>>
> >>> Replica exchange statistics
> >>> Repl  24999 attempts, 12500 odd, 12499 even
> >>> Repl  average probabilities:
> >>> Repl 0123456789   10   11   12
> >>> 13   14   15   16   17   18   19   20   21   22   23   24   25
> >>> Repl  .63  .63  .62  .62  .61  .61  .60  .60  .59  .59  .58  .59
>  .59
> >>> .60  .60  .61  .62  .62  .63  .64  .64  .65  .65  .66  .66
> >>>
> >>> Repl  number of exchanges:
> >>> Repl 0123456789   10   11   12
> >>> 13   14   15   16   17   18   19   20   21   22   23   24   25
> >>> Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424
> 7408
> >>> 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266
> >>>
> >>> Repl  average number of exchanges:
> >>> Repl 0123456789   10   11   12
> >>> 13   14   15   16   17   18   19   20   21   22   23   24   25
> >>> Repl  .63  .62  .63  .62  .61  .61  .60  .60  .59  .59  .58  .59
>  .59
> >>> .59  .60  .60  .61  .62  .63  .63  .63  .65  .65  .66  .66
> >>>
> >>> The averag

Re: [gmx-users] changing protonation state of a residue during a simulation

[Payman Pirzadeh]

Hello,
I am simulating a protein using side chain pKa values estimated from
PROPKA based on crystal structure of the protein. I re-estimated the pKa
of side chains after running 10 independent replica of 50ns (500ns in
total) of NPT simulations. It turned out that the average pKa of a
surface Glu was overestimated in the crystal structure (protonated), and
needs to be reconsidered (not protonated). I was wondering how I can
re-assign the protonation state of this single residue without going
through pdb2gmx (or may be I have to) to keep the current conformation
of the protein and currently equilibrated solvent molecules? Is there a
way to continue the current simulations I have and only change the
charge of this single surface Glu?
Thanks for your help.

Payman   



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Re: [gmx-users] xtc2dcd conversion

[Roland Schulz]

Hi,

you can use catdcd: www.ks.uiuc.edu/Development/MDTools/catdcd/

Roland

On Wed, May 15, 2013 at 3:14 AM, James Starlight  wrote:
>
> Dear Gromacs users!
>
> I want to find possible way for the conversion of the set of the Gromacs's
> xtc trajectories to the DCD format.
>
> The only possible way that I know for such conversion is the VMD. But it's
> very routine for the big set of the XTC's inputs.
>
>
> Thanks for help,
>
>
> James
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>



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Re: [gmx-users] g_cluster warning

[Mark Abraham]

Thanks for the report Sabine.

It would be nice if the original reporters could take the extra 5 seconds
to copy-paste and report the command lines they used. There are way too
many things that they or GROMACS could be doing wrong for any of us to
spend time guessing what is going on. :-)

Mark


On Wed, May 15, 2013 at 4:54 PM, Sabine Reisser wrote:

> Hi,
>
> by looking into the code I could figure out some things.
>
>
> WARNING: rmsd minimum 0 is below lowest rmsd value 0.0247473
>
> This warning comes from the -rmsmin option which is set to 0 by default
> and which controls the structure output.
>
> The problem with tpr/gro files is that g_cluster uses mass weighted RMSD
> calculation by default and if there are no masses (as in the gro file), it
> tries to assign masses from the atom name. This lead to masses of around
> 200 for H atoms which are called HG*, the program assumed this was mercury!
>
> So I'd strongly advise everybody to use tpr files within g_cluster. It
> would also be nice to insert a warning in g_cluster if atoms other than C,
> O, N, H, S are "found".
>
> Cheers
> Sabine
>
>
>
>
> On 05/14/2013 06:06 PM, Mark Abraham wrote:
>
>> Hi,
>>
>> I don't know. I don't know how to trigger it, and nobody has said how they
>> triggered it :-)
>>
>> Mark
>> On May 14, 2013 4:45 PM, "Preeti Choudhary" <
>> preetichoudhary18111989@gmail.**com >
>> wrote:
>>
>>  should we worry about the warning ???
>>>
>>>
>>> On Tue, May 14, 2013 at 7:19 PM, Mark Abraham >>
 wrote:
 We'd need a lot more info to start to understand why .tpr vs .gro
 does/should affect the result (or not)!

 Mark
 On May 14, 2013 2:32 PM, "Sabine Reisser" 

>>> wrote:
>>>
 Hi,
>
> I'm having the same warning, would also be interested in what it means.
>
> Additionally, I get different results if I use a tpr instead of a gro
>
 file

> in the -s option, using the same trajectory with -f. The results are
> completely different, for the gro file I get 42 while for the tpr file
>
 I
>>>
 get 2 clusters.
>
> Does anybody know why this is the case?
>
> Cheers
> Sabine
>
>
>
> On 05/10/2013 04:33 PM, Preeti Choudhary wrote:
>
>  hello everyone
>>
>> I am trying to cluster my data using g_cluster.I simulated the whole
>> protein. I did the g_cluster analysis with only certain region of the
>> protein which I specified using an index file.The program runs fine
>>
> and
>>>
 gives 1 cluster.My concern is the warning it gives which states that
>>
> :-
>>>
 WARNING: rmsd minimum 0 is below lowest rmsd value 0.0247473
>>
>>
>> what exactly this warning means ???
>>
>> -thanks
>>
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[gmx-users] bending angle between 2 vectors defined by cm of groups of atoms

[battis...@libero.it]

Dear users and experts,
do you know if it is possible make the bending angle calculation in the 
following case? 

I have got three groups (G1, G2, G3) into a system.
 I have to define the center of mass of each one. I have to calculate the 
bending angle defined by vector 1 and vector 2.
vector 1:  by the center of mass of G1 to the center of mass of G2.vector 2:  
by the center of mass of G2 to the center of mass of G3

Is it possible do this calculation with gromacs?
Thank you!
Anna
 
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Re: [gmx-users] g_cluster warning

[Sabine Reisser]

Hi,

by looking into the code I could figure out some things.

WARNING: rmsd minimum 0 is below lowest rmsd value 0.0247473

This warning comes from the -rmsmin option which is set to 0 by default and 
which controls the structure output.

The problem with tpr/gro files is that g_cluster uses mass weighted RMSD 
calculation by default and if there are no masses (as in the gro file), it 
tries to assign masses from the atom name. This lead to masses of around 200 
for H atoms which are called HG*, the program assumed this was mercury!

So I'd strongly advise everybody to use tpr files within g_cluster. It would also be nice 
to insert a warning in g_cluster if atoms other than C, O, N, H, S are "found".

Cheers
Sabine



On 05/14/2013 06:06 PM, Mark Abraham wrote:

Hi,

I don't know. I don't know how to trigger it, and nobody has said how they
triggered it :-)

Mark
On May 14, 2013 4:45 PM, "Preeti Choudhary" <
preetichoudhary18111...@gmail.com> wrote:


should we worry about the warning ???


On Tue, May 14, 2013 at 7:19 PM, Mark Abraham 
wrote:
We'd need a lot more info to start to understand why .tpr vs .gro
does/should affect the result (or not)!

Mark
On May 14, 2013 2:32 PM, "Sabine Reisser" 

wrote:

Hi,

I'm having the same warning, would also be interested in what it means.

Additionally, I get different results if I use a tpr instead of a gro

file

in the -s option, using the same trajectory with -f. The results are
completely different, for the gro file I get 42 while for the tpr file

I

get 2 clusters.

Does anybody know why this is the case?

Cheers
Sabine



On 05/10/2013 04:33 PM, Preeti Choudhary wrote:


hello everyone

I am trying to cluster my data using g_cluster.I simulated the whole
protein. I did the g_cluster analysis with only certain region of the
protein which I specified using an index file.The program runs fine

and

gives 1 cluster.My concern is the warning it gives which states that

:-

WARNING: rmsd minimum 0 is below lowest rmsd value 0.0247473


what exactly this warning means ???

-thanks


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Re: [gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be

[Justin Lemkul]

On 5/15/13 7:36 AM, aixintiankong wrote:

   i want to study how ligands change the conformations using the gromacs 
software and i want to run 100ns, but i don't konw how to reasonably set the  
nstxout nstvout nstenergy nstlog and nstxtcout.


There is no universal answer.  The main considerations are disk space and time 
scale on which pertinent events occur.  grompp will warn you if you are 
producing a large amount of data, which makes the disk space problem easy to 
assess.  As for the time scale of events, you will have to think about the types 
of motions you are hoping to see and save accordingly.


-Justin

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Department of Biochemistry
Virginia Tech
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Re: [gmx-users] simulate a protein covalently binding with a organic molecule

[Justin Lemkul]

On 5/15/13 7:30 AM, aixintiankong wrote:

Dear,
 Please help me . i want to simulate a systme of the protein covalently 
bind with a organic molecule.  Part of the model is standard resides and the 
rest it is nonstandard(HETNAM) resides. The two parts covalently bind to each 
other.  i don't know how to get the topology of the model.
 wait for you help


http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue

-Justin

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[gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be

[aixintiankong]

  i want to study how ligands change the conformations using the gromacs 
software and i want to run 100ns, but i don't konw how to reasonably set the  
nstxout nstvout nstenergy nstlog and nstxtcout.
 Thank you very much!
  



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[gmx-users] simulate a protein covalently binding with a organic molecule

[aixintiankong]

Dear,
Please help me . i want to simulate a systme of the protein covalently bind 
with a organic molecule.  Part of the model is standard resides and the rest it 
is nonstandard(HETNAM) resides. The two parts covalently bind to each other.  i 
don't know how to get the topology of the model.
wait for you help 
thank you very much!






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[gmx-users] simulate a protein covalently binding with a organic molecule

[aixintiankong]

Dear,
Please help me . i want to simulate a systme of the protein covalently bind 
with a organic molecule.  Part of the model is standard resides and the rest it 
is nonstandard(HETNAM) resides. The two parts covalently bind to each other.  i 
don't know how to get the topology of the model.
wait for you help 
thank you very much!
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Re: R: Re: [gmx-users] range angle calculated by g_sgangle

[Justin Lemkul]

On 5/15/13 3:50 AM, battis...@libero.it wrote:

Dear Justin,

thanks a lot for your reply that solve completely my problem.

I would like signal that in the manual of g_sgangle there is no enough
information about the three columns of the file sg_angle.xvg; furthermore the
axis label into the file sg_angle.xvg is wrong.
I suppose that this information will be useful for other users.



I will patch the code to fix this little issue.  All that needs to be added is a 
proper legend.


-Justin

--


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


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Re: [gmx-users] g_dist problem in Implicit solvent

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 5/14/13 11:37 PM, Tong Li wrote:

Hi Justin,

Really appreciate your prompt reply! I got the inconsistence, the atom index in
the original tpr file is different with the ones in xtc result file. However, I
have no ideas what caused this… Some atoms are not in the ‘tpr’ file, but appear
in the traj file (xtc) and also in the output geometry file (gro).



This is impossible.  If atoms are not in a .tpr file, they can't be written to 
configurations and trajectories.  Have you mixed up any of your files?  Use of 
gmxcheck and gmxdump will clarify what you have in what file.


-Justin


I was using absolute implicit solvent simulation, never used any or deduct any
water molecules from the simulation system. From geometry optimization, to nvt
relaxation, then steered MD simulation in nvt assemble.

Thanks a lot for your kind help!

Cheers,

Tong

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype  = cut-off

rcoulomb = 1.2

; Relative dielectric constant for the medium and the reaction field

epsilon_r= 2

epsilon_rf   = 0

; Method for doing Van der Waals

vdw-type = cut-off

; cut-off lengths

rvdw = 1.2

; Temperature coupling is on

tcoupl   = Berendsen  ; modified Berendsen thermostat

tc-grps  = Protein Non-Protein   ; two coupling groups - more
accurate

tau_t = 0.1  0.1  ; time constant, in ps

ref_t  = 310 310 ; reference temperature, one
for each group, in K

implicit-solvent = GBSA

algorithm  = HCT

rgbradii  = 1.2

; pull code

pull= umbrella

pull_geometry   = distance

pull_dim= Y Y Y

pull_start  = yes

pull_ngroups= 1

pull_group0 = non-Protein

pull_group1 = Protein

pull_init1  = 0

pull_rate1  = -2

pull_k1 = 2000  ; kJ mol^-1 nm^-2

pull_nstxout= 100  ; every 0.2 ps

pull_nstfout= 100  ; every 0.2 ps



--


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


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R: Re: [gmx-users] range angle calculated by g_sgangle

[battis...@libero.it]

Dear Justin,

thanks a lot for your reply that solve completely my problem.

I would like signal that in the manual of g_sgangle there is no enough 
information about the three columns of the file sg_angle.xvg; furthermore the 
axis label into the file sg_angle.xvg is wrong.
I suppose that this information will be useful for other users.

Thank you!

Anna

>Messaggio originale
>Da: jalem...@vt.edu
>Data: 14/05/2013 18.08
>A: "battis...@libero.it", "Discussion list for GROMACS 
users"
>Ogg: Re: [gmx-users] range angle calculated by g_sgangle
>
>
>
>On 5/14/13 11:03 AM, battis...@libero.it wrote:
>> Dear users and experts,
>>
>> why the angle calculated by g_sgangle, that are given in degrees, are only 
in the range  (-1, 1)?
>>
>
>The format of g_sgangle is time, cos(angle), angle.  Since values of cos
(angle) 
>are within { -1, 1 } that explains what you are seeing.
>
>-Justin
>
>-- 
>
>
>Justin A. Lemkul, Ph.D.
>Research Scientist
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
>


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Re: [gmx-users] Fwd: Static compilation of gromacs

[Mirco Wahab]

On 15.05.2013 06:41, Андрей Гончар wrote:

I know, but on target machine there is a gcc compilator version 4.1, and on
gromacs site they told that this version is broken and 4.5 should used
instead. So I try to compile it on machine with 4.5 version of gcc


Андрей, if there is *no fftw3f on the target machine* and
if it's an old system which will run its old system until
thrown out, then you could do the /'tough admin'/ solution.

Contact the admin/root of the target machine and let him copy
the files that show up after:

   $> cd /usr
   $> du -a | grep lib64/libfftw3

to the same location (/usr/lib64) on the target machine. This
will most probably work fine (I did so in many cases).

Another variant: Put these files into your user directory
on the target machine (/home/andrey/fftw3) and point
LD_LIBRARY_PATH to this directory by issuing (bash):

$> LD_LIBRARY_PATH=/home/andrey/fftw3:$LD_LIBRARY_PATH  mdrun -v

Regards,

M.

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Re: [gmx-users] Fwd: Static compilation of gromacs

[Alexey Shvetsov]

В письме от 15 мая 2013 08:41:14 пользователь Андрей Гончар написал:
> I know, but on target machine there is a gcc compilator version 4.1, and on
> gromacs site they told that this version is broken and 4.5 should used
> instead. So I try to compile it on machine with 4.5 version of gcc
> 

You can build gcc on target machine for example. also to simplify build you 
can take a look a http://prefix.gentoo.org for example.

> 
> 2013/5/15 Alexey Shvetsov 
> 
> > В письме от 15 мая 2013 00:11:49 пользователь Андрей Гончар написал:
> > > Hi. I'm trying to static compile gromacs from source, everything goes
> > 
> > well,
> > 
> > > but when I
> > > move it to another machine and try to launch mdrun I got a message:
> > > 
> > > mdrun: error while loading shared libraries: libfftw3f.so.3: cannot open
> > > shared object file: No such file or directory
> > > 
> > > I run ./configure with the following options:
> > > 
> > > ./configure --prefix=$PREF --enable-all-static --with-x=no --enable-mpi
> > > --without-xml --disable-shared --with-fft=fftw3
> > > 
> > > The goal is to compile gromacs on one computer and to use it on another.
> > 
> > I
> > 
> > > haven't root privileges on another machine so I decided to make a
> > > statically linked instance of gromacs, copy it to another computer and
> > 
> > use
> > 
> > > it from my home directory.
> > 
> > You dont need root privileges to install gromacs for example in
> > ${HOME}/usr
> > also its good idea to build gromacs on target machine
> > --
> > Best Regards,
> > Alexey 'Alexxy' Shvetsov
> > Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
> > Gatchina, Russia
> > Department of Molecular and Radiation Biophysics
> > Gentoo Team Ru
> > Gentoo Linux Dev
> > mailto:alexx...@gmail.com
> > mailto:ale...@gentoo.org
> > mailto:ale...@omrb.pnpi.spb.ru
> > --
> > 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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Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, 
Gatchina, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexx...@gmail.com
mailto:ale...@gentoo.org
mailto:ale...@omrb.pnpi.spb.ru

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[gmx-users] xtc2dcd conversion

[James Starlight]

Dear Gromacs users!

I want to find possible way for the conversion of the set of the Gromacs's
xtc trajectories to the DCD format.

The only possible way that I know for such conversion is the VMD. But it's
very routine for the big set of the XTC's inputs.


Thanks for help,


James
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