[gmx-users] Re: stepsize too small ... but potential energ negative!

[Anna Marabotti]

Dear Justin,
I would like to say that you were true, but it isn't! :-(
I launched the minimization steps first changing in my em.mdp file the
emstep from 0.1 to 0.01 as you suggested, then using directly your minim.mdp
file from the lysozyme tutorial to create the .tpr:

integrator  =  steep
emtol   =  1000.0
emstep  =  0.01
nsteps  =  5
nstlist =  1
ns_type =  grid
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
rvdw=  1.0
pbc =  xyz

In both cases, the calculation stops with the same error as previous. The
log file reports a similar (infinite) value for LJ and Coulomb at the first
step, then nothing more. 
I'm convincing myself that the problem is in the protein structure, not in
the parameters I used for minimization, but I really don't know what's
wrong. Moreover, I don't understand why mdrun goes for 37 steps without
giving me any output values. It doesn't say "I cannot minimize your
structure because it's too wrong for me", it doesn't fail to minimize it
arriving at a very high force or positive potential energy: it apparently
goes for some steps, but actually it seems to do nothing. It's not only the
fact that the structure doesn't minimize that is strange, in my opinion it's
more stranger the fact that I haven't any communication about something
wrong in my structure.

Any other help will be appreciated.
Thank you very much 
Anna
--

Message: 2
Date: Mon, 24 May 2010 10:08:27 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Re: stepsize too small ... but potential
energy  negative!
To: Discussion list for GROMACS users 
Message-ID: <4bfa885b.9040...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Anna Marabotti wrote:
> Dear Justin, dear Luca,
> here's the answer to your questions:
> - I'm currently using the "classical" forcefield gromos96 43a1 (choice "0"
> in pdb2gmx). After producing the topology, the only warning I see from
> pdb2gmx is this one: WARNING: there were 0 atoms with zero occupancy and
63
> atoms with occupancy unequal to one (out of 1583 atoms). Check your pdb
> file.
> However, atoms with occupancy <1 are present also in "regular" PDB files
(if
> I remember well, also in PDB files I used previously). Is this a problem?
> -  Box: I'm currently using a cubic box and I'm setting 1 nm of distance
> between solute and box with option -d (and also center the box). Looking
at
> the system I can't see any contact between the protein and the box walls.
I
> started by setting 0.8 nm and the problem was the same.
> - .mdp file: here it is:
> cpp =
> define  =  -DFLEXIBLE
> constraints =  none
> integrator  =  steep
> nsteps  =  5
> emtol   =  1000
> emstep  =  0.1

This step size is far too large!  Try something more like 0.01.

> nstlist =  5
> ns_type =  grid
> rlist   =  1.0
> coulombtype =  PME
> rcoulomb=  1.0
> rvdw=  1.2
> fourierspacing  =  0.12
> fourier_nx  =  0
> fourier_ny  =  0
> fourier_nz  =  0
> pme_order   =  4
> ewald_rtol  =  1e-5
> optimize_fft=  yes
> Tcoupl  =  no
> Pcoupl  =  no
> gen_vel =  no
> It's very similar to the one Justin suggested in its tutorial.

...except for numerous changes.

> - PR-MD: I'not interested in skipping the minimization and continue with
MD.
> I tried to launch a PR-MD step to see if the error produced in this step
was
> more informative, and try to understand what was the problem on my
> structure. I failed, however...
> 
> I would also add that this is not the first time that I'm using an
homology
> model produced by MODELLER to perform MD. All the checks I made on my
model
> tell me that it is a good model, so I really don't understand what's wrong
> with it.
> 
> Finally, I started from the structure deprived of the first residue in
order
> to see if that residue was the "bad" one, but the problem still persists
and
> the potential energy has the same negative value with the same order of
> magnitude.
> 

Likely due to a flawed .mdp file.  The algorithm is trying to take too large
of 
a step along the potential energy surface, causing bad geometry and infinite

forces.  A bit more finesse should solve this problem.

-Justin


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[gmx-users] The components on potential energy

[abdullah ahmed]

Hello, 
 
I would like to ask for some information about the potential energy term in the 
log file after minimization. I have used the OPLS-AA forcefield to conduct 
minimization. I understand that it is the addition of a group of energy terms 
(bond energy, angle, LJ ect..) however, I do not know the individual components 
that make up potential energy term. 

Thank you in advance,
Abdullah
  
_
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[gmx-users] about PRODRG

[fancy2012]

Dear GMX users,
 When I prepare the topology file of one small molecule using PRODRG, I find 
that the generated topology file is for another molecule. The only difference 
between the two molecules is that the latter one has one more double bond. How 
should I deal with such problems? Thanks very much!
 
All the best,
qinghua
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Re: [gmx-users] Re: the output of do_dssp

[Justin A. Lemkul]

Hsin-Lin wrote:

Hi, Justin:

Thank you for your reply.
I try to select the group, 'mainchain', when prompted, and get the quantity
of coil still larger than the number of residues of my protein.


Then some other elements of your system are being detected as containing 
relevant atoms.  What happens if you run do_dssp on a single structure 
containing only your protein?



The data is the same as the output that generated by the selection, "1.
Protein".
If I select backbone, I get the fatal error: 
Failed to execute command: /Prousr/statphys/hsinlin/dssp/dsspcmbi -na
ddhIPvCe ddJ6Yv7a > /dev/null 2> /dev/null 


And I don't understand even if I can run the selection, "backbone",
successfully.


No, you can't.


According the dssp web of wiki:
http://en.wikipedia.org/wiki/DSSP_%28protein%29
the hydrogen bonds are dicided by O, C, H, and N four atoms.
How can we get dssp analysis by backbone that includes only NCCNCCNCC.?



You can't - DSSP requires the presence of the carbonyl O in order to determine 
hydrogen bonding geometry.  If you don't have a full carbonyl, the analysis fails.


-Justin


Sincerely yours,
Hsin-Lin

Hsin-Lin wrote:

Hi,

I use do_dssp to generate xvg file collect the last line to make a plot.
There are something written in this way:
--
@ s0 legend "Structure"
@ s1 legend "Coil"
@ s2 legend "Bend"
0514   1
---
My system is dimer and each peptide has 6 residue.

Then you have a problem.  Your output indicates 14 residues are in a

random

coil, so either you have more than 12 total residues, or something went

wrong

in
the dssp calculation.


And the number I choose to analyze is "1. Protein".


Perhaps this is why you had a problem.  Normally, choosing "Protein" would
cause
the calculation to hang, but maybe that is not the case any more.  See

here

for
the proper group to choose and the rationale:

http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp


Now I have a question, if I want to calculate the percentage of

secondary

structure.
In the example above, is it calculated in this way 5/12=42%?


I'd question your results first...you don't have 12 residues in your
calculation, otherwise your protein is 14/12 = 117% random coil!  Also

realize

that (by default) the "Structure" term only includes alpha helix, beta

strand,

bend, and turn.  Other structural elements are not included.  That may or
may
not be what you want, depending on the structural elements of your

protein.

-Justin


Hsin-Lin
 



--


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: stepsize too small ... but potential energ negative!

[Justin A. Lemkul]

Anna Marabotti wrote:

Dear Justin,
I would like to say that you were true, but it isn't! :-(
I launched the minimization steps first changing in my em.mdp file the
emstep from 0.1 to 0.01 as you suggested, then using directly your minim.mdp
file from the lysozyme tutorial to create the .tpr:

integrator  =  steep
emtol   =  1000.0
emstep  =  0.01
nsteps  =  5
nstlist =  1
ns_type =  grid
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
rvdw=  1.0
pbc =  xyz

In both cases, the calculation stops with the same error as previous. The
log file reports a similar (infinite) value for LJ and Coulomb at the first
step, then nothing more. 
I'm convincing myself that the problem is in the protein structure, not in

the parameters I used for minimization, but I really don't know what's
wrong. Moreover, I don't understand why mdrun goes for 37 steps without
giving me any output values. It doesn't say "I cannot minimize your
structure because it's too wrong for me", it doesn't fail to minimize it
arriving at a very high force or positive potential energy: it apparently
goes for some steps, but actually it seems to do nothing. It's not only the
fact that the structure doesn't minimize that is strange, in my opinion it's
more stranger the fact that I haven't any communication about something
wrong in my structure.



This situation is really bizarre.  Can you send me your coordinate file and 
topology (off-list) so I can have a look?  It will be much faster if I can see 
for myself what's going on.


-Justin


Any other help will be appreciated.
Thank you very much 
Anna

--

Message: 2
Date: Mon, 24 May 2010 10:08:27 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Re: stepsize too small ... but potential
energy  negative!
To: Discussion list for GROMACS users 
Message-ID: <4bfa885b.9040...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Anna Marabotti wrote:

Dear Justin, dear Luca,
here's the answer to your questions:
- I'm currently using the "classical" forcefield gromos96 43a1 (choice "0"
in pdb2gmx). After producing the topology, the only warning I see from
pdb2gmx is this one: WARNING: there were 0 atoms with zero occupancy and

63

atoms with occupancy unequal to one (out of 1583 atoms). Check your pdb
file.
However, atoms with occupancy <1 are present also in "regular" PDB files

(if

I remember well, also in PDB files I used previously). Is this a problem?
-  Box: I'm currently using a cubic box and I'm setting 1 nm of distance
between solute and box with option -d (and also center the box). Looking

at

the system I can't see any contact between the protein and the box walls.

I

started by setting 0.8 nm and the problem was the same.
- .mdp file: here it is:
cpp =
define  =  -DFLEXIBLE
constraints =  none
integrator  =  steep
nsteps  =  5
emtol   =  1000
emstep  =  0.1


This step size is far too large!  Try something more like 0.01.


nstlist =  5
ns_type =  grid
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
rvdw=  1.2
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  4
ewald_rtol  =  1e-5
optimize_fft=  yes
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no
It's very similar to the one Justin suggested in its tutorial.


...except for numerous changes.


- PR-MD: I'not interested in skipping the minimization and continue with

MD.

I tried to launch a PR-MD step to see if the error produced in this step

was

more informative, and try to understand what was the problem on my
structure. I failed, however...

I would also add that this is not the first time that I'm using an

homology

model produced by MODELLER to perform MD. All the checks I made on my

model

tell me that it is a good model, so I really don't understand what's wrong
with it.

Finally, I started from the structure deprived of the first residue in

order

to see if that residue was the "bad" one, but the problem still persists

and

the potential energy has the same negative value with the same order of
magnitude.



Likely due to a flawed .mdp file.  The algorithm is trying to take too large
of 
a step along the potential energy surface, causing bad geometry and infinite


forces.  A bit more finesse should solve this problem.

-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

Re: [gmx-users] The components on potential energy

[Justin A. Lemkul]

abdullah ahmed wrote:

Hello,
 
I would like to ask for some information about the potential energy term 
in the log file after minimization. I have used the OPLS-AA forcefield 
to conduct minimization. I understand that it is the addition of a group 
of energy terms (bond energy, angle, LJ ect..) however, I do not know 
the individual components that make up potential energy term.




Read the primary literature for the OPLS-AA force field.  The functional form 
will be described there.  Generally, you should do this before running your 
simulation to understand the mechanics of the force field, its assumptions, pros 
and cons, etc.


-Justin


Thank you in advance,
Abdullah


Hotmail: Powerful Free email with security by Microsoft. Get it now. 





--


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] The components on potential energy

[Mark Abraham]

- Original Message -
From: abdullah ahmed 
Date: Tuesday, May 25, 2010 18:36
Subject: [gmx-users] The components on potential energy
To: gmx 

> 
Hello, 
>  
> I would like to ask for some information about the potential energy term in 
> the log file after minimization. I have used the OPLS-AA forcefield to 
> conduct minimization. I understand that it is the addition of a group of 
> energy terms (bond energy, angle, LJ ect..) however, I do not know the 
> individual components that make up potential energy term. 

Your question is unclear. Some such components are listed in the .log file, 
others are available with g_energy on the .edr file. If you don't know what 
they mean, start by reading the relevant manual sections.

Mark
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Re: [gmx-users] about PRODRG

[Justin A. Lemkul]

fancy2012 wrote:

Dear GMX users,
 When I prepare the topology file of one small molecule using PRODRG, I 
find that the generated topology file is for another molecule. The only 
difference between the two molecules is that the latter one has one more 
double bond. How should I deal with such problems? Thanks very much!
 


That's very odd, but it's simple to correct the affected bonded parameters and 
atom types (if necessary) to reflect the desired molecule.


Also note:

http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/PRODRG#Tips

-Justin


All the best,
qinghua
 



--


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] about PRODRG

[Mark Abraham]

- Original Message -
From: fancy2012 
Date: Tuesday, May 25, 2010 18:43
Subject: [gmx-users] about PRODRG
To: gmx-users 

> Dear GMX users,
>  When I prepare the topology file of one small molecule using PRODRG, I find 
> that the generated topology file is for another molecule. The only difference 
> between the two molecules is that the latter one has one more double bond. 
> How should I deal with such problems? Thanks very much!

It's not possible to have such confusion with well-formed input. It sounds like 
you got the charge or number of atoms wrong, or mismatched some files.

Mark
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[gmx-users] Re: stepsize too small ... but potential energy negative!

[Anna Marabotti]

Dear Justin,
to add other elements to find a solution to this problem, I repeated all the
Gromacs procedure until minimization on the file PDB I used as template to
model my protein. pdb2gmx warns that 232 atoms have non-zero occupancy, it's
because there are sidechains with alternative conformations, but for the
rest everything is OK. When I try to launch the mdrun to minimize the
protein, however, the range checking error appears:
 
Reading file 1WBE_min.tpr, VERSION 4.0.7 (double precision)

Steepest Descents:

   Tolerance (Fmax)   =  1.0e+03

   Number of steps=5

 

---

Program mdrun_d, VERSION 4.0.7

Source code file: nsgrid.c, line: 357

 

Range checking error:

Explanation: During neighborsearching, we assign each particle to a grid

based on its coordinates. If your system contains collisions or parameter

errors that give particles very high velocities you might end up with some

coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot

put these on a grid, so this is usually where we detect those errors.

Make sure your system is properly energy-minimized and that the potential

energy seems reasonable before trying again.

 

Variable ci has value -2147483648. It should have been within [ 0 .. 1728 ]

 

So I think definitely that the problem is in the protein structure arising
from some bad coordinates in the template I used to model my protein.

I have to wait for the approval of people working on this project to send
you coordinates and topologies of my model, but since I think that the error
in the model is strictly derived from the error in this public file, I will
send you privately the coordinates and topologies of this file. Please
remember that in my model there are some atoms with occupancy <1, but the
conformation of the sidechains is unique. I corrected by hand the occupancy
on my model, re-tried to minimize it and nothing changed: the same error
occurs. On the contrary, in this case, with this template file, the mdrun
did not start at all.

 

Once again thank you very much and best regards

Anna

 

Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma, 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Email: anna.marabo...@isa.cnr.it
Skype account: annam1972
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
 
"If you think you are too small to make a difference, try sleeping with a
mosquito"
 
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[gmx-users] tpr file

[Carla Jamous]

Hi everyone,


please I have an important question:
When I continue my simulation, I do: tpbconv -s .tpr -extend-s .tpr
mdrun -v -s .tpr
-cpi .cpt -cpo .cpt -o .trr -c .gro -x .xtc -e .edr -g .log

At one point of my simulation, I had a problem, the directory that contains
all my topology and parameter files  has been deleted.

So does it affect my simulation? Does gromacs need the topology and
parameters at each step or does it stock all of these in the .tpr file?

Thank you

Carla
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Re: [gmx-users] tpr file

[Justin A. Lemkul]

Carla Jamous wrote:

Hi everyone,


please I have an important question:
When I continue my simulation, I do: tpbconv -s .tpr -extend-s .tpr
mdrun -v -s 
.tpr -cpi .cpt -cpo .cpt -o .trr -c .gro -x .xtc -e .edr -g .log


At one point of my simulation, I had a problem, the directory that 
contains all my topology and parameter files  has been deleted.


So does it affect my simulation? Does gromacs need the topology and 
parameters at each step or does it stock all of these in the .tpr file?




The .tpr file contains all the necessary coordinates, velocities, simulation 
parameters, and topology information.  There is no repetitive reading from your 
.top file.  So if you lost your .top, you can still run a simulation.  Just 
don't lose your .tpr file, too...


-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


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Re: [gmx-users] tpr file

[Mark Abraham]

- Original Message -
From: Carla Jamous 
Date: Tuesday, May 25, 2010 22:54
Subject: [gmx-users] tpr file
To: Discussion list for GROMACS users 

> Hi everyone,
> 
> 
> please I have an important question: 
> When I continue my simulation, I do: tpbconv -s .tpr -extend    -s .tpr 
>     mdrun -v -s .tpr 
> -cpi .cpt -cpo .cpt
-o .trr -c .gro -x .xtc -e .edr -g .log
> 
> At one point of my simulation, I had a problem, the directory that contains 
> all my topology and parameter files  has been deleted.
> 
> So does it affect my simulation? Does gromacs need the topology and 
> parameters at each step or does it stock all of these in the .tpr file?

By design, everything necessary for mdrun is stored directly in the .tpr file, 
its other input files, or on its command line. So your simulation is fine as it 
is, or to continue.

Make backups! :-)

Mark
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Re: [gmx-users] question about Gromacs4.0.7: parallel run

[Yi Peng]

Hi, Justin,

Thank you so much. Now it works well.

Yi

On Mon, May 24, 2010 at 7:59 PM, Justin A. Lemkul  wrote:

>
>
> Yi Peng wrote:
>
>> Hi, everyone,
>>
>> Recently our school upgraded the clusters for us. And they install the
>> Gromacs-4.0.7 for us.  Before I always used Gromacs-4.0.3, the scripts used
>> for parallel running works well.
>>
>> My script is as follows:
>>
>> #PBS -l nodes=4:ppn=2
>> #PBS -N pr-impd1-wt
>> #PBS -j oe
>> module load gromacs
>> module load openmpi-intel
>> cd $PBS_O_WORKDIR
>> NPROCS=`wc -l < $PBS_NODEFILE`
>> /usr/local/bin/pbsdcp -s pr.tpr $TMPDIR
>> cd $TMPDIR
>> mpiexec mdrun -multi $NPROCS -maxh 100 -s pr.tpr -e pr.edr -o pr.trr -g
>> pr.log -c pr.gro
>> /usr/local/bin/pbsdcp -g '*' $PBS_O_WORKDIR
>> cd $PBS_O_WORKDIR
>>
>> But today I tried to use Gromacs-4.0.7 for this. It always has the error
>> message as follows:
>> ---
>> Program mdrun, VERSION 4.0.7
>> Source code file: gmxfio.c, line: 737
>>
>> Can not open file:
>> pr7.tpr
>> ---
>>
>> "Your Bones Got a Little Machine" (Pixies)
>>
>> Error on node 7, will try to stop all the nodes
>> Halting parallel program mdrun on CPU 7 out of 8
>>
>> gcq#212: "Your Bones Got a Little Machine" (Pixies)
>>
>>
>> ---
>> Program mdrun, VERSION 4.0.7
>> Source code file: gmxfio.c, line: 737
>>
>> Can not open file:
>> pr5.tpr
>> ---
>>
>> "Your Bones Got a Little Machine" (Pixies)
>>
>>
>> gcq#212: "Your Bones Got a Little Machine" (Pixies)
>>
>> Error on node 5, will try to stop all the nodes
>> Halting parallel program mdrun on CPU 5 out of 8
>>
>> ---
>> Program mdrun, VERSION 4.0.7
>> Source code file: gmxfio.c, line: 737
>>
>> Can not open file:
>> pr4.tpr
>> ---
>>
>> "Your Bones Got a Little Machine" (Pixies)
>>
>>
>> gcq#212: "Your Bones Got a Little Machine" (Pixies)
>>
>> Error on node 4, will try to stop all the nodes
>> Halting parallel program mdrun on CPU 4 out of 8
>> --
>> MPI_ABORT was invoked on rank 6 in communicator MPI_COMM_WORLD
>> with errorcode -1.
>>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> You may or may not see output from other processes, depending on
>> exactly when Open MPI kills them.
>> --
>>
>> How can I solve this problem. Where can I add number to each input  file
>> for pr.tpr?
>>
>>
> The use of -multi implies that you have a series of .tpr files beginning
> with zero, i.e. pr0.tpr, pr1.tpr, etc.  So the input files have to be named
> as mdrun expects them to be.  The name given to the -s flag is a prefix.
>  See, for instance:
>
> http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps
>
> -Justin
>
>  Thanks!
>>
>> Yi
>>
>>
> --
> 
>
> 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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[gmx-users] coarse grain dynamics

[ram bio]

Dear Gromacs Users,

I have done coarse grain simulation for 2 peptides in bilayer for
1000ns, and now i would like to know the hydrogen bond interactions
between these two peptides. Please let me know how to do this, i can
visualize the trajectory in VMD, but unable to calculate the hydrogen
bonding distance and the hydrogen bonds existing..

Thanks

Ram
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[gmx-users] Re: stepsize too small ... but potential energy negative!

[Anna Marabotti]

Dear Justin,

you are definitely true. I tested with Gromacs 4.0.7 a couple of other
proteins that were correctly minimized with the same machine and the
previous version of Gromacs, and both of them stopped with the
neighborsearching error. Then, I found a way to switch to version 4.0.5 on
the same machine, and I minimized pretty well my model...
Now the big difficulty will be saying to the administrators of the system
that hosts my simulations that their installation is faulty...and I fear you
will not able to help me...;-)

Thank you so much for all your invaluable help and time you spent on my
problem. I also want to thank Luca Mollica for his precious support during
these days.

Best regards
Anna

-Messaggio originale-
Da: Justin A. Lemkul [mailto:jalem...@vt.edu] 
Inviato: martedì 25 maggio 2010 15.28
A: Anna Marabotti
Oggetto: Re: R: coordinates and topologies of file "stepsize too small"


Hi Anna,

I strongly suspect the installation is faulty.  I see no other explanation.

Setting a box is easy: "editconf -c -bt dodecahedron."  It may appear
"strange" 
because most visualization software defaults to a triclinic rendering, but
you 
can use "trjconv -pbc mol -ur compact" to get the correct box appearance.
In 
the case of 1WBE, I used ~2000 fewer water molecules than your original
system.

-Justin

Anna Marabotti wrote:
> Dear Justin,
> this is probably the key of my problem! GROMACS 4.0.7 has been just
> installed on the machine I'm currently using, and this is my first
> calculation using it (before, I was using version 4.0.5.). I'm not able to
> answer to your question about compilers because I'm only a user of that
> machine, but now I will try to repeat calculations using some systems that
I
> successfully used with version 4.0.5, and will see what happens, and if
the
> problem will repeat, I will contact the sysadmin to check with him the
> installation!
> Thank you very much for your help, I will keep gmx-users updated with the
> (hopefully!) end of this story!
> 
> Let me ask you just a further little question: do you use some particular
> parameters when you solvate the system in a non-cubic box? I tried
sometimes
> in the past to use the dodecahedral box, but I obtained "strange" results,
> and therefore I preferred to switch to the cubic one, although there are
> much more water molecules to manage. Have you got some suggestions?
> 
> Many thanks again and best regards
> Anna
> 
> -Messaggio originale-
> Da: Justin A. Lemkul [mailto:jalem...@vt.edu] 
> Inviato: martedì 25 maggio 2010 14.55
> A: Anna Marabotti
> Oggetto: Re: coordinates and topologies of file "stepsize too small"
> 
> 
> Hi Anna,
> 
> I must admit I'm stumped.  I was able to minimize the 1WBE structure just
> fine, 
> both in vacuo (in a 10-nm cubic box) and in solution with a counterion 
> (dodecahedral solvent box, 1.0-nm solute-box distance).  Both procedures 
> proceeded without problems, so I doubt that anything is wrong with your
> template 
> structure.
> 
> What compilers did you use to build Gromacs?  Sometimes weird results
happen
> 
> from buggy compilers, but aside from your Gromacs installation being 
> nonfunctional, I don't know what's going on.  Have you successfully worked
> with 
> other systems with this particular Gromacs installation?
> 
> -Justin
> 

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Re: [gmx-users] coarse grain dynamics

[Nuno Azoia]

Hi there!

I never worked with coarse grain simulations, but if you used a coarse
grain methodology you didn't include all the atoms, so you didn't
included hydrogens. So now you can not see them, of course. They are not
there.

If you need to "know the hydrogen bond interactions" you need to do some
"all atoms" simulation, not coarse grain.

Nuno Azoia

On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote:
> Dear Gromacs Users,
> 
> I have done coarse grain simulation for 2 peptides in bilayer for
> 1000ns, and now i would like to know the hydrogen bond interactions
> between these two peptides. Please let me know how to do this, i can
> visualize the trajectory in VMD, but unable to calculate the hydrogen
> bonding distance and the hydrogen bonds existing..
> 
> Thanks
> 
> Ram

-- 
Nuno Gonçalo Azoia Lopes
 
Laboratório de Investigação em Acabamento
Departamento de Engenharia Têxtil
Universidade do Minho
Campus de Azurém
4800-058 Guimarães
Portugal
 
Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293
 
Mobile: +351 965 382 487
E-mail: naz...@det.uminho.pt
http://nazoia.net

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Re: [gmx-users] coarse grain dynamics

[Jared James Thompson]

There are programs around for reconstruction of full-atomistic representations
from coarse-grained representations, however. I don't know if there are any
available for the GROMACS architecture.




Quoting Nuno Azoia :

> Hi there!
> 
> I never worked with coarse grain simulations, but if you used a coarse
> grain methodology you didn't include all the atoms, so you didn't
> included hydrogens. So now you can not see them, of course. They are not
> there.
> 
> If you need to "know the hydrogen bond interactions" you need to do some
> "all atoms" simulation, not coarse grain.
> 
> Nuno Azoia
> 
> On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote:
> > Dear Gromacs Users,
> > 
> > I have done coarse grain simulation for 2 peptides in bilayer for
> > 1000ns, and now i would like to know the hydrogen bond interactions
> > between these two peptides. Please let me know how to do this, i can
> > visualize the trajectory in VMD, but unable to calculate the hydrogen
> > bonding distance and the hydrogen bonds existing..
> > 
> > Thanks
> > 
> > Ram
> 
> -- 
> Nuno Gonçalo Azoia Lopes
>  
> Laboratório de Investigação em Acabamento
> Departamento de Engenharia Têxtil
> Universidade do Minho
> Campus de Azurém
> 4800-058 Guimarães
> Portugal
>  
> Tel: +351 253 510 280 - Ext: 517 289
> Fax: +351 253 510 293
>  
> Mobile: +351 965 382 487
> E-mail: naz...@det.uminho.pt
> http://nazoia.net
> 
> --
> 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
> 


-- 
Jared James Thompson
Department of Medicinal Chemistry and Molecular Pharmacology
Laboratory for Computational Drug Design and Biology
RHPH 504C
Heine Pharmacy Building
575 Stadium Mall Drive
West Lafayette, IN  47907-2091
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Re: [gmx-users] coarse grain dynamics

[Esteban Gabriel Vega Hissi]

Hi,

To change between representations (atomistic <--> coarse grained), if you
are using the MARTINI FF, you can use the modified version of Gromacs 3.3,
check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt

If you don't want to switch to full-atomistic representation, check which CG
atom types are able to form hydrogen bonds and look for interactions between
them. Obviously, this will be an approximation.


Esteban G. Vega-Hissi
UNSL
San Luis
Argentina

--
On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson
wrote:

> There are programs around for reconstruction of full-atomistic
> representations
> from coarse-grained representations, however. I don't know if there are any
> available for the GROMACS architecture.
>
>
>
>
> Quoting Nuno Azoia :
>
> > Hi there!
> >
> > I never worked with coarse grain simulations, but if you used a coarse
> > grain methodology you didn't include all the atoms, so you didn't
> > included hydrogens. So now you can not see them, of course. They are not
> > there.
> >
> > If you need to "know the hydrogen bond interactions" you need to do some
> > "all atoms" simulation, not coarse grain.
> >
> > Nuno Azoia
> >
> > On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote:
> > > Dear Gromacs Users,
> > >
> > > I have done coarse grain simulation for 2 peptides in bilayer for
> > > 1000ns, and now i would like to know the hydrogen bond interactions
> > > between these two peptides. Please let me know how to do this, i can
> > > visualize the trajectory in VMD, but unable to calculate the hydrogen
> > > bonding distance and the hydrogen bonds existing..
> > >
> > > Thanks
> > >
> > > Ram
> >
> > --
> > Nuno Gonçalo Azoia Lopes
> >
> > Laboratório de Investigação em Acabamento
> > Departamento de Engenharia Têxtil
> > Universidade do Minho
> > Campus de Azurém
> > 4800-058 Guimarães
> > Portugal
> >
> > Tel: +351 253 510 280 - Ext: 517 289
> > Fax: +351 253 510 293
> >
> > Mobile: +351 965 382 487
> > E-mail: naz...@det.uminho.pt
> > http://nazoia.net
> >
> > --
> > 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
> >
>
>
> --
> Jared James Thompson
> Department of Medicinal Chemistry and Molecular Pharmacology
> Laboratory for Computational Drug Design and Biology
> RHPH 504C
> Heine Pharmacy Building
> 575 Stadium Mall Drive
> West Lafayette, IN  47907-2091
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] coarse grain dynamics

[ram bio]

thanks,

but i am using gromacs version 4.0.07

On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi
 wrote:
> Hi,
> To change between representations (atomistic <--> coarse grained), if you
> are using the MARTINI FF, you can use the modified version of Gromacs 3.3,
> check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt
> If you don't want to switch to full-atomistic representation, check which CG
> atom types are able to form hydrogen bonds and look for interactions between
> them. Obviously, this will be an approximation.
>
> Esteban G. Vega-Hissi
> UNSL
> San Luis
> Argentina
> --
> On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson 
> wrote:
>>
>> There are programs around for reconstruction of full-atomistic
>> representations
>> from coarse-grained representations, however. I don't know if there are
>> any
>> available for the GROMACS architecture.
>>
>>
>>
>>
>> Quoting Nuno Azoia :
>>
>> > Hi there!
>> >
>> > I never worked with coarse grain simulations, but if you used a coarse
>> > grain methodology you didn't include all the atoms, so you didn't
>> > included hydrogens. So now you can not see them, of course. They are not
>> > there.
>> >
>> > If you need to "know the hydrogen bond interactions" you need to do some
>> > "all atoms" simulation, not coarse grain.
>> >
>> > Nuno Azoia
>> >
>> > On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote:
>> > > Dear Gromacs Users,
>> > >
>> > > I have done coarse grain simulation for 2 peptides in bilayer for
>> > > 1000ns, and now i would like to know the hydrogen bond interactions
>> > > between these two peptides. Please let me know how to do this, i can
>> > > visualize the trajectory in VMD, but unable to calculate the hydrogen
>> > > bonding distance and the hydrogen bonds existing..
>> > >
>> > > Thanks
>> > >
>> > > Ram
>> >
>> > --
>> > Nuno Gonçalo Azoia Lopes
>> >
>> > Laboratório de Investigação em Acabamento
>> > Departamento de Engenharia Têxtil
>> > Universidade do Minho
>> > Campus de Azurém
>> > 4800-058 Guimarães
>> > Portugal
>> >
>> > Tel: +351 253 510 280 - Ext: 517 289
>> > Fax: +351 253 510 293
>> >
>> > Mobile: +351 965 382 487
>> > E-mail: naz...@det.uminho.pt
>> > http://nazoia.net
>> >
>> > --
>> > 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!
>> > 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
>> >
>>
>>
>> --
>> Jared James Thompson
>> Department of Medicinal Chemistry and Molecular Pharmacology
>> Laboratory for Computational Drug Design and Biology
>> RHPH 504C
>> Heine Pharmacy Building
>> 575 Stadium Mall Drive
>> West Lafayette, IN  47907-2091
>> --
>> 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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>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
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Re: [gmx-users] coarse grain dynamics

[Justin A. Lemkul]

ram bio wrote:

thanks,

but i am using gromacs version 4.0.07



I think the general consensus thus far is you won't be able to do what you want 
without significant effort to reconstruct your system, and perhaps then you 
should question whether any tools that seek to build optimal hydrogens from CG 
structures are going to bias the result.  Would those hydrogen bonds have 
actually formed in an AA simulation?  Hard to tell.  If you want to analyze 
hydrogen bonds, CG approximations are not probably sufficient.


This is a good exercise in planning your analysis before conducting your 
simulation.  You can probably estimate some sort of polar contacts from your CG 
representation, but not hydrogen bonds.


-Justin


On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi
 wrote:

Hi,
To change between representations (atomistic <--> coarse grained), if you
are using the MARTINI FF, you can use the modified version of Gromacs 3.3,
check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt
If you don't want to switch to full-atomistic representation, check which CG
atom types are able to form hydrogen bonds and look for interactions between
them. Obviously, this will be an approximation.

Esteban G. Vega-Hissi
UNSL
San Luis
Argentina
--
On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson 
wrote:

There are programs around for reconstruction of full-atomistic
representations
from coarse-grained representations, however. I don't know if there are
any
available for the GROMACS architecture.




Quoting Nuno Azoia :


Hi there!

I never worked with coarse grain simulations, but if you used a coarse
grain methodology you didn't include all the atoms, so you didn't
included hydrogens. So now you can not see them, of course. They are not
there.

If you need to "know the hydrogen bond interactions" you need to do some
"all atoms" simulation, not coarse grain.

Nuno Azoia

On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote:

Dear Gromacs Users,

I have done coarse grain simulation for 2 peptides in bilayer for
1000ns, and now i would like to know the hydrogen bond interactions
between these two peptides. Please let me know how to do this, i can
visualize the trajectory in VMD, but unable to calculate the hydrogen
bonding distance and the hydrogen bonds existing..

Thanks

Ram

--
Nuno Gonçalo Azoia Lopes

Laboratório de Investigação em Acabamento
Departamento de Engenharia Têxtil
Universidade do Minho
Campus de Azurém
4800-058 Guimarães
Portugal

Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293

Mobile: +351 965 382 487
E-mail: naz...@det.uminho.pt
http://nazoia.net

--
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--
Jared James Thompson
Department of Medicinal Chemistry and Molecular Pharmacology
Laboratory for Computational Drug Design and Biology
RHPH 504C
Heine Pharmacy Building
575 Stadium Mall Drive
West Lafayette, IN  47907-2091
--
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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] coarse grain dynamics

[Jared James Thompson]

I agree with Justin on this one. Simulations run using CG that is not optimized
for reconstruction may not actually reflect the type of interactions you are
looking for. The current result of this simulation may not directly correspond
to a full atomistic result, so even if a reconstruction were performed you would
most likely NOT be able to draw conclusions from it. 

Otherwise, everyone would run really fast simulations in CG, then reconstruct
their systems afterward. :)



Quoting "Justin A. Lemkul" :

> 
> 
> ram bio wrote:
> > thanks,
> > 
> > but i am using gromacs version 4.0.07
> > 
> 
> I think the general consensus thus far is you won't be able to do what you
> want 
> without significant effort to reconstruct your system, and perhaps then you 
> should question whether any tools that seek to build optimal hydrogens from
> CG 
> structures are going to bias the result.  Would those hydrogen bonds have 
> actually formed in an AA simulation?  Hard to tell.  If you want to analyze 
> hydrogen bonds, CG approximations are not probably sufficient.
> 
> This is a good exercise in planning your analysis before conducting your 
> simulation.  You can probably estimate some sort of polar contacts from your
> CG 
> representation, but not hydrogen bonds.
> 
> -Justin
> 
> > On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi
> >  wrote:
> >> Hi,
> >> To change between representations (atomistic <--> coarse grained), if you
> >> are using the MARTINI FF, you can use the modified version of Gromacs
> 3.3,
> >> check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt
> >> If you don't want to switch to full-atomistic representation, check which
> CG
> >> atom types are able to form hydrogen bonds and look for interactions
> between
> >> them. Obviously, this will be an approximation.
> >>
> >> Esteban G. Vega-Hissi
> >> UNSL
> >> San Luis
> >> Argentina
> >> --
> >> On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson
> 
> >> wrote:
> >>> There are programs around for reconstruction of full-atomistic
> >>> representations
> >>> from coarse-grained representations, however. I don't know if there are
> >>> any
> >>> available for the GROMACS architecture.
> >>>
> >>>
> >>>
> >>>
> >>> Quoting Nuno Azoia :
> >>>
>  Hi there!
> 
>  I never worked with coarse grain simulations, but if you used a coarse
>  grain methodology you didn't include all the atoms, so you didn't
>  included hydrogens. So now you can not see them, of course. They are
> not
>  there.
> 
>  If you need to "know the hydrogen bond interactions" you need to do
> some
>  "all atoms" simulation, not coarse grain.
> 
>  Nuno Azoia
> 
>  On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote:
> > Dear Gromacs Users,
> >
> > I have done coarse grain simulation for 2 peptides in bilayer for
> > 1000ns, and now i would like to know the hydrogen bond interactions
> > between these two peptides. Please let me know how to do this, i can
> > visualize the trajectory in VMD, but unable to calculate the hydrogen
> > bonding distance and the hydrogen bonds existing..
> >
> > Thanks
> >
> > Ram
>  --
>  Nuno Gonçalo Azoia Lopes
> 
>  Laboratório de Investigação em Acabamento
>  Departamento de Engenharia Têxtil
>  Universidade do Minho
>  Campus de Azurém
>  4800-058 Guimarães
>  Portugal
> 
>  Tel: +351 253 510 280 - Ext: 517 289
>  Fax: +351 253 510 293
> 
>  Mobile: +351 965 382 487
>  E-mail: naz...@det.uminho.pt
>  http://nazoia.net
> 
>  --
>  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
> 
> >>>
> >>> --
> >>> Jared James Thompson
> >>> Department of Medicinal Chemistry and Molecular Pharmacology
> >>> Laboratory for Computational Drug Design and Biology
> >>> RHPH 504C
> >>> Heine Pharmacy Building
> >>> 575 Stadium Mall Drive
> >>> West Lafayette, IN  47907-2091
> >>> --
> >>> 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
> >>
> >> --
> >> 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 

Re: [gmx-users] coarse grain dynamics

[ram bio]

Thanks for the comments and info, but is there any way to take a
particular  frame for eg. the last frame  of CG simulation and extend
the run into all-atom simulation further ...

On Tue, May 25, 2010 at 5:32 PM, Jared James Thompson
 wrote:
> I agree with Justin on this one. Simulations run using CG that is not 
> optimized
> for reconstruction may not actually reflect the type of interactions you are
> looking for. The current result of this simulation may not directly correspond
> to a full atomistic result, so even if a reconstruction were performed you 
> would
> most likely NOT be able to draw conclusions from it.
>
> Otherwise, everyone would run really fast simulations in CG, then reconstruct
> their systems afterward. :)
>
>
>
> Quoting "Justin A. Lemkul" :
>
>>
>>
>> ram bio wrote:
>> > thanks,
>> >
>> > but i am using gromacs version 4.0.07
>> >
>>
>> I think the general consensus thus far is you won't be able to do what you
>> want
>> without significant effort to reconstruct your system, and perhaps then you
>> should question whether any tools that seek to build optimal hydrogens from
>> CG
>> structures are going to bias the result.  Would those hydrogen bonds have
>> actually formed in an AA simulation?  Hard to tell.  If you want to analyze
>> hydrogen bonds, CG approximations are not probably sufficient.
>>
>> This is a good exercise in planning your analysis before conducting your
>> simulation.  You can probably estimate some sort of polar contacts from your
>> CG
>> representation, but not hydrogen bonds.
>>
>> -Justin
>>
>> > On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi
>> >  wrote:
>> >> Hi,
>> >> To change between representations (atomistic <--> coarse grained), if you
>> >> are using the MARTINI FF, you can use the modified version of Gromacs
>> 3.3,
>> >> check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt
>> >> If you don't want to switch to full-atomistic representation, check which
>> CG
>> >> atom types are able to form hydrogen bonds and look for interactions
>> between
>> >> them. Obviously, this will be an approximation.
>> >>
>> >> Esteban G. Vega-Hissi
>> >> UNSL
>> >> San Luis
>> >> Argentina
>> >> --
>> >> On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson
>> 
>> >> wrote:
>> >>> There are programs around for reconstruction of full-atomistic
>> >>> representations
>> >>> from coarse-grained representations, however. I don't know if there are
>> >>> any
>> >>> available for the GROMACS architecture.
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> Quoting Nuno Azoia :
>> >>>
>>  Hi there!
>> 
>>  I never worked with coarse grain simulations, but if you used a coarse
>>  grain methodology you didn't include all the atoms, so you didn't
>>  included hydrogens. So now you can not see them, of course. They are
>> not
>>  there.
>> 
>>  If you need to "know the hydrogen bond interactions" you need to do
>> some
>>  "all atoms" simulation, not coarse grain.
>> 
>>  Nuno Azoia
>> 
>>  On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote:
>> > Dear Gromacs Users,
>> >
>> > I have done coarse grain simulation for 2 peptides in bilayer for
>> > 1000ns, and now i would like to know the hydrogen bond interactions
>> > between these two peptides. Please let me know how to do this, i can
>> > visualize the trajectory in VMD, but unable to calculate the hydrogen
>> > bonding distance and the hydrogen bonds existing..
>> >
>> > Thanks
>> >
>> > Ram
>>  --
>>  Nuno Gonçalo Azoia Lopes
>> 
>>  Laboratório de Investigação em Acabamento
>>  Departamento de Engenharia Têxtil
>>  Universidade do Minho
>>  Campus de Azurém
>>  4800-058 Guimarães
>>  Portugal
>> 
>>  Tel: +351 253 510 280 - Ext: 517 289
>>  Fax: +351 253 510 293
>> 
>>  Mobile: +351 965 382 487
>>  E-mail: naz...@det.uminho.pt
>>  http://nazoia.net
>> 
>>  --
>>  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!
>>  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
>> 
>> >>>
>> >>> --
>> >>> Jared James Thompson
>> >>> Department of Medicinal Chemistry and Molecular Pharmacology
>> >>> Laboratory for Computational Drug Design and Biology
>> >>> RHPH 504C
>> >>> Heine Pharmacy Building
>> >>> 575 Stadium Mall Drive
>> >>> West Lafayette, IN  47907-2091
>> >>> --
>> >>> 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!
>> >>> Please don't post (un)subscribe requests to the list. Use the
>> >>> www inter

Re: [gmx-users] about PRODRG

[Lucio Ricardo Montero Valenzuela]

Try specifying manually the hybridization of the heavy atoms and the
protonation.
Best regards.

Lucio Montero.
Laboratorio del Dr. Federico Sánchez
Ext. 27666
Departamento de Biología Molecular de Plantas
Instituto de Biotecnología, UNAM
Cuernavaca, Morelos, 62210
El mar, 25-05-2010 a las 16:11 +0800, fancy2012 escribió:
> Dear GMX users,
>  When I prepare the topology file of one small molecule using PRODRG,
> I find that the generated topology file is for another molecule. The
> only difference between the two molecules is that the latter one has
> one more double bond. How should I deal with such problems? Thanks
> very much!
>  
> All the best,
> qinghua
>  
> -- 
> 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] coarse grain dynamics

[Justin A. Lemkul]

ram bio wrote:

Thanks for the comments and info, but is there any way to take a
particular  frame for eg. the last frame  of CG simulation and extend
the run into all-atom simulation further ...



There are tools out there to reconstruct an atomistic representation of a CG 
system (see link below, and poke around Google for a few minutes).  If you want 
to start a whole new simulation, that is certainly possible after (of course) 
regenerating your system topology to match the new system.


-Justin


On Tue, May 25, 2010 at 5:32 PM, Jared James Thompson
 wrote:

I agree with Justin on this one. Simulations run using CG that is not optimized
for reconstruction may not actually reflect the type of interactions you are
looking for. The current result of this simulation may not directly correspond
to a full atomistic result, so even if a reconstruction were performed you would
most likely NOT be able to draw conclusions from it.

Otherwise, everyone would run really fast simulations in CG, then reconstruct
their systems afterward. :)



Quoting "Justin A. Lemkul" :



ram bio wrote:

thanks,

but i am using gromacs version 4.0.07


I think the general consensus thus far is you won't be able to do what you
want
without significant effort to reconstruct your system, and perhaps then you
should question whether any tools that seek to build optimal hydrogens from
CG
structures are going to bias the result.  Would those hydrogen bonds have
actually formed in an AA simulation?  Hard to tell.  If you want to analyze
hydrogen bonds, CG approximations are not probably sufficient.

This is a good exercise in planning your analysis before conducting your
simulation.  You can probably estimate some sort of polar contacts from your
CG
representation, but not hydrogen bonds.

-Justin


On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi
 wrote:

Hi,
To change between representations (atomistic <--> coarse grained), if you
are using the MARTINI FF, you can use the modified version of Gromacs

3.3,

check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt
If you don't want to switch to full-atomistic representation, check which

CG

atom types are able to form hydrogen bonds and look for interactions

between

them. Obviously, this will be an approximation.

Esteban G. Vega-Hissi
UNSL
San Luis
Argentina
--
On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson



wrote:

There are programs around for reconstruction of full-atomistic
representations
from coarse-grained representations, however. I don't know if there are
any
available for the GROMACS architecture.




Quoting Nuno Azoia :


Hi there!

I never worked with coarse grain simulations, but if you used a coarse
grain methodology you didn't include all the atoms, so you didn't
included hydrogens. So now you can not see them, of course. They are

not

there.

If you need to "know the hydrogen bond interactions" you need to do

some

"all atoms" simulation, not coarse grain.

Nuno Azoia

On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote:

Dear Gromacs Users,

I have done coarse grain simulation for 2 peptides in bilayer for
1000ns, and now i would like to know the hydrogen bond interactions
between these two peptides. Please let me know how to do this, i can
visualize the trajectory in VMD, but unable to calculate the hydrogen
bonding distance and the hydrogen bonds existing..

Thanks

Ram

--
Nuno Gonçalo Azoia Lopes

Laboratório de Investigação em Acabamento
Departamento de Engenharia Têxtil
Universidade do Minho
Campus de Azurém
4800-058 Guimarães
Portugal

Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293

Mobile: +351 965 382 487
E-mail: naz...@det.uminho.pt
http://nazoia.net

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--
Jared James Thompson
Department of Medicinal Chemistry and Molecular Pharmacology
Laboratory for Computational Drug Design and Biology
RHPH 504C
Heine Pharmacy Building
575 Stadium Mall Drive
West Lafayette, IN  47907-2091
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[gmx-users] A question on execusion speed

[Paymon Pirzadeh]

Hello,
I have question regarding the execution time of a trajectory. I used to
run my trajectory at 265K or 275K and at the end of the log file the
speed was reported as e.g. 1.18 ns/day. Recently, I changed the
temperature to 288K and now my simulation is not finished in the
assigned wall time (240 hours). The potential and total energy and other
parameters in the log file looks fine. Is there really sth going on with
temperature or the cluster I am running the jobs on?!
Regards,

Paymon 

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Re: [gmx-users] A question on execusion speed

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

Hello,
I have question regarding the execution time of a trajectory. I used to
run my trajectory at 265K or 275K and at the end of the log file the
speed was reported as e.g. 1.18 ns/day. Recently, I changed the
temperature to 288K and now my simulation is not finished in the
assigned wall time (240 hours). The potential and total energy and other
parameters in the log file looks fine. Is there really sth going on with
temperature or the cluster I am running the jobs on?!


I can't think of a reason why simply changing the temperature would drastically 
alter the speed of the simulation.  Look to the hardware.  When I've had random 
decreases in performance, it's because a node is having issues or the 
interconnect is bugging out.


-Justin


Regards,

Paymon 



--


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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[gmx-users] How to combine two gro files in one big file

[Yan Gao]

Hi there,

I want to simulate two molecules which are identical, and one is
rotated/translated from another. I have the gro file for one molecule.

I tried editconf, which helped manipulate the molecule. Then I want to
combine it with the original gro file, so that the two identical molecules
are placed in one file. I searched the manual but could not find a proper
command. Could anyone help? Thanks.

-- 
Yan
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[gmx-users] Restarting after NVT: continuation error

[VANDANA KUMARI]

Hello Gromacs Users,

I am trying to make tpr file for NPT equilibration after NVT equilibration using

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

I am using  parameter " continuation = yes " in npt.mdp  for restarting after 
NVT, but I am getting this warning massage:

 WARNING 1 [file npt.mdp, line unknown]:
  Unknown left-hand 'continuation' in parameter file

Please help me with this issue.

Thank you
--
Vandana






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RE: [gmx-users] How to combine two gro files in one big file

[VANDANA KUMARI]

Hi Yan,

You can do it by converting your both gro file into pdb files and concatenating 
both  pdb files into one file . and you can convert pdb into gro using editconf
steps are as follows:

1. editconf -f 1.gro -o 1.pdb
2. editconf -f 2.gro -o 2.pdb

3. cat 1.pdb 2.pdb > both.pdb

you need to delete unnecessary line i.e. CRYST1 or END from you both.pdb file

4. editconf -f both.pdb -o both.gro


--
Vandana Kumari

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Yan Gao [y1...@ucsd.edu]
Sent: Tuesday, May 25, 2010 5:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] How to combine two gro files in one big file

Hi there,

I want to simulate two molecules which are identical, and one is 
rotated/translated from another. I have the gro file for one molecule.

I tried editconf, which helped manipulate the molecule. Then I want to combine 
it with the original gro file, so that the two identical molecules are placed 
in one file. I searched the manual but could not find a proper command. Could 
anyone help? Thanks.

--
Yan
-- 
gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Restarting after NVT: continuation error

[Amit Choubey]

On Tue, May 25, 2010 at 2:32 PM, VANDANA KUMARI <
kumar...@buckeyemail.osu.edu> wrote:

>
> Hello Gromacs Users,
>
> I am trying to make tpr file for NPT equilibration after NVT equilibration
> using
>
> grompp -f npt.mdp -c nvt.gro -t nvt.trr -p topol.top -n index.ndx -o
> npt.tpr
>

> I am using  parameter " continuation = yes " in npt.mdp  for restarting
> after NVT, but I am getting this warning massage:
>

>  WARNING 1 [file npt.mdp, line unknown]:
>   Unknown left-hand 'continuation' in parameter file
>
>
well to continue why dont you use the same velocities ; just say gen_vel =
no

amit

> Please help me with this issue.
>
> Thank you
> --
> Vandana
>
>
>
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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RE: [gmx-users] Restarting after NVT: continuation error

[VANDANA KUMARI]

Hi Amit,

thanks for the reply. I am using gen_vel = no in my mdp file.but I am wondering 
why I am getting warning message when I am using "continuation = yes" or 
"continuation = no ". grompp is not recognizing continuation as parameter.
Am I doing something wrong?

Thanks,
--
Vandana Kumari

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Amit Choubey [kgp.a...@gmail.com]
Sent: Tuesday, May 25, 2010 5:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Restarting after NVT: continuation error



On Tue, May 25, 2010 at 2:32 PM, VANDANA KUMARI 
mailto:kumar...@buckeyemail.osu.edu>> wrote:

Hello Gromacs Users,

I am trying to make tpr file for NPT equilibration after NVT equilibration using

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

I am using  parameter " continuation = yes " in npt.mdp  for restarting after 
NVT, but I am getting this warning massage:

 WARNING 1 [file npt.mdp, line unknown]:
  Unknown left-hand 'continuation' in parameter file


well to continue why dont you use the same velocities ; just say gen_vel = no

amit
Please help me with this issue.

Thank you
--
Vandana







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Re: [gmx-users] Restarting after NVT: continuation error

[Justin A. Lemkul]

VANDANA KUMARI wrote:

Hi Amit,

thanks for the reply. I am using gen_vel = no in my mdp file.but I am 
wondering why I am getting warning message when I am using "continuation 
= yes" or "continuation = no ". grompp is not recognizing continuation 
as parameter.

Am I doing something wrong?


What version of Gromacs are you using?  The "continuation" keyword was 
introduced in the 4.0.x series to replace "unconstrained_start" from versions up 
to, and including 3.3.3.


-Justin



Thanks,
--
Vandana Kumari

*From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on 
behalf of Amit Choubey [kgp.a...@gmail.com]

*Sent:* Tuesday, May 25, 2010 5:51 PM
*To:* Discussion list for GROMACS users
*Subject:* Re: [gmx-users] Restarting after NVT: continuation error



On Tue, May 25, 2010 at 2:32 PM, VANDANA KUMARI 
mailto:kumar...@buckeyemail.osu.edu>> wrote:


 
Hello Gromacs Users,


I am trying to make tpr file for NPT equilibration after NVT
equilibration using

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


I am using  parameter " continuation = yes " in npt.mdp  for
restarting after NVT, but I am getting this warning massage:


 WARNING 1 [file npt.mdp, line unknown]:
  Unknown left-hand 'continuation' in parameter file


well to continue why dont you use the same velocities ; just say gen_vel 
= no


amit

Please help me with this issue.

Thank you
--
Vandana







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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] How to combine two gro files in one big file

[Justin A. Lemkul]

VANDANA KUMARI wrote:

Hi Yan,

You can do it by converting your both gro file into pdb files and 
concatenating both  pdb files into one file . and you can convert pdb 
into gro using editconf

steps are as follows:

1. editconf -f 1.gro -o 1.pdb
2. editconf -f 2.gro -o 2.pdb

3. cat 1.pdb 2.pdb > both.pdb

you need to delete unnecessary line i.e. CRYST1 or END from you both.pdb 
file


4. editconf -f both.pdb -o both.gro 


Conversion back and forth between .pdb and .gro is not required (but it does 
work).  The main point of creating a concatenated file is that both molecules 
are placed correctly within the same box, so for each:


editconf -f 1.gro -o 1_newbox.gro -center x y z -box x y z
(and the same for molecule 2)

Getting the molecule positions and box vectors right is the real trick.

Then concatenate, remove unnecessary box and header lines in the middle of the 
file, correct the atom count and you're done.


-Justin




--
Vandana Kumari

*From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on 
behalf of Yan Gao [y1...@ucsd.edu]

*Sent:* Tuesday, May 25, 2010 5:33 PM
*To:* Discussion list for GROMACS users
*Subject:* [gmx-users] How to combine two gro files in one big file

Hi there,

I want to simulate two molecules which are identical, and one is 
rotated/translated from another. I have the gro file for one molecule.


I tried editconf, which helped manipulate the molecule. Then I want to 
combine it with the original gro file, so that the two identical 
molecules are placed in one file. I searched the manual but could not 
find a proper command. Could anyone help? Thanks.


--
Yan



--


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] A question on execusion speed

[Mark Abraham]

- Original Message -
From: "Justin A. Lemkul" 
Date: Wednesday, May 26, 2010 3:16
Subject: Re: [gmx-users] A question on execusion speed
To: Discussion list for GROMACS users 

> 
> 
> Paymon Pirzadeh wrote:
> >Hello,
> >I have question regarding the execution time of a trajectory. I 
> used to
> >run my trajectory at 265K or 275K and at the end of the log 
> file the
> >speed was reported as e.g. 1.18 ns/day. Recently, I changed the
> >temperature to 288K and now my simulation is not finished in the
> >assigned wall time (240 hours). The potential and total energy 
> and other
> >parameters in the log file looks fine. Is there really sth 
> going on with
> >temperature or the cluster I am running the jobs on?!
> 
> I can't think of a reason why simply changing the temperature 
> would drastically alter the speed of the simulation.  Look 
> to the hardware.  When I've had random decreases in 
> performance, it's because a node is having issues or the 
> interconnect is bugging out.

Indeed. Obviously one should use gmxcheck to compare the two .tpr, and be 
confident the options to mdrun and the job script conditions were constant, 
before casting nasturtiums!

Mark
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Re: [gmx-users] large sim box

[Yan Gao]

Hi Mark,

Thank you for your comments! They are very helpful.

I still have several questions regarding your comments:
1. Which constraints should I apply for 2fs stepsize? hbonds, all-bonds,
h-angles, all-angles
I am simulating molecules that contain carbon nanotubes and polymer chains.
May I have your suggestions based on your experience? Thanks.

2.If I understand correctly, it is enough to use the default value for
xtc-precision = 1000.
I am not quite understand about this. Does 1000 means that it is calculated
with precision of 0.001 nm? and 100 for 1e-6 nm? Thanks.

3. Regarding the MPI, may I have your suggestions on any illustrative
examples of parallelization with MPI for gromacs?
 How can I know if the cluster support MPI? The cluster I am using have
linux system.
 It seems from the FAQ that I need to re-configure the Gromacs to enable
mpi. Do I need additional software/program to support the parallelization?
Can I implement the parallelization just like I implement the single
processor task? or with several more bash commands? Thanks.

Thank you very much for your time and help!

Young




On Mon, May 24, 2010 at 1:02 PM, Mark Abraham wrote:

> - Original Message -
> From: Yan Gao 
> Date: Tuesday, May 25, 2010 3:02
> Subject: [gmx-users] large sim box
> To: Discussion list for GROMACS users 
>
> > Hi There,
> >
> > I want to use a large simulation box. I did a trial
> with 15 * 15 * 15 nm box for 100 steps. genbox_d generates 110k water
> molecules, or 330k atoms.
> >
> > It looks like that gromacs can run that
>  large number of atoms. I am sure it will take a long long long time.
> However if I really want to simulate it, is there any way that I can
> increase the speed? (except using a better cpu, or paralleling it)
> Thanks.
>
> You can control the cost through choice of algorithm and implementation.
> That means you need to learn how they work and whether some trade-offs are
> suitable for you. That's going to mean lots of reading, and some
> experimentation on more tractable systems. Learn to walk before you try to
> run! However, the only serious way to approach a system this large is with
> parallelization. Also, reconsider your use of double precision.
>
> > My second question is that: If I have to use clusters or super
> computer, which one is better? and, do I need a particular
> software/program to paralleling it? Thanks.
>
> GROMACS does parallelization using MPI, which will be available on any
> machine you can find. There are platforms for which GROMACS does not have
> the specially-optimized non-bonded inner loops - avoid such platforms if you
> have the choice. You should read the 2008 GROMACS JCTC paper.
>
> >
> > I put my .mdp below:
> > integrator   = md
> > dt
>  = 0.002
> > ; duration  2000 ps
> > nsteps   = 100
> > comm_mode
>   = linear
> > nstcomm = 1
> > ; dump config every 300 fs
> >
> nstxout  = 10
> > nstvout  = 10
> > nstfout
>   = 10
>
> Writing output of all of energies, forces and velocities this often is a
> waste of time in production simulations. Adjacent data points 10 MD steps
> apart will be strongly correlated, even if you plan to use the force and/or
> velocity data. Consider the needs of your analysis, and probably plan to use
> nstxtcout instead of any of these.
>
> > nstcheckpoint= 100
> > nstlog
>  = 10
> > nstenergy= 10
> > nstxtcout= 10
> >
> xtc-precision= 100
>
> Read what this does.
>
> > nstlist  = 1
> > ns_type
>  = grid
> > pbc   = xyz
> > rlist=
>  1.0;1.0
> > coulombtype  = PME
> > rcoulomb
>  = 1.0;1.0
> >
> fourierspacing = 0.2;0.1
>
> That will noticeably reduce the cost of PME, but its effect on accuracy is
> not well known.
>
> > pme_order = 4
> > ewald_rtol
>   = 1e-5
> > optimize_fft = yes
> > vdwtype =
> cut-off
> > rvdw = 1.0;1.0
> > tcoupl
>  = Nose-Hoover
> >
> tc_grps  = system
>
> This is often a poor choice. grompp probably told you that.
>
> > tau_t= 0.5
> > ref_t
>  = 300.0
> > Pcoupl   = no
> > annealing = no
> > gen_vel
>  = no
> > gen_temp = 300.0
> >
> gen_seed = 173529
> > constraints  = none
>
> You must use constraints if you wish a 2fs timestep.
>
> > ;energy_excl
>  = C_H C_H
> > constraint_algorithm =  lincs
> > unconstrained_start
>   = no
> > lincs_order = 4
> > lincs_iter = 1
>
> Mark
> --
> 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.
> 

Re: [gmx-users] large sim box

[Mark Abraham]

- Original Message -
From: Yan Gao 
Date: Wednesday, May 26, 2010 9:19
Subject: Re: [gmx-users] large sim box
To: Discussion list for GROMACS users 

> Hi Mark,
> 
> Thank you for your comments! They are very helpful.
> 
> I still have several questions regarding your comments:
> 1. Which constraints should I apply for 2fs stepsize? hbonds, all-bonds, 
> h-angles, all-angles

Probably all-bonds, but there's no substitute for reading in learning about 
such things. Start with the GROMACS manual (which is an excellent resource!) 
and the papers to which it refers. Then consult some literature on systems 
similar to yours to get an idea what others think is sound. Do all the tutorial 
material you can get your hands on.
 
> I am simulating molecules that contain carbon nanotubes and polymer chains.
> May I have your suggestions based on your experience? Thanks.

Sorry, I don't have any there, and there's doubtless a range.

> 2.If I understand correctly, it is enough to use the default value for 
> xtc-precision = 1000. 
> I am not quite understand about this. Does 1000 means that it is calculated 
> with precision of 0.001 nm? and 100 for 1e-6 nm? Thanks.

Sounds right. Again, check the manual, section 7.3

> 3. Regarding the MPI, may I have your suggestions on any illustrative 
> examples of parallelization with MPI for gromacs?

I'm not sure what you're looking for. There are 
http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions,
 and reports of MPI simulations in the JCTC paper I linked last time. There's 
tutorial material out there in Google land that probably guides you through 
running such calculations.

> How can I know if the cluster support MPI? The cluster I am using have linux 
>system.

Ask the admins, see what software is installed, etc. Do be aware that unless 
the interconnect is fast (i.e. better than gigabit ethernet) then you will not 
see much benefit from parallelization.

>  It seems from the FAQ that I need to re-configure the Gromacs to enable mpi. 
> Do I need additional software/program to support the parallelization? Can I 
> implement the parallelization just like I implement the single processor 
> task? or with several more bash commands? Thanks.

"Implement" implies writing code, which you do not need or want to do. See 
http://www.lam-mpi.org/tutorials/lam/ for some information.

Mark
 
> Thank you very much for your time and help!
> 
> Young
> 
> 
> 
> 
> On Mon, May 24, 2010 at 1:02 PM, Mark Abraham  wrote:



> - Original Message -
> 
From: Yan Gao 
> 
Date: Tuesday, May 25, 2010 3:02
> 
Subject: [gmx-users] large sim box
> 
To: Discussion list for GROMACS users 

> 
> 
> Hi There,
> 
>
> 
> I want to use a large simulation box. I did a trial
> 
with 15 * 15 * 15 nm box for 100 steps. genbox_d generates 110k water
> 
molecules, or 330k atoms.
> 
>
> 
> It looks like that gromacs can run that
> 
 large number of atoms. I am sure it will take a long long long time.
> 
However if I really want to simulate it, is there any way that I can
> 
increase the speed? (except using a better cpu, or paralleling it)
> 
Thanks.

> 

> You can control the cost through choice of algorithm and implementation. That 
> means you need to learn how they work and whether some trade-offs are 
> suitable for you. That's going to mean lots of reading, and some 
> experimentation on more tractable systems. Learn to walk before you try to 
> run! However, the only serious way to approach a system this large is with 
> parallelization. Also, reconsider your use of double precision.




> 
> 
> My second question is that: If I have to use clusters or super
> 
computer, which one is better? and, do I need a particular
> 
software/program to paralleling it? Thanks.

> 

> GROMACS does parallelization using MPI, which will be available on any 
> machine you can find. There are platforms for which GROMACS does not have the 
> specially-optimized non-bonded inner loops - avoid such platforms if you have 
> the choice. You should read the 2008 GROMACS JCTC paper.




> 
> 
>
> 
> I put my .mdp below:
> 
> integrator   = md
> 
> dt  
> 
 = 0.002
> 
> ; duration  2000 ps
> 
> nsteps   = 100
> 
> comm_mode   
> 
  = linear
> 
> nstcomm             = 1
> 
> ; dump config every 300 fs
> 
>
> 
nstxout  = 10
> 
> nstvout  = 10
> 
> nstfout   
> 
      = 10

> 

> Writing output of all of energies, forces and velocities this often is a 
> waste of time in production simulations. Adjacent data points 10 MD steps 
> apart will be strongly correlated, even if you plan to use the force and/or 
> velocity data. Consider the needs of your analysis, and probably plan to use 
> nstxtcout instead of any of these.




> 
> 
> nstcheckpoint    = 100
> 
> nstlog  
> 
 = 10
> 
> nstenergy    = 10
> 
> nstxtcout    = 10
> 
>
> 
xtc-precisi

Re: [gmx-users] How to combine two gro files in one big file

[Yan Gao]

Thank you Vandana and Justin, the cat command solve the problem.

Regarding the removement of the unnecessary lines in the middle, is there a
command that can do it automatically? or one has to make code by self?
Thanks.

Yan

On Tue, May 25, 2010 at 3:25 PM, Justin A. Lemkul  wrote:

>
>
> VANDANA KUMARI wrote:
>
>> Hi Yan,
>>
>> You can do it by converting your both gro file into pdb files and
>> concatenating both  pdb files into one file . and you can convert pdb into
>> gro using editconf
>> steps are as follows:
>>
>> 1. editconf -f 1.gro -o 1.pdb
>> 2. editconf -f 2.gro -o 2.pdb
>>
>> 3. cat 1.pdb 2.pdb > both.pdb
>>
>> you need to delete unnecessary line i.e. CRYST1 or END from you both.pdb
>> file
>>
>> 4. editconf -f both.pdb -o both.gro
>>
>
> Conversion back and forth between .pdb and .gro is not required (but it
> does work).  The main point of creating a concatenated file is that both
> molecules are placed correctly within the same box, so for each:
>
> editconf -f 1.gro -o 1_newbox.gro -center x y z -box x y z
> (and the same for molecule 2)
>
> Getting the molecule positions and box vectors right is the real trick.
>
> Then concatenate, remove unnecessary box and header lines in the middle of
> the file, correct the atom count and you're done.
>
> -Justin
>
>
>
>>
>> --
>> Vandana Kumari
>> 
>> *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
>> behalf of Yan Gao [y1...@ucsd.edu]
>> *Sent:* Tuesday, May 25, 2010 5:33 PM
>> *To:* Discussion list for GROMACS users
>> *Subject:* [gmx-users] How to combine two gro files in one big file
>>
>> Hi there,
>>
>> I want to simulate two molecules which are identical, and one is
>> rotated/translated from another. I have the gro file for one molecule.
>>
>> I tried editconf, which helped manipulate the molecule. Then I want to
>> combine it with the original gro file, so that the two identical molecules
>> are placed in one file. I searched the manual but could not find a proper
>> command. Could anyone help? Thanks.
>>
>> --
>> Yan
>>
>>
> --
> 
>
> 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 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
>



-- 
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: yan.gao.2...@gmail.com
-- 
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 combine two gro files in one big file

[Justin A. Lemkul]

Yan Gao wrote:

Thank you Vandana and Justin, the cat command solve the problem.

Regarding the removement of the unnecessary lines in the middle, is 
there a command that can do it automatically? or one has to make code by 
self? Thanks.




That's a trivial exercise for a simple text editor.

-Justin


Yan

On Tue, May 25, 2010 at 3:25 PM, Justin A. Lemkul > wrote:




VANDANA KUMARI wrote:

Hi Yan,

You can do it by converting your both gro file into pdb files
and concatenating both  pdb files into one file . and you can
convert pdb into gro using editconf
steps are as follows:

1. editconf -f 1.gro -o 1.pdb
2. editconf -f 2.gro -o 2.pdb

3. cat 1.pdb 2.pdb > both.pdb

you need to delete unnecessary line i.e. CRYST1 or END from you
both.pdb file

4. editconf -f both.pdb -o both.gro


Conversion back and forth between .pdb and .gro is not required (but
it does work).  The main point of creating a concatenated file is
that both molecules are placed correctly within the same box, so for
each:

editconf -f 1.gro -o 1_newbox.gro -center x y z -box x y z
(and the same for molecule 2)

Getting the molecule positions and box vectors right is the real trick.

Then concatenate, remove unnecessary box and header lines in the
middle of the file, correct the atom count and you're done.

-Justin




--
Vandana Kumari

*From:* gmx-users-boun...@gromacs.org

[gmx-users-boun...@gromacs.org
] on behalf of Yan Gao
[y1...@ucsd.edu ]
*Sent:* Tuesday, May 25, 2010 5:33 PM
*To:* Discussion list for GROMACS users
*Subject:* [gmx-users] How to combine two gro files in one big file

Hi there,

I want to simulate two molecules which are identical, and one is
rotated/translated from another. I have the gro file for one
molecule.

I tried editconf, which helped manipulate the molecule. Then I
want to combine it with the original gro file, so that the two
identical molecules are placed in one file. I searched the
manual but could not find a proper command. Could anyone help?
Thanks.

-- 
Yan



-- 



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 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




--
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: yan.gao.2...@gmail.com 


--


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] Restarting after NVT: continuation error

[VANDANA KUMARI]

Justin,

Thanks, Its working on Gromacs4.0.7.
 
--
Vandana Kumari

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Tuesday, May 25, 2010 6:23 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Restarting after NVT: continuation error

VANDANA KUMARI wrote:
> Hi Amit,
>
> thanks for the reply. I am using gen_vel = no in my mdp file.but I am
> wondering why I am getting warning message when I am using "continuation
> = yes" or "continuation = no ". grompp is not recognizing continuation
> as parameter.
> Am I doing something wrong?

What version of Gromacs are you using?  The "continuation" keyword was
introduced in the 4.0.x series to replace "unconstrained_start" from versions up
to, and including 3.3.3.

-Justin

>
> Thanks,
> --
> Vandana Kumari
> 
> *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
> behalf of Amit Choubey [kgp.a...@gmail.com]
> *Sent:* Tuesday, May 25, 2010 5:51 PM
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] Restarting after NVT: continuation error
>
>
>
> On Tue, May 25, 2010 at 2:32 PM, VANDANA KUMARI
> mailto:kumar...@buckeyemail.osu.edu>> wrote:
>
>
> Hello Gromacs Users,
>
> I am trying to make tpr file for NPT equilibration after NVT
> equilibration using
>
> grompp -f npt.mdp -c nvt.gro -t nvt.trr -p topol.top -n index.ndx -o
> npt.tpr
>
>
> I am using  parameter " continuation = yes " in npt.mdp  for
> restarting after NVT, but I am getting this warning massage:
>
>
>  WARNING 1 [file npt.mdp, line unknown]:
>   Unknown left-hand 'continuation' in parameter file
>
>
> well to continue why dont you use the same velocities ; just say gen_vel
> = no
>
> amit
>
> Please help me with this issue.
>
> Thank you
> --
> Vandana
>
>
>
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> 
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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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[gmx-users] PMF in vacuum

[Eudes Fileti]

Hi gmx-users,
I'm trying to simulate a umbrella sampling PMF between two benzene
molecules
in vacuum. My protocol is working fine, my histograms have good overlap and
the curves I have got are quite reasonable.

However I have noticed that some options in my .mdp file can significantly
change
the depth of the well. Also the curves can not go to zero at long distances.
For example, if I use PBC I get a reasonably good value for the minimum of
the PMF
but from a certain separation it starts to increase slightly in a linear
fashion
instead of going to zero. On the other hand, if I make pbc = no, I get an
acceptable curve,
with the PMF going to zero, but with the minimum too high.

Someone could give me any tips on the best set of parameters to calculate
this PMF in a vacuum?
bests
eef
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4996-0196
http://fileti.ufabc.edu.br
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[gmx-users] PMF in vacuum

[chris . neale]

Dear Eudes:

Can you please elaborate on your description? What .mdp options are  
you using? What exactly do your curves look like (you can post  
pictures to photobucket or some other online service and link them  
here)? If you suspect that you are doing something wrong, then we need  
to understand exactly what you are doing and exactly what you are  
seeing in order to help.


Chris.

-- original message --

Hi gmx-users,
I'm trying to simulate a umbrella sampling PMF between two benzene
molecules
in vacuum. My protocol is working fine, my histograms have good overlap and
the curves I have got are quite reasonable.

However I have noticed that some options in my .mdp file can significantly
change
the depth of the well. Also the curves can not go to zero at long distances.
For example, if I use PBC I get a reasonably good value for the minimum of
the PMF
but from a certain separation it starts to increase slightly in a linear
fashion
instead of going to zero. On the other hand, if I make pbc = no, I get an
acceptable curve,
with the PMF going to zero, but with the minimum too high.

Someone could give me any tips on the best set of parameters to calculate
this PMF in a vacuum?
bests
eef

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[gmx-users] Re: the output of do_dssp

[Hsin-Lin]

Hi, Justin
 
Thank you for your patience.
According your reply, I used trjconv to write only protein group into
another file.
I execute do_dssp again in group "protein"and "mainchain" respectively but
still get coils more than total residues.
Why?
 
Hsin-Lin
 
 
Hsin-Lin wrote:
> Hi, Justin:
> 
> Thank you for your reply.
> I try to select the group, 'mainchain', when prompted, and get the
quantity
> of coil still larger than the number of residues of my protein.
 
Then some other elements of your system are being detected as containing 
relevant atoms.  What happens if you run do_dssp on a single structure 
containing only your protein?
 
> The data is the same as the output that generated by the selection, "1.
> Protein".
> If I select backbone, I get the fatal error: 
> Failed to execute command: /Prousr/statphys/hsinlin/dssp/dsspcmbi -na
> ddhIPvCe ddJ6Yv7a > /dev/null 2> /dev/null 
> 
> And I don't understand even if I can run the selection, "backbone",
> successfully.
 
No, you can't.
 
> According the dssp web of wiki:
> http://en.wikipedia.org/wiki/DSSP_%28protein%29
> the hydrogen bonds are dicided by O, C, H, and N four atoms.
> How can we get dssp analysis by backbone that includes only
NCCNCCNCC.?
> 
 
You can't - DSSP requires the presence of the carbonyl O in order to
determine 
hydrogen bonding geometry.  If you don't have a full carbonyl, the analysis
fails.
 
-Justin
 
> Sincerely yours,
> Hsin-Lin
>> Hsin-Lin wrote:
>>> Hi,
>>> 
>>> I use do_dssp to generate xvg file collect the last line to make a plot.
>>> There are something written in this way:
>>> --
>>> @ s0 legend "Structure"
>>> @ s1 legend "Coil"
>>> @ s2 legend "Bend"
>>> 0514   1
>>> ---
>>> My system is dimer and each peptide has 6 residue.
>> Then you have a problem.  Your output indicates 14 residues are in a
> random
>> coil, so either you have more than 12 total residues, or something went
> wrong
>> in
>> the dssp calculation.
>> 
>>> And the number I choose to analyze is "1. Protein".
>>> 
>> Perhaps this is why you had a problem.  Normally, choosing "Protein"
would
>> cause
>> the calculation to hang, but maybe that is not the case any more.  See
> here
>> for
>> the proper group to choose and the rationale:
>> 
>> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
>> 
>>> Now I have a question, if I want to calculate the percentage of
> secondary
>>> structure.
>>> In the example above, is it calculated in this way 5/12=42%?
>>> 
>> I'd question your results first...you don't have 12 residues in your
>> calculation, otherwise your protein is 14/12 = 117% random coil!  Also
> realize
>> that (by default) the "Structure" term only includes alpha helix, beta
> strand,
>> bend, and turn.  Other structural elements are not included.  That may or
>> may
>> not be what you want, depending on the structural elements of your
> protein.
>> -Justin
>> 
>>> Hsin-Lin
>  
> 

 

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