Re: [gmx-users] g_cluster for concoord output?

[Tsjerk Wassenaar]

Hi Albert,

pdb is mentioned valid input for both -f (trajectory) and -s
(reference). So you can use the file you have for both:

g_cluster -s disco.pdb -f disco.pdb [...]

Cheers,

Tsjerk

On Tue, Apr 3, 2012 at 8:23 AM, Albert  wrote:
> Dear:
>
>    I've generated a disoc.pdb file by concoord and does any one have any
> idea how to analyze it by Gromacs g_cluster? when I read the manual of
> g_cluter, it will require
>
>  -f       traj.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
>  -s      topol.tpr  Input, Opt.  Structure+mass(db): tpr tpb tpa gro g96 pdb
>  -n      index.ndx  Input, Opt.  Index file
>  -dm       rmsd.xpm  Input, Opt.  X PixMap compatible matrix file
>
>
> but the concoord output is a single pdb file.
>
> thank you very much
>
> best wishes
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

AW: [gmx-users] the mdrun "-v"

[Rausch, Felix]

Hey Acoot,

The “–v” option simply means “verbose”, so mdrun outputs a bit more information 
(for example a nice finish time estimation) than it would do without “-v”. I 
doubt that giving a little bit more output to the console will influence the 
run time significantly. My advice: Just try it out ;)

Cheers,
Felix

Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Acoot Brett
Gesendet: Dienstag, 3. April 2012 08:19
An: Discussion list for GROMACS users
Betreff: [gmx-users] the mdrun "-v"


Dear All,

For the function of mdrun. will you please introduce the time difference for 
the whole mdrun with or without "-v"? I suppose with "-v" will need some 
calculation time, but I am not sure whether the time spent is significant.

Cheers,

Acoot
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_cluster for concoord output?

[Albert]

Dear:

I've generated a disoc.pdb file by concoord and does any one have 
any idea how to analyze it by Gromacs g_cluster? when I read the manual 
of g_cluter, it will require


  -f   traj.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
  -s  topol.tpr  Input, Opt.  Structure+mass(db): tpr tpb tpa gro 
g96 pdb

  -n  index.ndx  Input, Opt.  Index file
 -dm   rmsd.xpm  Input, Opt.  X PixMap compatible matrix file


but the concoord output is a single pdb file.

thank you very much

best wishes
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] the mdrun "-v"

[Acoot Brett]

Dear All,

For the function of mdrun. will you please introduce 
the time difference for the whole mdrun with or without "-v"? I suppose 
with "-v" will need some calculation time, but I am not sure whether the
 time spent is significant.

Cheers,

Acoot-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] how to get a minimized structure pdb

[Mark Abraham]

On 03/04/12, balaji nagarajan  wrote:

> 
> 
> 
> 
> 
> 
> 
> 
> 
> Dear Users ! 
> 
> I have done a minimization for a tetrapeptide in a water box
> 
> with conjugate gradient minimization of 1000 steps
> 
> when I convert it to pdb as below 
>  
> 
> trjconv -f em.trr -o min.pdb -s em.tpr << EOF
> 0
> EOF
> 
> 
> the out put pdb has many structures 
> as follows 
> 
> MODEL 0 
> 
> MODEL 1
> 
> MODEL  2  
> 
> but the minimized pdb is single structre , 
> 
> what does these structures mean. 
> 
> how to obtain a single structre. 
> 
> my mimization input file is as follows
> --
> define   = -DFLEXIBLE
> constraints  = none
> integrator   = cg
> dt   = 0.001 ; ps !
> nsteps   = 1000
> nstlist  = 10
> ns_type  = grid
> rlist= 1.0
> coulombtype  = PME
> rcoulomb = 1.0
> vdwtype  = cut-off
> rvdw = 1.0
> optimize_fft = yes
> ;
> ;Energy minimizing stuff
> ;
> emtol= 10.0
> emstep   = 0.01
> 
> energygrps = protein SOL
> 
> 
> thanks in advance Dear Users ! 
> 
> I have done a minimization for a tetrapeptide in a water box
> 
> with conjugate gradient minimization of 1000 steps
> 
> when I convert it to pdb as below 
>  
> 
> trjconv -f em.trr -o min.pdb -s em.tpr << EOF
> 0
> EOF
> 
> 
> 

 
That will convert the contents of the trajectory file into a pseudo-trajectory 
in .pdb format. Hence you see multiple models. So you can simply look only at 
the last model, or direct trjconv to only convert the last trajectory frame, or 
perhaps use the file written by mdrun -c. You could have pre-solved the problem 
by writing the -c file in .pdb format by choosing mdrun -s yourem.tpr -c 
yourfinalstructure.pdb. 
 
Mark 
 

> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Dear Users ! 
> 
> I have done a minimization for a tetrapeptide in a water box
> 
> with conjugate gradient minimization of 1000 steps
> 
> when I convert it to pdb as below 
>  
> 
> trjconv -f em.trr -o min.pdb -s em.tpr << EOF
> 0
> EOF
> 
> 
> the out put pdb has many structures 
> as follows 
> 
> MODEL 0 
> 
> MODEL 1
> 
> MODEL  2  
> 
> but the minimized pdb is single structre , 
> 
> what does these structures mean. 
> 
> how to obtain a single structre. 
> 
> my mimization input file is as follows
> --
> define   = -DFLEXIBLE
> constraints  = none
> integrator   = cg
> dt   = 0.001 ; ps !
> nsteps   = 1000
> nstlist  = 10
> ns_type  = grid
> rlist= 1.0
> coulombtype  = PME
> rcoulomb = 1.0
> vdwtype  = cut-off
> rvdw = 1.0
> optimize_fft = yes
> ;
> ;Energy minimizing stuff
> ;
> emtol= 10.0
> emstep   = 0.01
> 
> energygrps = protein SOL
> 
> 
> thanks in advance Dear Users ! 
> 
> I have done a minimization for a tetrapeptide in a water box
> 
> with conjugate gradient minimization of 1000 steps
> 
> when I convert it to pdb as below 
>  
> 
> trjconv -f em.trr -o min.pdb -s em.tpr << EOF
> 0
> EOF
> 
> 
> the out put pdb has many structures 
> as follows 
> 
> MODEL 0 
> 
> MODEL 1
> 
> MODEL  2  
> 
> but the minimized pdb is single structre , 
> 
> what does these structures mean. 
> 
> how to obtain a single structre. 
> 
> my mimization input file is as follows
> --
> define   = -DFLEXIBLE
> constraints  = none
> integrator   = cg
> dt   = 0.001 ; ps !
> nsteps   = 1000
> nstlist  = 10
> ns_type  = grid
> rlist= 1.0
> coulombtype  = PME
> rcoulomb = 1.0
> vdwtype  = cut-off
> rvdw = 1.0
> optimize_fft = yes
> ;
> ;Energy minimizing stuff
> ;
> emtol= 10.0
> emstep   = 0.01
> 
> energygrps = protein SOL
> 
> 
> thanks in advance 
> 
> 
> 
> 

 
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] how to get a minimized structure pdb

[balaji nagarajan]

Dear Users ! 

I have done a minimization for a tetrapeptide in a water box

with conjugate gradient minimization of 1000 steps

when I convert it to pdb as below 
 

trjconv -f em.trr -o min.pdb -s em.tpr << EOF
0
EOF


the out put pdb has many structures 
as follows 

MODEL 0 

MODEL 1

MODEL  2  

but the minimized pdb is single structre , 

what does these structures mean. 

how to obtain a single structre. 

my mimization input file is as follows
--
define   = -DFLEXIBLE
constraints  = none
integrator   = cg
dt   = 0.001 ; ps !
nsteps   = 1000
nstlist  = 10
ns_type  = grid
rlist= 1.0
coulombtype  = PME
rcoulomb = 1.0
vdwtype  = cut-off
rvdw = 1.0
optimize_fft = yes
;
;Energy minimizing stuff
;
emtol= 10.0
emstep   = 0.01

energygrps = protein SOL


thanks in advance Dear Users ! 

I have done a minimization for a tetrapeptide in a water box

with conjugate gradient minimization of 1000 steps

when I convert it to pdb as below 
 

trjconv -f em.trr -o min.pdb -s em.tpr << EOF
0
EOF


the out put pdb has many structures 
as follows 

MODEL 0 

MODEL 1

MODEL  2  

but the minimized pdb is single structre , 

what does these structures mean. 

how to obtain a single structre. 

my mimization input file is as follows
--
define   = -DFLEXIBLE
constraints  = none
integrator   = cg
dt   = 0.001 ; ps !
nsteps   = 1000
nstlist  = 10
ns_type  = grid
rlist= 1.0
coulombtype  = PME
rcoulomb = 1.0
vdwtype  = cut-off
rvdw = 1.0
optimize_fft = yes
;
;Energy minimizing stuff
;
emtol= 10.0
emstep   = 0.01

energygrps = protein SOL


thanks in advance -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] how to get a minimized structure pdb

[balaji nagarajan]

Dear Users ! 

I have done a minimization for a tetrapeptide in a water box

with conjugate gradient minimization of 1000 steps

when I convert it to pdb as below 
 

trjconv -f em.trr -o min.pdb -s em.tpr << EOF
0
EOF


the out put pdb has many structures 
as follows 

MODEL 0 

MODEL 1

MODEL  2  

but the minimized pdb is single structre , 

what does these structures mean. 

how to obtain a single structre. 

my mimization input file is as follows
--
define   = -DFLEXIBLE
constraints  = none
integrator   = cg
dt   = 0.001 ; ps !
nsteps   = 1000
nstlist  = 10
ns_type  = grid
rlist= 1.0
coulombtype  = PME
rcoulomb = 1.0
vdwtype  = cut-off
rvdw = 1.0
optimize_fft = yes
;
;Energy minimizing stuff
;
emtol= 10.0
emstep   = 0.01

energygrps = protein SOL


thanks in advance 

  -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] on the Umbrella Sampling on-line tutorial

[Acoot Brett]

Dear All,


I planned to use the method introduced in the Umbrella Sampling on-line 
tutorial of Justin Lemkul 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html).
 

But if a peptide is surrounded by a protein, which means the opening of the 
protein-complex is not large enough to allow the peptide to leave the protein 
without significantly breaking the conformation of the protein in the 
protein-peptide complex, is the Umbrella Sampling method still valid for the 
binding energy calculation?

Will you please also show me in which part of the tutorial the direction of 
pull-apart is defined? We should process it in a direction the peptide can 
leave the protein, not the direction protein will bind the peptide much 
strongly.

I am looking
 forward to getting a reply from you.

Cheers,

Acoot-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom

[Mark Abraham]

 
 
On 03/04/12, Andrew DeYoung  wrote:

> Hi,
> 
> Is it possible to compute the total electrostatic energy of an atom over
> time?  By "total," I mean including all of the terms (short range Coulomb,
> 1-4 Coulomb, and Ewald), not just the short range Coulomb and 1-4 Coulomb.
> 
> This question is somewhat related to a question I asked last week (
> http://lists.gromacs.org/pipermail/gmx-users/2012-March/069745.html ), and
> to which I received a great answer.  But my specific question now is: is it
> possible to calculate the Ewald term due to a particular atom?  Or is it
> impossible to decouple the Ewald calculation among individual atoms or or
> sets of pairs of atoms? 
> 
> For example, I would like to determine the electrostatic energy between atom
> 455 and the "rest" of the system (i.e., all other atoms in the system).  To
> try this, I added an entry "a" to my .ndx file:
> 
> [ a ]
> 455
> 
> I then added a directive to my .mdp file:
> 
> energygrps = a
> 
> I then run grompp and mdrun, passing my .ndx file to grompp.  (Note: in my
> .mdp file, I specify that energies should be saved every timestep: nstenergy
> = 1.)  Then I run g_energy on the .edr file that resulted from mdrun.  I am
> given the following energy terms to extract: 
> 
> ---
>   1  Bond 2  Angle3  Ryckaert-Bell.   4  LJ-14
> 
>   5  Coulomb-14   6  LJ-(SR)  7  Coulomb-(SR) 8
> Coul.-recip.  
>   9  Potential   10  Kinetic-En. 11  Total-Energy12
> Conserved-En. 
>  13  Temperature 14  Pressure15  Constr.-rmsd16  Vir-XX
> 
>  17  Vir-XY  18  Vir-XZ  19  Vir-YX  20  Vir-YY
> 
>  21  Vir-YZ  22  Vir-ZX  23  Vir-ZY  24  Vir-ZZ
> 
>  25  Pres-XX 26  Pres-XY 27  Pres-XZ 28  Pres-YX
> 
>  29  Pres-YY 30  Pres-YZ 31  Pres-ZX 32  Pres-ZY
> 
>  33  Pres-ZZ 34  #Surf*SurfTen   35  Mu-X36  Mu-Y
> 
>  37  Mu-Z38  Coul-SR:a-a 39  LJ-SR:a-a   40  Coul-14:a-a
> 
>  41  LJ-14:a-a   42  Coul-SR:a-rest  43  LJ-SR:a-rest44
> Coul-14:a-rest
>  45  LJ-14:a-rest46  Coul-SR:rest-rest
> 
>  47  LJ-SR:rest-rest 48  Coul-14:rest-rest
> 
>  49  LJ-14:rest-rest 50  T-System
> ---
> 
> Choices 42 and 44 are two parts of what I would like: short range Coulomb
> and 1-4 Coulomb energy terms for a-rest.  But is it possible to somehow also
> calculate the Ewald term for a-rest?

 
Not easily, and the value of it would be debatable even if you could compute 
it. Someone did post a several-step method a few years ago using mdrun -rerun 
and perhaps tpbconv -zeroq that achieved something like the decomposition of 
the reciprocal-space term you seem to be after.
 
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/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: how to g_select bound water molecules

[Yun Shi]

OK. I have a protein "ab" and ligand "lig", and I want to select the bound
water between them. So I used

g_select -f trajout.xtc -s mdrun.tpr -n index.ndx -select '"boundwaters"
resname SOL and within 0.4 of group "ab" and within 0.4 of group "lig"' -on
boundwaters.ndx

Then I can use the ndx file to do other things. The hard part is what after
-select


On Mon, Apr 2, 2012 at 5:11 PM, Dallas Warren wrote:

>  For future reference of others that may struggle with g_select, it would
> be a very good idea for you to put on the emailing list how you achieved it.
> 
>
> ** **
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
>
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail. 
>
> ** **
>
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *Yun Shi
> *Sent:* Tuesday, 3 April 2012 9:58 AM
> *To:* Discussion list for GROMACS users
> *Subject:* [gmx-users] Re: how to g_select bound water molecules
>
> ** **
>
> Never mind. I got it.
>
> On Mon, Apr 2, 2012 at 4:20 PM, Yun Shi  wrote:
>
> Hello all,
>
> Can anyone tell me how to get in "help examples" in g_select by typing
> some commands?
>
> Anyway, I want to select bound waters between my ligand and protein using
> -select 'resname SOL & within 0.5 ...'. Any idea?
>
> Thanks for any suggestion.
>
> Yun
>
> ** **
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] on the Umbrella Sampling on-line tutorial

[chris . neale]

Dear Acoot:

I'll reply to general topics, not to the tutorial in particular.

If the opening is not large enough to allow the peptide to exit, then  
the surrounding protein will need to change its conformation to permit  
unbinding. This can happen, but you need (a) to have sufficiently long  
sampling times to permit the required conformational change and (b)  
starting structures in which the peptide is near the umbrella center  
and do not crash during simulation.


The US method is always valid, but it is not always the best choice.  
You might try using the free energy code to implement a thermodynamic  
cycle. Nevertheless, one imagines that the protein does actually need  
to open up during peptide binding and so you will still need to sample  
protein opening/closing in order to obtain equilibrium (i.e. correct)  
binding free energies because you need to sample the unbound protein  
at equilibrium. That is to say that a thermodynamic cycle may appear  
converged when in fact it is not, because you have not converged the  
unbound state of the protein. In any event, be careful with your  
convergence analysis.


This would be a good system for which to attempt both US and  
double-decoupling approaches and use the results of each to ensure  
that you are not missing some important conformational states.


That said, I highly doubt that it is possible to converge the free  
energies of induced-fit peptide-protein binding with any available  
atomistic computational method using contemporary computational  
resources. The lower bound of required sampling times is certainly on  
the order of 10 us per umbrella and I bet that the actual value is a  
few orders of magnitude larger. I have less experience with the free  
energy code than I do with US, but I suspect that the required  
sampling times are also very long for a system like this.


Chris.

-- original message --

Dear All,

I planned to use the method introduced in the Umbrella Sampling  
on-line tutorial of Justin Lemkul  
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html).


But if a peptide is surrounded by a protein, which means the opening  
of the protein-complex is not large enough to allow the peptide to  
leave the protein without significantly breaking the conformation of  
the protein in the protein-peptide complex, is the Umbrella Sampling  
method still valid for the binding energy calculation?


Will you please also show me in which part of the tutorial the  
direction of pull-apart is defined? We should process it in a  
direction the peptide can leave the protein, not the direction protein  
will bind the peptide much strongly.


I am looking forward to getting a reply from you.

Cheers,

Acoot


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] the mdrun -reprod in gromacs 4.5.5

[Acoot Brett]

Dear All,

For gromcas 4.5.5 mdrun, is "-reprod (reproducibility)" is the default function 
or not?

If not the default function, then how shod we input value for "-reprod" in 
order to get high reproducibility? The value should be "yes" or "no"? The 
on-line manual explanation on it makes me confusing.

I am looking forward to getting your reply.

Cheers,

Acoot
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom

[Andrew DeYoung]

Hi,

Is it possible to compute the total electrostatic energy of an atom over
time?  By "total," I mean including all of the terms (short range Coulomb,
1-4 Coulomb, and Ewald), not just the short range Coulomb and 1-4 Coulomb.

This question is somewhat related to a question I asked last week (
http://lists.gromacs.org/pipermail/gmx-users/2012-March/069745.html ), and
to which I received a great answer.  But my specific question now is: is it
possible to calculate the Ewald term due to a particular atom?  Or is it
impossible to decouple the Ewald calculation among individual atoms or or
sets of pairs of atoms? 

For example, I would like to determine the electrostatic energy between atom
455 and the "rest" of the system (i.e., all other atoms in the system).  To
try this, I added an entry "a" to my .ndx file:

[ a ]
455

I then added a directive to my .mdp file:

energygrps = a

I then run grompp and mdrun, passing my .ndx file to grompp.  (Note: in my
.mdp file, I specify that energies should be saved every timestep: nstenergy
= 1.)  Then I run g_energy on the .edr file that resulted from mdrun.  I am
given the following energy terms to extract: 

---
  1  Bond 2  Angle3  Ryckaert-Bell.   4  LJ-14

  5  Coulomb-14   6  LJ-(SR)  7  Coulomb-(SR) 8
Coul.-recip.  
  9  Potential   10  Kinetic-En. 11  Total-Energy12
Conserved-En. 
 13  Temperature 14  Pressure15  Constr.-rmsd16  Vir-XX

 17  Vir-XY  18  Vir-XZ  19  Vir-YX  20  Vir-YY

 21  Vir-YZ  22  Vir-ZX  23  Vir-ZY  24  Vir-ZZ

 25  Pres-XX 26  Pres-XY 27  Pres-XZ 28  Pres-YX

 29  Pres-YY 30  Pres-YZ 31  Pres-ZX 32  Pres-ZY

 33  Pres-ZZ 34  #Surf*SurfTen   35  Mu-X36  Mu-Y

 37  Mu-Z38  Coul-SR:a-a 39  LJ-SR:a-a   40  Coul-14:a-a

 41  LJ-14:a-a   42  Coul-SR:a-rest  43  LJ-SR:a-rest44
Coul-14:a-rest
 45  LJ-14:a-rest46  Coul-SR:rest-rest

 47  LJ-SR:rest-rest 48  Coul-14:rest-rest

 49  LJ-14:rest-rest 50  T-System
---

Choices 42 and 44 are two parts of what I would like: short range Coulomb
and 1-4 Coulomb energy terms for a-rest.  But is it possible to somehow also
calculate the Ewald term for a-rest?

Thank you kindly! 

Andrew DeYoung
Carnegie Mellon University 

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] on the Umbrella Sampling on-line tutorial

[Acoot Brett]

Dear All,

I planned to use the method introduced in the Umbrella Sampling on-line 
tutorial of Justin Lemkul 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html).
 

But if a peptide is surrounded by a protein, which means the opening of the 
protein-complex is not large enough to allow the peptide to leave the protein 
without significantly breaking the conformation of the protein in the 
protein-peptide complex, is the Umbrella Sampling method still valid for the 
binding energy calculation?

Will you please also show me in which part of the tutorial the direction of 
pull-apart is defined? We should process it in a direction the peptide can 
leave the protein, not the direction protein will bind the peptide much 
strongly.

I am looking forward to getting a reply from you.

Cheers,

Acoot
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] How to compile the template.c when GMX is builded with cmake

[chris . neale]

Dear Users:

I was previously able to compile template.c after I compiled gromacs  
with autoconf. I was unable to compile templae.c, however, I used  
cmake to compile gromacs. This is from gromacs-4.5.4.


I tried "cmake ." in the template directory with no success:

cmake .gpc-f102n084-$ cmake .
-- The C compiler identification is Intel
-- The CXX compiler identification is Intel
-- Check for working C compiler:  
/home/scinet/gpc/intel/ics/composer_xe_2011_sp1.6.233/bin/intel64/icc
-- Check for working C compiler:  
/home/scinet/gpc/intel/ics/composer_xe_2011_sp1.6.233/bin/intel64/icc  
-- works

-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler:  
/home/scinet/gpc/intel/ics/composer_xe_2011_sp1.6.233/bin/intel64/icpc
-- Check for working CXX compiler:  
/home/scinet/gpc/intel/ics/composer_xe_2011_sp1.6.233/bin/intel64/icpc  
-- works

-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- checking for module 'libmd'
--   package 'libmd' not found
CMake Error at CMakeLists.txt:42 (message):
  libmd not found, source GMXRC.


-- Configuring incomplete, errors occurred!

###

For this test, I used the template.c that came with gromacs.

This issue has previously been posted to the list (see below) but I  
was unable to find any answers to that previous querry.


I also looked at the README that came in the template directory and  
find it to be apparently autoconf specific, with no directions for  
cmake.


Thank you,
Chris.

quoting http://www.mail-archive.com/gmx-users@gromacs.org/msg39347.html

How to compile the template.c when GMX is builded with cmake

Bert
Thu, 31 Mar 2011 10:15:22 -0700

Dear all,

When GMX is builded with cmake, how to compile the template.c? I used
to make the template.c by the command "make -f MakefileXXX", but it
can not work in version 4.5. Thanks for your suggestions.

Best regards,
Bert
--




--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

RE: [gmx-users] Re: how to g_select bound water molecules

[Dallas Warren]

For future reference of others that may struggle with g_select, it would be a 
very good idea for you to put on the emailing list how you achieved it.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Yun Shi
Sent: Tuesday, 3 April 2012 9:58 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] Re: how to g_select bound water molecules

Never mind. I got it.
On Mon, Apr 2, 2012 at 4:20 PM, Yun Shi 
mailto:yunsh...@gmail.com>> wrote:
Hello all,

Can anyone tell me how to get in "help examples" in g_select by typing some 
commands?

Anyway, I want to select bound waters between my ligand and protein using 
-select 'resname SOL & within 0.5 ...'. Any idea?

Thanks for any suggestion.

Yun

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

RE: [gmx-users] a question related to the extending of md

[Dallas Warren]

Also, it is easy to join the two .edr files together, using eneconv

However, it is probably better for you to simply start again and get the 
simulation to complete in one go.  It should not take long to do.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Dallas Warren
Sent: Tuesday, 3 April 2012 9:37 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] a question related to the extending of md

What .edr files are listed in the directory?

Seems simply a case that the first section of the trajectory energy file has a 
separate file name to the last, i.e. the results weren't appended to the 
initial .edr file.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org 
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Acoot Brett
Sent: Tuesday, 3 April 2012 9:13 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: [gmx-users] a question related to the extending of md


   Dear All,

I am raning the 100 ps npt according to the on-line tutorial. For the computer 
reason it stops at about  less than50 ps.

Then I
$ tpbconv -s npt.tpr -until 100 -o 100npt.tpr


mdrun -s 100npt.tpr -cpi npt.cpt -v

After completes I analyzee the g-energy. But xgrace shows for pressure and 
dnsity, the x-axis is only from 0 to a little more than 50 ps, and I cannot get 
the results for x-axis from 0 to 100 ps.

I am looking forward to getting a reply from you on how to solve the probelm.

Cheers,

Acoot
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: how to g_select bound water molecules

[Yun Shi]

Never mind. I got it.

On Mon, Apr 2, 2012 at 4:20 PM, Yun Shi  wrote:

> Hello all,
>
> Can anyone tell me how to get in "help examples" in g_select by typing
> some commands?
>
> Anyway, I want to select bound waters between my ligand and protein using
> -select 'resname SOL & within 0.5 ...'. Any idea?
>
> Thanks for any suggestion.
>
> Yun
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

RE: [gmx-users] a question related to the extending of md

[Dallas Warren]

What .edr files are listed in the directory?

Seems simply a case that the first section of the trajectory energy file has a 
separate file name to the last, i.e. the results weren't appended to the 
initial .edr file.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Acoot Brett
Sent: Tuesday, 3 April 2012 9:13 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: [gmx-users] a question related to the extending of md


   Dear All,

I am raning the 100 ps npt according to the on-line tutorial. For the computer 
reason it stops at about  less than50 ps.

Then I
$ tpbconv -s npt.tpr -until 100 -o 100npt.tpr


mdrun -s 100npt.tpr -cpi npt.cpt -v

After completes I analyzee the g-energy. But xgrace shows for pressure and 
dnsity, the x-axis is only from 0 to a little more than 50 ps, and I cannot get 
the results for x-axis from 0 to 100 ps.

I am looking forward to getting a reply from you on how to solve the probelm.

Cheers,

Acoot
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] how to g_select bound water molecules

[Yun Shi]

Hello all,

Can anyone tell me how to get in "help examples" in g_select by typing some
commands?

Anyway, I want to select bound waters between my ligand and protein using
-select 'resname SOL & within 0.5 ...'. Any idea?

Thanks for any suggestion.

Yun
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] a question related to the extending of md

[Acoot Brett]

 
   Dear All,
 
I am raning the 100 ps npt according to the on-line tutorial. For the computer 
reason it stops at about  less than50 ps.
 
Then I$ tpbconv -s npt.tpr  -until 100 -o 100npt.tpr
 
 mdrun -s 100npt.tpr -cpi npt.cpt -v
 
After completes I analyzee the g-energy. But xgrace shows for pressure and 
dnsity, the x-axis is only from 0 to a little more than 50 ps, and I cannot get 
the results for x-axis from 0 to 100 ps.
 
I am looking forward to getting a reply from you on how to solve the probelm.
 
Cheers,
 
Acoot-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] ions error

[Justin A. Lemkul]

Eduardo Oliveira wrote:

OK, thanks for the info.

I'm running GROMACS 4.5.5

Here is my genion command:

genion_d -s sistema_stpr.tpr -o sistema_ion.gro -nname CL- -nn 3 -nq -1 
-p sistema.top


I chose the GROMOS force filed.



Refer to the second paragraph of genion -h.

-Justin



*De:* Justin A. Lemkul 
*Para:* Eduardo Oliveira ; Discussion list for 
GROMACS users 

*Enviadas:* Segunda-feira, 2 de Abril de 2012 16:55
*Assunto:* Re: [gmx-users] ions error



Eduardo Oliveira wrote:
 > Hi all,
 >
 > After a ran grompp_d in prepration for a Steepest Descente 
Minimizations with constraints i got the folowing error message:

 >
 > Fatal error:
 > No such moleculetype CL-
 >
 > I don know for shure but i think that i forgot to modify some of the 
files with the numbers os CL- ions I've introduced into the system.

 >

No, the error is complaining about the ion name, not the number.  If the 
numbering mismatched, you'd get something different.  Check ions.itp for 
proper naming for your force field.


 > Here is the command line:
 >
 > grommp_d -f stpr.mdp -c sistema_ions.gro -p sistema.top -o 
sistema_stpr.tpr


The more relevant information would have been your genion command, force 
field name, and Gromacs version.


-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






--


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/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] ions error

[Justin A. Lemkul]

Eduardo Oliveira wrote:

Hi all,

After a ran grompp_d in prepration for a Steepest Descente Minimizations 
with constraints i got the folowing error message:


Fatal error:
No such moleculetype CL-

I don know for shure but i think that i forgot to modify some of the 
files with the numbers os CL- ions I've introduced into the system.




No, the error is complaining about the ion name, not the number.  If the 
numbering mismatched, you'd get something different.  Check ions.itp for proper 
naming for your force field.



Here is the command line:

grommp_d -f stpr.mdp -c sistema_ions.gro -p sistema.top -o sistema_stpr.tpr


The more relevant information would have been your genion command, force field 
name, and Gromacs version.


-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 listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] ions error

[Eduardo Oliveira]

Hi all,

After a ran grompp_d in prepration for a Steepest Descente Minimizations with 
constraints i got the folowing error message:

Fatal error:
No such moleculetype CL-


I don know for shure but i think that i forgot to modify some of the files with 
the numbers os CL- ions I've introduced into the system.

Here is the command line:

grommp_d -f stpr.mdp -c sistema_ions.gro -p sistema.top -o sistema_stpr.tpr

Thanks in advance.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] em fatal error!

[Erik Marklund]

2 apr 2012 kl. 16.02 skrev lina:

> On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila  wrote:
>> We are trying to do simulation of lysozyme in water.
>> 
>> step with problem : energy minimization.
>> 
>> command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c
>> 1AKI_solv_ions.gro -p topol.top -o em.tpr
>> 
>>  :-)  G  R  O  M  A  C  S  (-:
>> 
>> Getting the Right Output Means no Artefacts in Calculating Stuff
>> 
>> :-)  VERSION 4.0.5  (-:
>> 
>> 
>>   Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>>Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>  Copyright (c) 2001-2008, The GROMACS development team,
>> check out http://www.gromacs.org for more information.
>> 
>>  This program is free software; you can redistribute it and/or
>>   modify it under the terms of the GNU General Public License
>>  as published by the Free Software Foundation; either version 2
>>  of the License, or (at your option) any later version.
>> 
>> :-)  grompp  (-:
>> 
>> Option Filename  Type Description
>> 
>>   -f  minim.mdp  Input, Opt!  grompp input file with MD parameters
>>  -po  mdout.mdp  Output   grompp input file with MD parameters
>>   -c 1AKI_solv_ions.gro  InputStructure file: gro g96 pdb tpr tpb
>> tpa
>>   -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>>  -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>>   -n  index.ndx  Input, Opt.  Index file
>>   -p  topol.top  InputTopology file
>>  -pp  processed.top  Output, Opt. Topology file
>>   -o em.tpr  Output   Run input file: tpr tpb tpa
>>   -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>>   -e   ener.edr  Input, Opt.  Energy file: edr ene
>> 
>> Option   Type   Value   Description
>> --
>> -[no]h   bool   no  Print help info and quit
>> -niceint0   Set the nicelevel
>> -[no]v   bool   yes Be loud and noisy
>> -timereal   -1  Take frame at or first after this time.
>> -[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
>> sites
>> -maxwarn int0   Number of allowed warnings during input
>> processing
>> -[no]zerobool   no  Set parameters for bonded interactions without
>> defaults to zero instead of generating an error
>> -[no]renum   bool   yes Renumber atomtypes and minimize number of
>> atomtypes
>> 
>> 
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
>> checking input for internal consistency...
>> processing topology...
>> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp
>> Generated 332520 of the 332520 non-bonded parameter combinations
>> Generating 1-4 interactions: fudge = 0.5
>> Generated 332520 of the 332520 1-4 parameter combinations
>> Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
>> Excluding 3 bonded neighbours molecule type 'Protein_A'
>> Excluding 2 bonded neighbours molecule type 'SOL'
>> 
>> ---
>> Program grompp, VERSION 4.0.5
> 
> You use Version 4.0.5.
> 
> If I remember correctly, the earlier version has different pname.
> (seems one is NA+, one is NA)
> 
> If I were you, I would update to latest version and try.

Upgrading may be a good thing for many reasons. To see what are the names of 
ions, check ions.itp.

> 
>> Source code file: toppush.c, line: 1641
>> 
>> Fatal error:
>> No such moleculetype NA
>> 
>> what should we do
>> 
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

---

Re: [gmx-users] charges

[David van der Spoel]

On 2012-04-02 20:40, R.Perez Garcia wrote:

Dear prof. van der Spoel,
I know.. Dr. Alex de Vries is supervising me for my colloquium.
Unfortunately (for me), they are very busy and (mainly) I am doing four
months stage at Perugia universityv (It) which means I can not
personally ask...so I prefer to ask the list.
Thank you for your answer, even if the literature concerning virtual
charges is not a lot, I will keep looking.
Best regards: R


It's in the manual.
[ virtual_sites2 ]
; k i j type constant
3  1 2 1  0.5

will give you a virtual site 3 half-way atoms 1 & 2.



On 02-04-12, *David van der Spoel *  wrote:

On 2012-04-02 20:29, R.Perez Garcia wrote:
>Dear GROMACS users,
>I would like to place the charge more localized in the "bonds region"
>and not exactly in the atoms.
>Please let me know if you know there is a way to do this in GROMACS.
>Thank you in advance, R
>
>
Yes, using virtual sites.
There's an expert group of gromacs users at the department of
biophysical chemistry at your university, Marrink. You may want to
talk to then.

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists






--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] charges

[R.Perez Garcia]

Dear prof. van der Spoel,
I know.. Dr. Alex de Vries is supervising me for my colloquium. Unfortunately 
(for me), they are very busy and (mainly) I am doing four months stage at 
Perugia universityv (It) which means I can not personally ask...so I prefer to 
ask the list.
Thank you for your answer, even if the literature concerning virtual charges is 
not a lot, I will keep looking.
Best regards: R

On 02-04-12, David van der Spoel   wrote:
> On 2012-04-02 20:29, R.Perez Garcia wrote:
> >Dear GROMACS users,
> >I would like to place the charge more localized in the "bonds region"
> >and not exactly in the atoms.
> >Please let me know if you know there is a way to do this in GROMACS.
> >Thank you in advance, R
> >
> >
> Yes, using virtual sites.
> There's an expert group of gromacs users at the department of biophysical 
> chemistry at your university, Marrink. You may want to talk to then.
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.se    http://folding.bmc.uu.se
> -- 
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface 
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] charges

[David van der Spoel]

On 2012-04-02 20:29, R.Perez Garcia wrote:

Dear GROMACS users,
I would like to place the charge more localized in the "bonds region"
and not exactly in the atoms.
Please let me know if you know there is a way to do this in GROMACS.
Thank you in advance, R



Yes, using virtual sites.
There's an expert group of gromacs users at the department of 
biophysical chemistry at your university, Marrink. You may want to talk 
to then.


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] charges

[R.Perez Garcia]

Dear GROMACS users,
I would like to place the charge more localized in the "bonds region" and not 
exactly in the atoms.
Please let me know if you know there is a way to do this in GROMACS.
Thank you in advance, R 
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Editing of the existing system

[James Starlight]

By the way

Today I've examined in vacuum minimisation outputs more carefully (
watching in vmd trr ) and found that conformation of the loops in the
docked regions were changed after long CG minimisation.

Then I've resolvate my system and add ions and run STEEP minimisation of
that system.

After this I've decreasing integration step to the from 0.001 to 0.0001.

Unfortunatelly the error was the same

starting with the LINK warnings like

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002089, max 0.082711 (between atoms 1387 and 1388)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length


and ending with the exploiding of my system as well with the eror like

step 29: Water molecule starting at atom 42310 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates


Also I've changed COM groups ( to the System value in one case as well as
placing the second protein group to the common group with the first protein
and membrane in the second case ). But the result was the same.


Is there any  suggestions or should I start with another conformation of
first protein ?


James



2 апреля 2012 г. 9:56 пользователь James Starlight
написал:

> Justin,
>
> Thanks again for attention to my problem.
>
>
> I've checked my system and found that the problem was exactly in the 1388
> atom ( wich is not properly minimized in accordance to the log files). This
> atom is the Cb atom of Gln residue wich placed between one loop of the
> protein and docked alpha helix of the peptide. The  surrounding of that
> atom ( It's likely that other intracellular loops of the receptor as well
> as long N term protect this side chain to rotate during the minimisation ).
> When I've checked pdb files produced by exploding system I've found that
> some atoms ( from that loops) were moved from the pereodic boundaries (
> I've obtain very big system as the conseqyence surrounding by some single
> atoms. So it all look like as big artifact :) )
>
> So it seems that I need to use slightly different initial conformation of
> the receptor because minimisation could not to resolve such crushes.
>
>
> Thanks again
>
>
> James
>
> 1 апреля 2012 г. 21:37 пользователь Justin A. Lemkul написал:
>
>
>>
>> James Starlight wrote:
>>
>>> Justin,
>>>
>>> Sorry again for the delay.
>>>
>>> I've finished minimise my system with the CG algorithm in double
>>> precision ( after steep minimisation )
>>> but the output was
>>>
>>> Stepsize too small, or no change in energy.
>>> Converged to machine precision,
>>> but not to the requested precision Fmax < 0.1
>>>
>>> Than I've tried to equilibrate this system with the NVT conditions and
>>> obtain old error about collapse of my system :)
>>>
>>>  I've found logs of both minimisation ( the step minimisation log was
>>> very big I've coppied only end part of this output data )  and attach it to
>>> this topic.
>>>
>>>
>> Both of these log files indicate that EM was likely fine.  For future
>> reference, the following sections were all I was asking for all along:
>>
>> From CG:
>> Potential Energy  = -5.96597537065782e+05
>> Maximum force =  1.42815783701700e+02 on atom 1388
>> Norm of force =  1.58963638409829e+00
>>
>> From steep:
>> Potential Energy  = -5.7233788e+05
>> Maximum force =  7.0209003e+02 on atom 1388
>> Norm of force =  1.1310696e+01
>>
>> CG gives you the better minimization, overall, as expected.  Atom 1388
>> bears the maximum force, but it is not of problematic magnitude.
>>
>>
>>  Also I've run minimisation in vacuum as you've told me but this results
>>> would be aviable tomorrow.
>>>
>>>
>> It's probably not necessary, after all.  I was guessing at that point
>> based on incomplete information.
>>
>>
>>  Could you tell me whats exactly wrong with that system and is there
>>> possible ways to fix the problem?
>>>
>>>
>> As I've said before, the only strange thing you seem to be doing is with
>> your comm-grps.  Change this setting to "System" and see if it runs.
>>  Otherwise, I can find no reason for the immediate instability.  If it
>> still crashes, perhaps decrease the time step for the initial equilibration.
>>
>>
>> -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 listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search

Re: [gmx-users] em fatal error!

[lina]

On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila  wrote:
> We are trying to do simulation of lysozyme in water.
>
> step with problem : energy minimization.
>
> command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c
> 1AKI_solv_ions.gro -p topol.top -o em.tpr
>
>  :-)  G  R  O  M  A  C  S  (-:
>
>     Getting the Right Output Means no Artefacts in Calculating Stuff
>
>     :-)  VERSION 4.0.5  (-:
>
>
>   Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>    Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>  Copyright (c) 2001-2008, The GROMACS development team,
>     check out http://www.gromacs.org for more information.
>
>  This program is free software; you can redistribute it and/or
>   modify it under the terms of the GNU General Public License
>  as published by the Free Software Foundation; either version 2
>  of the License, or (at your option) any later version.
>
>     :-)  grompp  (-:
>
> Option Filename  Type Description
> 
>   -f  minim.mdp  Input, Opt!  grompp input file with MD parameters
>  -po  mdout.mdp  Output   grompp input file with MD parameters
>   -c 1AKI_solv_ions.gro  Input    Structure file: gro g96 pdb tpr tpb
> tpa
>   -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>  -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>   -n  index.ndx  Input, Opt.  Index file
>   -p  topol.top  Input    Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o em.tpr  Output   Run input file: tpr tpb tpa
>   -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>   -e   ener.edr  Input, Opt.  Energy file: edr ene
>
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -nice    int    0   Set the nicelevel
> -[no]v   bool   yes Be loud and noisy
> -time    real   -1  Take frame at or first after this time.
> -[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
>     sites
> -maxwarn int    0   Number of allowed warnings during input
> processing
> -[no]zero    bool   no  Set parameters for bonded interactions without
>     defaults to zero instead of generating an error
> -[no]renum   bool   yes Renumber atomtypes and minimize number of
>     atomtypes
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> ---
> Program grompp, VERSION 4.0.5

You use Version 4.0.5.

If I remember correctly, the earlier version has different pname.
(seems one is NA+, one is NA)

If I were you, I would update to latest version and try.

> Source code file: toppush.c, line: 1641
>
> Fatal error:
> No such moleculetype NA
>
> what should we do
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: Carbohydrate simulation: problem with the terminal atoms

[Justin A. Lemkul]

khuchtumur wrote:

Hi Justin,

Thank you for writing this clarification. I'm still having a bit of a
problem with the anomeric -OH group giving LINCS warnings during
equilibration though. 


I am trying to parametrize a beta-lactose molecule in g53a6. Following are
the steps I followed.
1) Draw lactose in Avogadro
2) Use PRODRG to get ITP template
3) Change the charges and charge groups in accordance with Oostenbrink et al
2004 and Lins et al 2005.
4) Change the bonds and angles in accordance with Oostenbrink et al, which
matches Lins et al
5) Check the improper dihedrals for chiral centers
6) Set up the proper dihedrals using Lins et al. 
7) Set the exclusion you mentioned here (between O5 and H1)

8) Change the C-C-C-O5 specification from Lins et al to CCCO1 specification
as in your post (explained below)

This gives the following charges and dihedrals:

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  LAT  O2 1   -0.642  15.9994   
 2 H 1  LAT H2 10.410   1.0080   
 3   CH1 1  LAT  C2 10.232  13.0190   
 4   CH1 1  LAT  C3 20.232  13.0190   
 5OA 1  LAT  O3 2   -0.642  15.9994   
 6 H 1  LAT H3 20.410   1.0080   
 7   CH1 1  LAT  C4 30.232  13.0190   
 8OA 1  LAT  O4 3   -0.642  15.9994   
 9 H 1  LAT H4 30.410   1.0080   
10   CH1 1  LAT  C5 40.376  13.0190   
11   CH2 1  LAT  C6 50.232  14.0270   
12OA 1  LAT  O6 5   -0.642  15.9994   
13 H 1  LAT H6 50.410   1.0080   
14OA 1  LAT  O5 4   -0.480  15.9994   
15   CH1 1  LAT  C1 40.232  13.0190   
16OA 1  LAT  O1 4   -0.360  15.9994   
17   CH1 1  LAT C4' 40.232  13.0190 ;'

18   CH1 1  LAT C3' 60.232  13.0190 ;'
19OA 1  LAT O3' 6   -0.642  15.9994 ;'
20 H 1  LAT H3' 60.410   1.0080   
21   CH1 1  LAT C2' 70.232  13.0190 ;'

22OA 1  LAT O2' 7   -0.642  15.9994 ;'
23 H 1  LAT H2' 70.410   1.0080   
24   CH1 1  LAT C1' 80.232  13.0190 ;'

25OA 1  LAT O1' 8   -0.538  15.9994 ;'
26 H 1  LAT H1' 80.410   1.0080   
27OA 1  LAT O5' 8   -0.480  15.9994 ;'

28   CH1 1  LAT C5' 80.376  13.0190 ;'
29   CH2 1  LAT C6' 90.232  14.0270 ;'
30OA 1  LAT O6' 9   -0.642  15.9994 ;'
31 H 1  LAT H6' 90.410   1.0080   


[ dihedrals ]

   2   1   3  15   1  gd_30
;   2   1   3   4   1  gd_30
   1   3  15  16   1  gd_18
;   1   3  15  14   1  gd_18
   1   3   4   5   1  gd_18
   1   3   4   7   1  gd_17
;   3  15  16  17   1  gd_29
   3  15  14  10   1  gd_29
   3   4   5   6   1  gd_30
   3   4   7   8   1  gd_17
   3   4   7  10   1  gd_34
  15   3   4   7   1  gd_34
  15   3   4   5   1  gd_17
  16  15   3   4   1  gd_17
  16  15   3   4   1  gd_34
  14  15   3   4   1  gd_17
;  14  15   3   4   1  gd_34
;   6   5   4   7   1  gd_30
   5   4   7   8   1  gd_18
   5   4   7  10   1  gd_17
   4   7   8   9   1  gd_30
   4   7  10  11   1  gd_34
   4   7  10  14   1  gd_17
;   4   7  10  14   1  gd_34
;   9   8   7  10   1  gd_30
   8   7  10  11   1  gd_17
;   8   7  10  14   1  gd_18
;   7  10  11  12   1  gd_1
   7  10  14  15   1  gd_29
  13  12  11  10   1  gd_30
  12  11  10  14   1  gd_3
  12  11  10  14   1  gd_35
;  11  10  14  15   1  gd_29
  14  15  16  17   1  gd_2
  14  15  16  17   1  gd_32
  15  16  17  18   1  gd_30
;  15  16  17  28   1  gd_29
  16  17  18  19   1  gd_18
  16  17  18  21   1  gd_17
  16  17  28  29   1  gd_17
;  16  17  28  27   1  gd_18
;  17  18  19  20   1  gd_30
  17  18  21  22   1  gd_17
  17  18  21  24   1  gd_34
;  17  28  29  30   1  gd_17
  17  28  27  24   1  gd_29
  19  18  17  28   1  gd_17
  18  17  28  29   1  gd_34
  18  17  28  27   1  gd_17
;  18  17  28  27   1  gd_34
  21  18  17  28   1  gd_34
  20  19  18  21   1  gd_30
  19  18  21  22   1  gd_18
  19  18  21  24   1  gd_17
;  18  21  22  23   1  gd_30
  18  21  24  25   1  gd_17
  18  21  24  25   1  gd_34
  18  21  24  27   1  gd_17
;  18  21  24  27   1  gd_34 
  23  22  21  24   1  gd_30

  22  21  24  25   1  gd_18
;  22  21  24  27   1  gd_18
;  21  24  25  26   1  gd_30
  21  24  27  28   1  gd_29
  26  25  24  27   1 

Re: [gmx-users] em fatal error!

[Tsjerk Wassenaar]

Hi Ankita,

>> command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c
>> 1AKI_solv_ions.gro -p topol.top -o em.tpr

It is very unwise to run such things as root.

By the way, if you follow a tutorial and refer to it, please send a link.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] em fatal error!

[rama david]

Hi Ankita ,
   The error is  self-explanatory  , and simple to interpret it.
  You check the Topology file and see the last line that showing
added ions ...
What was your genion  COMMAND LINE
Have a nice day
Rama


On Mon, Apr 2, 2012 at 3:19 PM, Erik Marklund  wrote:
>
> 2 apr 2012 kl. 11.27 skrev ankita oindrila:
>
> We are trying to do simulation of lysozyme in water.
>
> step with problem : energy minimization.
>
> command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c
> 1AKI_solv_ions.gro -p topol.top -o em.tpr
>
>  :-)  G  R  O  M  A  C  S  (-:
>
>     Getting the Right Output Means no Artefacts in Calculating Stuff
>
>     :-)  VERSION 4.0.5  (-:
>
>
>   Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>    Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>  Copyright (c) 2001-2008, The GROMACS development team,
>     check out http://www.gromacs.org for more information.
>
>  This program is free software; you can redistribute it and/or
>   modify it under the terms of the GNU General Public License
>  as published by the Free Software Foundation; either version 2
>  of the License, or (at your option) any later version.
>
>     :-)  grompp  (-:
>
> Option Filename  Type Description
> 
>   -f  minim.mdp  Input, Opt!  grompp input file with MD parameters
>  -po  mdout.mdp  Output   grompp input file with MD parameters
>   -c 1AKI_solv_ions.gro  Input    Structure file: gro g96 pdb tpr tpb
> tpa
>   -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>  -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>   -n  index.ndx  Input, Opt.  Index file
>   -p  topol.top  Input    Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o em.tpr  Output   Run input file: tpr tpb tpa
>   -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>   -e   ener.edr  Input, Opt.  Energy file: edr ene
>
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -nice    int    0   Set the nicelevel
> -[no]v   bool   yes Be loud and noisy
> -time    real   -1  Take frame at or first after this time.
> -[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
>     sites
> -maxwarn int    0   Number of allowed warnings during input
> processing
> -[no]zero    bool   no  Set parameters for bonded interactions without
>     defaults to zero instead of generating an error
> -[no]renum   bool   yes Renumber atomtypes and minimize number of
>     atomtypes
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> ---
> Program grompp, VERSION 4.0.5
> Source code file: toppush.c, line: 1641
>
> Fatal error:
> No such moleculetype NA
>
> what should we do
>
>
> Have a look at http://www.gromacs.org/Documentation/Errors
>
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> ---
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Pleas

[gmx-users] Re: Williams

[wmiranda]

Hello!
What`s the meaning of the error "hi (0.00) <= lo (0.00)" that
outputs g_cluster?
Which the purpose of the option -rmsmin of g_cluster?
Thanks

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Problems with simulation on multi-nodes cluster

[Mark Abraham]

On 2/04/2012 7:13 PM, James Starlight wrote:

Mark,

As I've told previously I have problems with the running simulation in 
multi-node mode.


Yup, and my bet is you can't run any other software on multiple MPI 
nodes either, because your MPI system is not set up correctly, or maybe 
is too old. We can't help with that, since it's nothing to do with GROMACS.




I checked logs of such simulations and fond like this

Will use 10 particle-particle and 6 PME only nodes
This is a guess, check the performance at the end of the log file
Using 6 separate PME nodes

This simulation was run on the 2 nodes ( 2*8 CPUs). And I've never 
obtain the same notions about PME nodes when I've launch my systems on 
the singe node.


Not surprising. Running in parallel is a lot more tricky than running in 
serial, and so there's lots of software engineering that supports it. 
See manual 3.15 and 3.17.5. Running at near-maximum efficiency in 
parallel requires you understand some of that, but by default it will 
"just run" almost all the time.


Might it be that some special options for the PME nodes are needed in 
the mdp file to be defined ?


Not in the sense you mean. There are not normally any .mdp changes 
necessary to support parallelism, and you get told about them when they 
arise. The trace back below clearly indicates that the problem occurs as 
GROMACS goes to set up the parallel communication infrastructure, which 
has nothing directly to do with the .mdp contents.


Mark



James

20 ? 2012 ?. 18:02  Mark Abraham 
mailto:mark.abra...@anu.edu.au>> ???:


On 20/03/2012 10:35 PM, James Starlight wrote:

Could someone tell me what tell the below error

Getting Loaded...
Reading file MD_100.tpr, VERSION 4.5.4 (single precision)
Loaded with Money


Will use 30 particle-particle and 18 PME only nodes
This is a guess, check the performance at the end of the log file
[ib02:22825] *** Process received signal ***
[ib02:22825] Signal: Segmentation fault (11)
[ib02:22825] Signal code: Address not mapped (1)
[ib02:22825] Failing at address: 0x10
[ib02:22825] [ 0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xf030) [0x7f535903e03$
[ib02:22825] [ 1]
/usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x7e23) [0x7f535$
[ib02:22825] [ 2]
/usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x8601) [0x7f535$
[ib02:22825] [ 3]
/usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x8bab) [0x7f535$
[ib02:22825] [ 4]
/usr/lib/openmpi/lib/openmpi/mca_btl_sm.so(+0x42af) [0x7f5353$
[ib02:22825] [ 5]
/usr/lib/libopen-pal.so.0(opal_progress+0x5b) [0x7f535790506b]
[ib02:22825] [ 6] /usr/lib/libmpi.so.0(+0x37755) [0x7f5359282755]
[ib02:22825] [ 7]
/usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so(+0x1c3a) [0x7f$
[ib02:22825] [ 8]
/usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so(+0x7fae) [0x7f$
[ib02:22825] [ 9] /usr/lib/libmpi.so.0(ompi_comm_split+0xbf)
[0x7f535926de8f]
[ib02:22825] [10] /usr/lib/libmpi.so.0(MPI_Comm_split+0xdb)
[0x7f535929dc2b]
[ib02:22825] [11]
/usr/lib/libgmx_mpi_d.openmpi.so.6(gmx_setup_nodecomm+0x19b) $
[ib02:22825] [12] mdrun_mpi_d.openmpi(mdrunner+0x46a) [0x40be7a]
[ib02:22825] [13] mdrun_mpi_d.openmpi(main+0x1256) [0x407206]
[ib02:22825] [14]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd) [0x7f$
[ib02:22825] [15] mdrun_mpi_d.openmpi() [0x407479]
[ib02:22825] *** End of error message ***

--
mpiexec noticed that process rank 36 with PID 22825 on node
ib02 exited on sign$

--


I've obtained it when I've tried to use my system on
multi-node station ( there is no problem on single node). Does
this problem with the cluster system or something wrong with
parameters of my simulation?


The trace back suggests your MPI system is not configured
correctly for your hardware.

Mark

-- 
gmx-users mailing list gmx-users@gromacs.org


http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists






-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe reque

Re: [gmx-users] Adding Born Radii for implicit solvent MD

[Mark Abraham]

On 2/04/2012 7:57 PM, german.erlenk...@pharmazie.uni-halle.de wrote:

Dear Gromacs-Users,

I want to do a MD with implicit solvent.
During this I'll get the following erros.

GB parameter(s) missing or negative for atom type 'ca'

GB parameter(s) missing or negative for atom type 'OS'

GB parameter(s) missing or negative for atom type 'nh'

GB parameter(s) missing or negative for atom type 'c3'

GB parameter(s) missing or negative for atom type 'ha'

GB parameter(s) missing or negative for atom type 'hn'

GB parameter(s) missing or negative for atom type 'h1'

GB parameter(s) missing or negative for atom type 'h4'

GB parameter(s) missing or negative for atom type 'OW_spc'

GB parameter(s) missing or negative for atom type 'HW_spc'

GB parameter(s) missing or negative for atom type 'Na'

GB parameter(s) missing or negative for atom type 'Cl'


It seems that I have to add the Born-Radii for these atoms.
I have the Radii, but I don't know where I have to add them neither
what will be the right syntax.

Do I have to add the information in the itp-file for the ligand, the
complex or in gbsa.itp?


See manual 5.3.5. The lookup is done by atomtype, so the best approach 
is to make a local copy of the whole forcefield directory to your 
working directory, modify probably gbsa.itp. pdb2gmx will (be able to) 
pick up the local copy when generating the .top, so that grompp will 
find the parameters later.


Mrak
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: GPU support on GROMACS

[Szilárd Páll]

Hi,

> thought you can help with this...

I'd appreciate if you kept future conversation on the mailing list.

> The GROMACS website says Geforce GTX 560 Ti is supported. How about GTX 560?

Yes, they are. All Fermi-class cards are supported.

--
Szilárd


> Thanks,
> G
>
> --
> Gaurav Goel, PhD
> Assistant Professor
> Department of Chemical Engineering
> Indian Institute of Technology, Delhi
> Hauz Khas, New Delhi 110016
> India
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Adding Born Radii for implicit solvent MD

[german . erlenkamp]

Dear Gromacs-Users,

I want to do a MD with implicit solvent.
During this I'll get the following erros.

GB parameter(s) missing or negative for atom type 'ca'

GB parameter(s) missing or negative for atom type 'OS'

GB parameter(s) missing or negative for atom type 'nh'

GB parameter(s) missing or negative for atom type 'c3'

GB parameter(s) missing or negative for atom type 'ha'

GB parameter(s) missing or negative for atom type 'hn'

GB parameter(s) missing or negative for atom type 'h1'

GB parameter(s) missing or negative for atom type 'h4'

GB parameter(s) missing or negative for atom type 'OW_spc'

GB parameter(s) missing or negative for atom type 'HW_spc'

GB parameter(s) missing or negative for atom type 'Na'

GB parameter(s) missing or negative for atom type 'Cl'


It seems that I have to add the Born-Radii for these atoms.
I have the Radii, but I don't know where I have to add them neither
what will be the right syntax.

Do I have to add the information in the itp-file for the ligand, the
complex or in gbsa.itp?

Thanks for your help in advance.

Best regards,

German
-- 
German Erlenkamp
Institut fuer Pharmazeutische Chemie
Martin-Luther-Universitaet Halle
Wolfgang-Langenbeck-Str.4
06120 Halle/ Saale

E-Mail: german.erlenk...@pharmazie.uni-halle.de
Phone: (49)345 - 55 25 194
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] em fatal error!

[Erik Marklund]

2 apr 2012 kl. 11.27 skrev ankita oindrila:

> We are trying to do simulation of lysozyme in water.
> 
> step with problem : energy minimization.
> 
> command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c 
> 1AKI_solv_ions.gro -p topol.top -o em.tpr
> 
>  :-)  G  R  O  M  A  C  S  (-:
> 
> Getting the Right Output Means no Artefacts in Calculating Stuff
> 
> :-)  VERSION 4.0.5  (-:
> 
> 
>   Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>  Copyright (c) 2001-2008, The GROMACS development team,
> check out http://www.gromacs.org for more information.
> 
>  This program is free software; you can redistribute it and/or
>   modify it under the terms of the GNU General Public License
>  as published by the Free Software Foundation; either version 2
>  of the License, or (at your option) any later version.
> 
> :-)  grompp  (-:
> 
> Option Filename  Type Description
> 
>   -f  minim.mdp  Input, Opt!  grompp input file with MD parameters
>  -po  mdout.mdp  Output   grompp input file with MD parameters
>   -c 1AKI_solv_ions.gro  InputStructure file: gro g96 pdb tpr tpb tpa
>   -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>  -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>   -n  index.ndx  Input, Opt.  Index file
>   -p  topol.top  InputTopology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o em.tpr  Output   Run input file: tpr tpb tpa
>   -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>   -e   ener.edr  Input, Opt.  Energy file: edr ene
> 
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -niceint0   Set the nicelevel
> -[no]v   bool   yes Be loud and noisy
> -timereal   -1  Take frame at or first after this time.
> -[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
> sites
> -maxwarn int0   Number of allowed warnings during input processing
> -[no]zerobool   no  Set parameters for bonded interactions without
> defaults to zero instead of generating an error
> -[no]renum   bool   yes Renumber atomtypes and minimize number of
> atomtypes
> 
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
> 
> ---
> Program grompp, VERSION 4.0.5
> Source code file: toppush.c, line: 1641
> 
> Fatal error:
> No such moleculetype NA
> 
> what should we do

Have a look at http://www.gromacs.org/Documentation/Errors


> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] em fatal error!

[ankita oindrila]

*We are trying to do simulation of lysozyme in water.*

step with problem : energy minimization.

command given: *[root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c
1AKI_solv_ions.gro -p topol.top -o em.tpr*

 :-)  G  R  O  M  A  C  S  (-:

Getting the Right Output Means no Artefacts in Calculating Stuff

:-)  VERSION 4.0.5  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

:-)  grompp  (-:

Option Filename  Type Description

  -f  minim.mdp  Input, Opt!  grompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c 1AKI_solv_ions.gro  InputStructure file: gro g96 pdb tpr tpb
tpa
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n  index.ndx  Input, Opt.  Index file
  -p  topol.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -o em.tpr  Output   Run input file: tpr tpb tpa
  -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e   ener.edr  Input, Opt.  Energy file: edr ene

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint0   Set the nicelevel
-[no]v   bool   yes Be loud and noisy
-timereal   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
sites
-maxwarn int0   Number of allowed warnings during input
processing
-[no]zerobool   no  Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum   bool   yes Renumber atomtypes and minimize number of
atomtypes


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 2 bonded neighbours molecule type 'SOL'

---
Program grompp, VERSION 4.0.5
Source code file: toppush.c, line: 1641

*Fatal error:
No such moleculetype NA*

what should we do
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Problems with simulation on multi-nodes cluster

[James Starlight]

Mark,

As I've told previously I have problems with the running simulation in
multi-node mode.

I checked logs of such simulations and fond like this

Will use 10 particle-particle and 6 PME only nodes
This is a guess, check the performance at the end of the log file
Using 6 separate PME nodes

This simulation was run on the 2 nodes ( 2*8 CPUs). And I've never obtain
the same notions about PME nodes when I've launch my systems on the singe
node. Might it be that some special options for the PME nodes are needed in
the mdp file to be defined ?

James

20 марта 2012 г. 18:02 пользователь Mark Abraham
написал:

> On 20/03/2012 10:35 PM, James Starlight wrote:
>
>> Could someone tell me what tell the below error
>>
>> Getting Loaded...
>> Reading file MD_100.tpr, VERSION 4.5.4 (single precision)
>> Loaded with Money
>>
>>
>> Will use 30 particle-particle and 18 PME only nodes
>> This is a guess, check the performance at the end of the log file
>> [ib02:22825] *** Process received signal ***
>> [ib02:22825] Signal: Segmentation fault (11)
>> [ib02:22825] Signal code: Address not mapped (1)
>> [ib02:22825] Failing at address: 0x10
>> [ib02:22825] [ 0] /lib/x86_64-linux-gnu/**libpthread.so.0(+0xf030)
>> [0x7f535903e03$
>> [ib02:22825] [ 1] /usr/lib/openmpi/lib/openmpi/**mca_pml_ob1.so(+0x7e23)
>> [0x7f535$
>> [ib02:22825] [ 2] /usr/lib/openmpi/lib/openmpi/**mca_pml_ob1.so(+0x8601)
>> [0x7f535$
>> [ib02:22825] [ 3] /usr/lib/openmpi/lib/openmpi/**mca_pml_ob1.so(+0x8bab)
>> [0x7f535$
>> [ib02:22825] [ 4] /usr/lib/openmpi/lib/openmpi/**mca_btl_sm.so(+0x42af)
>> [0x7f5353$
>> [ib02:22825] [ 5] /usr/lib/libopen-pal.so.0(**opal_progress+0x5b)
>> [0x7f535790506b]
>> [ib02:22825] [ 6] /usr/lib/libmpi.so.0(+0x37755) [0x7f5359282755]
>> [ib02:22825] [ 7] /usr/lib/openmpi/lib/openmpi/**mca_coll_tuned.so(+0x1c3a)
>> [0x7f$
>> [ib02:22825] [ 8] /usr/lib/openmpi/lib/openmpi/**mca_coll_tuned.so(+0x7fae)
>> [0x7f$
>> [ib02:22825] [ 9] /usr/lib/libmpi.so.0(ompi_**comm_split+0xbf)
>> [0x7f535926de8f]
>> [ib02:22825] [10] /usr/lib/libmpi.so.0(MPI_Comm_**split+0xdb)
>> [0x7f535929dc2b]
>> [ib02:22825] [11] 
>> /usr/lib/libgmx_mpi_d.openmpi.**so.6(gmx_setup_nodecomm+0x19b)
>> $
>> [ib02:22825] [12] mdrun_mpi_d.openmpi(mdrunner+**0x46a) [0x40be7a]
>> [ib02:22825] [13] mdrun_mpi_d.openmpi(main+**0x1256) [0x407206]
>> [ib02:22825] [14] /lib/x86_64-linux-gnu/libc.so.**6(__libc_start_main+0xfd)
>> [0x7f$
>> [ib02:22825] [15] mdrun_mpi_d.openmpi() [0x407479]
>> [ib02:22825] *** End of error message ***
>> --**--**
>> --
>> mpiexec noticed that process rank 36 with PID 22825 on node ib02 exited
>> on sign$
>> --**--**
>> --
>>
>>
>> I've obtained it when I've tried to use my system on multi-node station (
>> there is no problem on single node). Does this problem with the cluster
>> system or something wrong with parameters of my simulation?
>>
>
> The trace back suggests your MPI system is not configured correctly for
> your hardware.
>
> 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/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] another g_tune_pme problem

[Carsten Kutzner]

On Apr 1, 2012, at 8:01 PM, Albert wrote:

> Hello:
>   I am trying to test g_tune_pme in workstation by command:
> 
> g_tune_pme_d -v -s md.tpr -o bm.trr -cpi md.cpt -cpo bm.cpt -g bm.log -launch 
> -nt 16 &
> 
> but it stopped immediately with following logs. I complied gromacs with a -d 
> in each module such as mdrun_d and I aliased mdrun_d to mdrun in the shell. 
> However, my g_tune_pme still claimed that it cannot execute md_run..
Hi,

so what does benchtest.log say?

Carsten

> 
> thank you very much
> 
> 
> --log--
> back Off! I just backed up perf.out to ./#perf.out.5#
> Will test 3 tpr files.
> Will try runs with 4 - 8 PME-only nodes.
>   Note that the automatic number of PME-only nodes and no separate PME nodes 
> are always tested.
> 
> Back Off! I just backed up benchtest.log to ./#benchtest.log.5#
> 
> ---
> Program g_tune_pme_d, VERSION 4.5.5
> Source code file: gmx_tune_pme.c, line: 631
> 
> Fatal error:
> Cannot execute mdrun. Please check benchtest.log for problems!
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> "Once Again Let Me Do This" (Urban Dance Squad)
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists