[gmx-users] drawing the plots

[Sajad Ahrari]

hello dear Gromacs users
i have Gromacs4.5.3 installed on suse11.1.but when i run commands like" 
g_gyrate 
-s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg"i can't see any plot drawn. 

although the command is run with no error.
by the way i have the package "package xmgrace-5.1.21-27.91.x86_64" already 
installed. 

thanks!
sajad
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Re: [gmx-users] the ligand have more than one molecules

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear users,

Is there anyone has a tutorial of the ligand have more than one molecules?


Perhaps you can describe in more detail what it is you hope to accomplish.  The 
procedure for dealing with multiple ligands is, in principle, no different from 
a single ligand.  There are not tutorials available for every variation of a 
procedure.


-Justin


For example:
*_topol.top:_*
[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
*ligandname  * 3

Thanks in advance
--
Ahmet YILDIRIM



--


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


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[gmx-users] the ligand have more than one molecules

[ahmet yıldırım]

Dear users,

Is there anyone has a tutorial of the ligand have more than one molecules?
For example:
*topol.top:*
[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
*ligandname  * 3

Thanks in advance
-- 
Ahmet YILDIRIM
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Re: [gmx-users] Adding water to protein to start the simulation process

[Thomas Evangelidis]

Indeed  :-)


2011/4/16 João Henriques 

> With all due respect, this is clearly a RT*M moment.
>
> * = F
>
> Joao Henriques
>
> On Fri, Apr 15, 2011 at 1:03 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> Monisha Hajra wrote:
>>
>>> Hi Justin,
>>>
>>> I am trying to follow the protocol only.
>>>  More than the Gromacs own website, I find
>>> http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production link is
>>> more useful.
>>>
>>>
>> Clearly.  This is one of many tutorials linked from the site I posted
>> before.
>>
>> However, I am stuck at one step which is mentioned :
>>> http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html
>>>
>>> I am not able to understand how to create traj.trr, traj.xtc and ener.edr
>>> file. Remaining all is self explained in the previous link.
>>>
>>>
>> These files are output by mdrun, i.e. actually running a simulation.
>>
>> -Justin
>>
>> Really appreciate any help.
>>>
>>> Regards
>>> Monisha
>>>
>>>
>>> On Fri, Apr 15, 2011 at 8:06 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>>
>>>
>>>
>>>Monisha Hajra wrote:
>>>
>>>Hi User,
>>>
>>>I have a protein which I have modeled by Homology modelling. The
>>>modeled protein has no water molecules in its surrounding
>>>environment.
>>>
>>>How should I add water molecule so that I can start the
>>>simulation process?
>>>
>>>
>>>Please refer to the abundant tutorial material on the website:
>>>
>>>http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use
>>>
>>> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>>>
>>>-Justin
>>>
>>>Regards
>>>Monisha
>>>
>>>
>>>-- 
>>>
>>>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
>>>
>>>
>>>
>> --
>> 
>>
>> 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
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>>
>
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> gmx-users mailing listgmx-users@gromacs.org
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-- 

==

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tev...@bioacademy.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [gmx-users] Adding water to protein to start the simulation process

[João Henriques]

With all due respect, this is clearly a RT*M moment.

* = F

Joao Henriques

On Fri, Apr 15, 2011 at 1:03 PM, Justin A. Lemkul  wrote:

>
>
> Monisha Hajra wrote:
>
>> Hi Justin,
>>
>> I am trying to follow the protocol only.
>>  More than the Gromacs own website, I find
>> http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production link is
>> more useful.
>>
>>
> Clearly.  This is one of many tutorials linked from the site I posted
> before.
>
> However, I am stuck at one step which is mentioned :
>> http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html
>>
>> I am not able to understand how to create traj.trr, traj.xtc and ener.edr
>> file. Remaining all is self explained in the previous link.
>>
>>
> These files are output by mdrun, i.e. actually running a simulation.
>
> -Justin
>
> Really appreciate any help.
>>
>> Regards
>> Monisha
>>
>>
>> On Fri, Apr 15, 2011 at 8:06 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Monisha Hajra wrote:
>>
>>Hi User,
>>
>>I have a protein which I have modeled by Homology modelling. The
>>modeled protein has no water molecules in its surrounding
>>environment.
>>
>>How should I add water molecule so that I can start the
>>simulation process?
>>
>>
>>Please refer to the abundant tutorial material on the website:
>>
>>http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use
>>
>> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>>
>>-Justin
>>
>>Regards
>>Monisha
>>
>>
>>-- 
>>
>>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
>>
>>
>>
> --
> 
>
> 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
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Re: [gmx-users] Adding water to protein to start the simulation process

[Justin A. Lemkul]

Monisha Hajra wrote:

Hi Justin,

I am trying to follow the protocol only.
 
More than the Gromacs own website, I find 
http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production link is 
more useful.




Clearly.  This is one of many tutorials linked from the site I posted before.


However, I am stuck at one step which is mentioned :
http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html

I am not able to understand how to create traj.trr, traj.xtc and 
ener.edr file. Remaining all is self explained in the previous link.




These files are output by mdrun, i.e. actually running a simulation.

-Justin


Really appreciate any help.

Regards
Monisha


On Fri, Apr 15, 2011 at 8:06 PM, Justin A. Lemkul > wrote:




Monisha Hajra wrote:

Hi User,

I have a protein which I have modeled by Homology modelling. The
modeled protein has no water molecules in its surrounding
environment.

How should I add water molecule so that I can start the
simulation process?


Please refer to the abundant tutorial material on the website:

http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation

-Justin

Regards
Monisha


-- 



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


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--


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


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[gmx-users] Re: Genbox command question

[Fabian Casteblanco]

Thank you Justin.

Your explanation really helped.  I was actually using 4.0.5, not 4.0.1
(my mistake).  Your explanations explained everything very well.
Thanks again for your help!

On Fri, Apr 15, 2011 at 3:33 PM, Fabian Casteblanco
 wrote:
> Hello,
>
> I'm trying to place 1000 molecules of 1-propanol using CHARMM FF
> parameters in a -box 6 6 6.   After minimization, I realized that for
> a single molecule, the potential was slightly above 0, '+24 kJ/mol' to
> be exact, with electrostatic coloumb potential the greatest
> contributor.  I used the same thing with OPLSA FF parameters and got a
> '+3 kJ/mol'.  I realize that when I place 1000 of these molecules, the
> potential will be very high since the potentials are positive to begin
> with.  When I placed 1000 molecules using:
>
> -     "genbox -ci propanol.gro -nmol 1000 -box 6 6 6 -o prop1000.gro"
>
> I resulted with a box full of 1000 molecules in that specific box size
> on gromacs 4.0.1.  I did the same on the latest gromacs 4.5 but it
> ended up taking longer and the last line stating 'killed'.  I redid it
> with a box 7 7 7 and it worked on gromacs 4.5.   However, after I
> energy minimized both 1000 molecules (box 6 6 6 on gromacs 4.0.1) and
> (box 7 7 7 on gromacs 4.5), the first gave me a large negative
> potential energy (-6000 kJ/mol) after taking a long time and the
> second box gave me a somewhat large 2*10^3 kJ/mol.  I am still new to
> Gromacs but I'm confused on why a certain box size worked on one
> version of gromacs and the other didnt.  I assume that the difference
> in potential energies is since the 2nd box has way more space for
> these molecules therefore they are not as well equilibrated as the
> more compact box of size 6 6 6.  Why does my box size that worked on
> gromacs4.0.1 work and on 4.5 it states killed as the last line and
> only works redoing it with a bigger box size.
>
> Thank you so much for your time and help ahead of time.
>
> --
> Best regards,
>
> Fabian F. Casteblanco
> Rutgers University --
> Chemical Engineering PhD Student
> C: +908 917 0723
> E:  fabian.castebla...@gmail.com
>



-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
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Re: [gmx-users] Genbox command question

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Hello,

I'm trying to place 1000 molecules of 1-propanol using CHARMM FF
parameters in a -box 6 6 6.   After minimization, I realized that for
a single molecule, the potential was slightly above 0, '+24 kJ/mol' to
be exact, with electrostatic coloumb potential the greatest
contributor.  I used the same thing with OPLSA FF parameters and got a
'+3 kJ/mol'.  I realize that when I place 1000 of these molecules, the
potential will be very high since the potentials are positive to begin
with.  When I placed 1000 molecules using:



This is not necessarily true.  Isolated molecules can have positive potential 
energies due to unsatisfied interactions, but in a condensed phase, the presence 
of other molecules produces negative energies due to favorable van der Waals and 
hydrogen bonding interactions.



- "genbox -ci propanol.gro -nmol 1000 -box 6 6 6 -o prop1000.gro"

I resulted with a box full of 1000 molecules in that specific box size
on gromacs 4.0.1.  I did the same on the latest gromacs 4.5 but it
ended up taking longer and the last line stating 'killed'.  I redid it
with a box 7 7 7 and it worked on gromacs 4.5.   However, after I
energy minimized both 1000 molecules (box 6 6 6 on gromacs 4.0.1) and
(box 7 7 7 on gromacs 4.5), the first gave me a large negative
potential energy (-6000 kJ/mol) after taking a long time and the


Simulations with version 4.0.1 will be extremely slow due to a critical bug that 
was introduced.  You should not use version 4.0.1; it was removed from the 
website within hours of its release due to series performance problems.



second box gave me a somewhat large 2*10^3 kJ/mol.  I am still new to


A more expanded system will have unsatisfied interactions, thus positive energy.


Gromacs but I'm confused on why a certain box size worked on one
version of gromacs and the other didnt.  I assume that the difference


That's hard to pinpoint.  If you have a 7-nm cubic box, gentle equilibration 
should produce a reasonable density and a much lower potential.



in potential energies is since the 2nd box has way more space for
these molecules therefore they are not as well equilibrated as the
more compact box of size 6 6 6.  Why does my box size that worked on


Energy minimization and equilibration dynamics are different.  A more dense 
system is simply more favorable.  You can certainly achieve an equivalent result 
with proper NPT equilibration.


-Justin


gromacs4.0.1 work and on 4.5 it states killed as the last line and
only works redoing it with a bigger box size.

Thank you so much for your time and help ahead of time.

--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com


--


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


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[gmx-users] Genbox command question

[Fabian Casteblanco]

Hello,

I'm trying to place 1000 molecules of 1-propanol using CHARMM FF
parameters in a -box 6 6 6.   After minimization, I realized that for
a single molecule, the potential was slightly above 0, '+24 kJ/mol' to
be exact, with electrostatic coloumb potential the greatest
contributor.  I used the same thing with OPLSA FF parameters and got a
'+3 kJ/mol'.  I realize that when I place 1000 of these molecules, the
potential will be very high since the potentials are positive to begin
with.  When I placed 1000 molecules using:

- "genbox -ci propanol.gro -nmol 1000 -box 6 6 6 -o prop1000.gro"

I resulted with a box full of 1000 molecules in that specific box size
on gromacs 4.0.1.  I did the same on the latest gromacs 4.5 but it
ended up taking longer and the last line stating 'killed'.  I redid it
with a box 7 7 7 and it worked on gromacs 4.5.   However, after I
energy minimized both 1000 molecules (box 6 6 6 on gromacs 4.0.1) and
(box 7 7 7 on gromacs 4.5), the first gave me a large negative
potential energy (-6000 kJ/mol) after taking a long time and the
second box gave me a somewhat large 2*10^3 kJ/mol.  I am still new to
Gromacs but I'm confused on why a certain box size worked on one
version of gromacs and the other didnt.  I assume that the difference
in potential energies is since the 2nd box has way more space for
these molecules therefore they are not as well equilibrated as the
more compact box of size 6 6 6.  Why does my box size that worked on
gromacs4.0.1 work and on 4.5 it states killed as the last line and
only works redoing it with a bigger box size.

Thank you so much for your time and help ahead of time.

--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
--
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[gmx-users] Pressure coupling problem

[Fabian Casteblanco]

Thank you Justin and Peter for your responses.  I tried extending the time
on the npt equilibration.  It helped but not much.  My final pressure after
the MD run was about 1.15 bar compared to ref_p which was set to 1 bar.
Peter, I will try to analyze the potential error using RMSD and Drift.

Thanks.

On Mon, Apr 11, 2011 at 4:55 PM, Fabian Casteblanco <
fabian.castebla...@gmail.com> wrote:

> Hi,
>
> I'm still in my first few months of using Gromacs.  I started by creating
> an *.itp and *.top file for *Ethanol* using CHARMM force field
> parameters.  I made the molecule and it looked fine, put 1000 molecules in a
> box, energy minimized it to a negative potential energy, viewed it on VMD,
> again looks fine.  When I started running the NVT script, I set it equal to
> a ref_T of 298 K.  It equilibrated at the temperature.  Then I tried using
> an NPT script to equilibrate it to a ref_p of 1 bar.  This is where I get
> the problem.  The output shows the density is close to the actual
> experimental value of 0.789 g/cm^3.  But for some reason, my pressure never
> gets an average of 1 bar.  It keeps oscillating, which I understand is
> normal, but the average is always 1.3 or 1.4 bar (it seems the longer I let
> it run, the larger the average pressure; 1.38 for 50,000 steps,dt=0.002 and
> 1.45 for 75,000 steps,dt=0.002).  I don't understand why the ref_p of 1 bar
> is not working when I run this NPT.mdp script file.  My simple goal is to
> have 1000 molecules of ethanol using CHARMM ff parameters at 25degC and 1
> bar and somewhere near the experimental density.
>
> I would really appreciate anybody's help!  I'm new to this but I'm eager to
> keep getting better.
>
> Thanks.
>
> *NVT SCRIPT  (this works fine and takes me to 298 K)*
> File Edit Options Buffers Tools Help
> title   =CHARMM ETHANOL  NVT equilibration
> ;define =-DPOSRES   ;position restrain the protein
> ;Run parameters
> integrator  =md ;leap-frog algorithm
> nsteps  =5  ;2 * 5 = 100 ps
> dt  =0.002  ;2fs
> ;Output control
> nstxout =100;save coordinates every 0.2 ps
> nstvout =100;save velocities every 0.2 ps
> nstenergy   =100;save energies every 0.2 ps
> nstlog  =100;update log file every 0.2 ps
> ;Bond parameters
> continuation=no ;first dynamics run
> constraint_algorithm=lincs  ;holonomic constraints
> constraints =all-bonds  ;all bonds (even heavy atom-H
> bonds)constraind
> lincs_iter  =1  ;accuracy of LINCS
> lincs_order =4  ;also related to accuracy
> ;Neighborhood searching
> ns_type =grid   ;search neighboring grid cells
> nstlist =5  ;10 fs
> rlist   =1.0;short-range neighborlist cutoff (in nm)
> rcoulomb=1.0;short-range electrostatic cutoff (in nm)
> rvdw=1.0;short-range van der Waals cutoff (in nm)
> ;Electrostatics
> coulombtype =PME;Particle Mesh Ewald for long-range
> electrostat\
> ;ics
> pme_order   =4  ;cubic interpolation
> fourierspacing  =0.16   ;grid spacing for FFT
> ;Temperature coupling is on
> tcoupl  =V-rescale  ;modified Berendsen thermostat
> tc_grps =SYSTEM   ;two coupling groups - more accurate
> tau_t   =0.1;0.1  ;time constant, in ps
> ref_t   =298;25   ;reference temperature, one for
> each \
> ;group, in K
> ;Pressure coupling is off
> pcoupl  =no ;no pressure coupling in NVT
> ;Periodic boundary conditions
> pbc =xyz; 3-D PBC
> ;Dispersion correction
> DispCorr=EnerPres   ;account for cut-off vdW scheme
> ;Velocity generation
> gen_vel =yes;assign velocities from Maxwell
> distribution
> gen_temp=25 ;temperature for Maxwell distribution
> gen_seed=-1 ;generate a random seed
> ;END
>
> *NPT SCRIPT*
> File Edit Options Buffers Tools Help
> title   =Ethanol npt equilibration
> ;define =-DPOSRES   ;position restrain the protein
> ;Run parameters
> integrator  =md ;leap-frog algorithm
> nsteps  =5  ;2 * 5 = 100 ps
> dt  =0.002  ;2fs
> ;Output control
> nstxout =100;save coordinates every 0.2 ps
> nstvout =100;save velocities every 0.2 ps
> nstenergy   =100;save energies every 0.2 ps
> nstlog  =100;update log file every 0.2 ps
> ;Bond parameters
> continuation=yes;Restarting after NVT
> constraint_algorithm=lincs  ;holonomic constraints
> constraints =all-bonds  ;all bonds (even heavy atom-H
> bonds)constraind
> lincs_iter  =1  ;accuracy of LINCS
> lincs_order =4  ;als

Re: [gmx-users] RMSF: Different results for same residue

[Francesco Oteri]

Il 15/04/2011 18:45, Alok Jain ha scritto:

Hi,

I am simulating a tetrameric protein in membrane. The simulation is
for 30ns. I wish to calculate RMSF for just one monomer (A).
I thought of doing this in two ways,

1. I input the residue numbers for the monomer A by creating an
index.ndx file to calculate RMSF only for the selected monomer CA
atoms.
g_rmsf -f  *.xtc -s *.tpr -od rmsdev.xvg -n index.ndx

2. I calculate RMSF for the complete protein CA atoms
g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg

I find the output from these to commands for the same monomer A
residues are different. The second command calculates a very high RMSF
for the same residues.
Why is it so ?? Or am I making a mistake at some place ??

Thanks in advance.

Alok
The reason is that in the two cases you used two different groups to fit 
the protein.
Different fit generates different result. If you try to calculate RMSF, 
fitting on the subunit B, you will find a third result. I guess the 
subunit B should fluctuate less than case 2)



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Re: [gmx-users] RMSF: Different results for same residue

[Justin A. Lemkul]

Alok Jain wrote:

Hi,

I am simulating a tetrameric protein in membrane. The simulation is
for 30ns. I wish to calculate RMSF for just one monomer (A).
I thought of doing this in two ways,

1. I input the residue numbers for the monomer A by creating an
index.ndx file to calculate RMSF only for the selected monomer CA
atoms.
g_rmsf -f  *.xtc -s *.tpr -od rmsdev.xvg -n index.ndx

2. I calculate RMSF for the complete protein CA atoms
g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg

I find the output from these to commands for the same monomer A
residues are different. The second command calculates a very high RMSF
for the same residues.
Why is it so ?? Or am I making a mistake at some place ??



The selected index group has a least-squares fit performed on it.  If the 
fitting group is different, the output RMSF will be different.  In case (1) 
you're doing the fitting and establishing a reference for RMSF from just one 
monomer and then doing the calculation on that group.  In case (2) you're using 
the whole protein for the calculation.


-Justin


Thanks in advance.

Alok


--


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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Energy minimization error

[Kavyashree M]

Ok thanks

On Fri, Apr 15, 2011 at 9:56 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> Dear gromacs users,
>>
>> While doing energy minimization for a protein (from pdb), with oplsaa
>> force field
>> and tip4p water model, there was an error and em stopped -
>>
>> Fatal error:
>> A charge group moved too far between two domain decomposition steps
>> This usually means that your system is not well equilibrated
>>
>> What is the correction for this?
>>
>>
> Build a more reasonable starting structure.  Somewhere you have atomic
> overlap or otherwise unresolvable geometry such that you have atoms flying
> across the system, as the error message indicates (although somewhat
> obliquely).
>
> The screen/log output from mdrun should print where the high forces are, or
> which atoms are having constraint problems, etc.  Investigate these atoms in
> your starting structure and/or EM trajectory and determine an appropriate
> solution based on what you find.
>
> -Justin
>
>
>  Thanking you
>> With regards
>> kavya
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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[gmx-users] RMSF: Different results for same residue

[Alok Jain]

Hi,

I am simulating a tetrameric protein in membrane. The simulation is
for 30ns. I wish to calculate RMSF for just one monomer (A).
I thought of doing this in two ways,

1. I input the residue numbers for the monomer A by creating an
index.ndx file to calculate RMSF only for the selected monomer CA
atoms.
g_rmsf -f  *.xtc -s *.tpr -od rmsdev.xvg -n index.ndx

2. I calculate RMSF for the complete protein CA atoms
g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg

I find the output from these to commands for the same monomer A
residues are different. The second command calculates a very high RMSF
for the same residues.
Why is it so ?? Or am I making a mistake at some place ??

Thanks in advance.

Alok
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Re: [gmx-users] Energy minimization error

[Justin A. Lemkul]

Kavyashree M wrote:

Dear gromacs users,

While doing energy minimization for a protein (from pdb), with oplsaa 
force field

and tip4p water model, there was an error and em stopped -

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated

What is the correction for this?



Build a more reasonable starting structure.  Somewhere you have atomic overlap 
or otherwise unresolvable geometry such that you have atoms flying across the 
system, as the error message indicates (although somewhat obliquely).


The screen/log output from mdrun should print where the high forces are, or 
which atoms are having constraint problems, etc.  Investigate these atoms in 
your starting structure and/or EM trajectory and determine an appropriate 
solution based on what you find.


-Justin


Thanking you
With regards
kavya



--


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


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[gmx-users] Energy minimization error

[Kavyashree M]

Dear gromacs users,

While doing energy minimization for a protein (from pdb), with oplsaa force
field
and tip4p water model, there was an error and em stopped -

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated

What is the correction for this?

Thanking you
With regards
kavya
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[gmx-users] mdrun_mpi in HP_MPI LSF/SLURM setup

[Larcombe, Lee]

Hi gmx-users

We have an HPC setup running HP_MPI and LSF/SLURM. Gromacs 4.5.3 has been 
compiled with mpi support
The compute nodes on the system contain 2 x dual core Xeons which the system 
sees as 4 processors

An LSF script called gromacs_run.lsf is as shown below

#BSUB -N
#BSUB -J "gromacsTest5"
#BSUB -u l.larco...@cranfield.ac.uk
#BSUB -n 4
#BSUB -q short
#BSUB -o %J.log
mpirun -srun mdrun_mpi -v -s xxx.tpr -o xxx.trr

Queued with:

Bsub < gromacs_run.lsf

This is intended to run 1 mdrun on a single node using all four cores of the 
two xeons. The result is that although the job is only submitted to one compute 
node, 4 mdruns are launched on each of the 4 cores = 16 jobs. These are all the 
same as if mdrun has not been compiled with mpi support.

If I tell srun to start just one task with "mpirun -srun -n1 mdrun_mpi -v -s 
xxx.tpr –o xxx.trr" it starts one job on each core instead of 4:

NNODES=1, MYRANK=0, HOSTNAME=comp195
NNODES=1, MYRANK=0, HOSTNAME=comp195
NNODES=1, MYRANK=0, HOSTNAME=comp195
NNODES=1, MYRANK=0, HOSTNAME=comp195

Logs show 4 mdrun_mpi starts, 4 file read ins and I get 4 of all run files in 
CWD. I am sure that mdrun_mpi is indeed compiled with mpi support - although 
our sysadmin did that, not me. For example, if I try and execute "mdrun_mpi –h" 
I get a message from HP–MPI and have to execute "mpirun mdrun_mpi –h" to see 
the help text.

Does anyone have any experience of running with this setup  - any ideas?

Thanks
Lee
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Re: [gmx-users] Adding water to protein to start the simulation process

[Justin A. Lemkul]

Monisha Hajra wrote:

Hi User,

I have a protein which I have modeled by Homology modelling. The modeled 
protein has no water molecules in its surrounding environment.


How should I add water molecule so that I can start the simulation process?



Please refer to the abundant tutorial material on the website:

http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation

-Justin


Regards
Monisha 



--


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


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[gmx-users] Adding water to protein to start the simulation process

[Monisha Hajra]

Hi User,

I have a protein which I have modeled by Homology modelling. The modeled
protein has no water molecules in its surrounding environment.

How should I add water molecule so that I can start the simulation process?

Regards
Monisha
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[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3

[chris . neale]

Based on your use of:

sc-sigma = 0.3

I wonder what happens with 4.5.3 when you set the env.var.  
GMX_SCSIGMA_MIN to 0


quoting http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x

"for free-energy calculations sc-sigma now also sets the minimum  
soft-core sigma (old tpr files retain the old behavior, which can be  
enforced by setting the env.var. GMX_SCSIGMA_MIN to 0)"


-- original message --

Dear Gromacs users,

   One example of my mdp files with lambda=0.5 is like the following:

integrator   = md
tinit= 0
dt   = 0.004
nsteps   = 25
simulation_part  = 1
comm_mode= Linear
nstcomm  = 10


nstlist  = 2
ns_type  = grid
pbc  = xyz
periodic_molecules   = no
rlist= 1.4


coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.4
epsilon_r= 1
epsilon_rf   = 1
vdw_type = cut-off
rvdw = 1.4
fourierspacing   = 0.168
pmeorder = 4
ewald_rtol   = 1.0e-5
ewald_geometry   = 3d
optimize_fft = yes


tcoupl   = v-rescale
tc-grps  = ioq !ioq
tau_t= 0.1 0.1
ref_t= 298.15 298.15
pcoupl   = Berendsen
Pcoupltype   = Isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0


constraints  = all-bonds
constraint_algorithm = lincs
lincs_order  = 4
lincs_iter   = 1

free_energy  = yes
init_lambda  = 0.5
delta_lambda = 0
foreign_lambda   =
sc-alpha = 0.7
sc-power = 1
sc-sigma = 0.3
nstdhdl  = 10
separate-dhdl-file   = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing  = 0.1
couple-moltype   =
couple-lambda0   = vdw-q
couple-lambda1   = vdw-q
couple-intramol  = no

The system has 1 Chloride ion with ffG43a1 force field parameter and SPC
water molecules with heavy hydrogen in a cubic box of size 3 nm. I have
sampled 21 lambda windows ranging from 0 to 1.

   The values are converged by block averaging.

   Regards,
   Yan

On Thu, Apr 14, 2011 at 3:35 PM,  wrote:


Dear Yan:

If you want to get to the bottom of this then (a) please report your mdp
files and (b) show some evidence that your values are converged by, for
instance, block averaging the run-time.

Chris.

-- original message --

Dear Gromacs users,

 I got different free energy values by Thermodynamic Integration (TI) in
Gromacs 4.0.7 and 4.5.3.

 When I calculated the hydration free energy of Chloride ion by using
Thermodynamic Integration method, the results for the free energy of
un-charging the Chloride ion from q=-e to 0 in SPC water are 359+/-6 kJ/mol
in Gromacs 4.0.7 and 385 +/-6 kJ/mol in Gromacs 4.5.3, respectively.

 The literature value is 392 kJ/mol (J. Phys. Chem. 1996, 100, 1206-1215,
Table 6), which is close to the result in Gromacs 4.5.3 but not in 4.0.7.

 As a check, Gromacs 3.3.1 gave the result as 381+/-3 kJ/mol.

 I searched the mail list and the bugzilla of Gromacs but didn't find
explanation for this issue of version.

 Does anyone know the reason for the different TI free energy values in
those different version of Gromacs?

--



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[gmx-users] Re: micelles and trjconv -pbc cluster

[jim jack]

Dear Tsjerk and Ran,  Thanks for the routines you sent me! I will try to 
apply them as soon as possible.
Best regards 
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Re: [gmx-users] Re: Trajectory visualization

[Erik Marklund]

Your results are not affected by isualization, are they? Just keep a 
copy of the original trajectory for analysis.


Erik

bharat gupta skrev 2011-04-15 07.08:
Reduicng no. of frames means breaking the simulation into smaller 
frames ... will it affect the result ??


On Thu, Apr 14, 2011 at 10:06 PM, Mark Abraham 
mailto:mark.abra...@anu.edu.au>> wrote:


On 15/04/2011 2:49 PM, bharat gupta wrote:

Hi,

I have done a simulation of 10ns but while viewing the
trajectory in VMD I am getting some problems. After loading
the .gro and .xtc file VMD stops working .. I used trjconv to
compress the file but VMD doesnot read frames from tat file...
How can I visualize the trajectories??


How do you mean "does not read frames from that file"? Can you
read an .xtc of one frame?

Maybe VMD is running out of memory. Use trjconv to reduce the
number of frames and try again.

Mark
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 




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---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] free energy perturbation

[Jignesh Patel]

Hello,

I am doing free energy perturbation for ethane to methanol conversion. Can
anybody tell me which of the following way is right to define virtual site
for hydrogen?

[ virtual_sites2 ]
  3 2 1 1 0.00

or

[ virtual_sites2 ]
  3 2 1 1 1.00

Thanking you in anticipation.

With regards,
Jignesh
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Re: [gmx-users] Fwd: genbox

[Mark Abraham]

On 15/04/2011 5:16 PM, leila separdar wrote:




I have .gro and .top of a nanoparticle at temperature 1K and I want to
add the simulation box some other atoms at temperature 300K. is there
any body knows how can I do it. I have  used (genbox -cp
nanoparticle.gro -ci otheratom.gro -p nanoparticle.top -o out) but it
add more than atoms than I expect for example if there is 600 other
atoms in otheratom,gro file this command add 2000 atoms to
simulation box and also nanoparticle.top does not update.
thanks in advance



Justin answered this earlier today.

Mark
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Re: [gmx-users] Re: Trajectory visualization

[Dommert Florian]

On Fri, 2011-04-15 at 15:15 +1000, Mark Abraham wrote:
> On 15/04/2011 3:08 PM, bharat gupta wrote: 
> > Reduicng no. of frames means breaking the simulation into smaller
> > frames ... will it affect the result ??
> 
> You can use trjconv -dt to reduce the number of frames per unit time,
> not just chopping into segments. Whether it affects your result is
> something only you can answer, because only you know what you are
> trying to do.
> 
> Mark
> 

And if you want to play a little bit around, you can also tell VMD if
you want read every step of the xtc file. In the frame section of the
molecule file browser, there is an option stride. Increase this number
and VMD will read just every n-th step and you can avoid using trjconv
for many many times.

/Flo


> > 
> > On Thu, Apr 14, 2011 at 10:06 PM, Mark Abraham
> >  wrote: 
> > On 15/04/2011 2:49 PM, bharat gupta wrote:
> > Hi,
> > 
> > I have done a simulation of 10ns but while viewing
> > the trajectory in VMD I am getting some problems.
> > After loading the .gro and .xtc file VMD stops
> > working .. I used trjconv to compress the file but
> > VMD doesnot read frames from tat file... How can I
> > visualize the trajectories??
> > 
> > 
> > How do you mean "does not read frames from that file"? Can
> > you read an .xtc of one frame?
> > 
> > Maybe VMD is running out of memory. Use trjconv to reduce
> > the number of frames and try again.
> > 
> > Mark
> > -- 
> > gmx-users mailing listgmx-users@gromacs.org
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> > 
> > 
> > -- 
> > Bharat
> > Ph.D. Candidate
> > Room No. : 7202A, 2nd Floor
> > Biomolecular Engineering Laboratory
> > Division of Chemical Engineering and Polymer Science
> > Pusan National University
> > Busan -609735
> > South Korea
> > Lab phone no. - +82-51-510-3680, +82-51-583-8343 
> > Mobile no. - 010-5818-3680
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> > 
> 
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-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658


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Re: [gmx-users] Different TI free energy values in 4.0.7 and 4.5.3

[Yan Chai]

Dear GROMACS users,

  As another check, I simulated the hydration of Sodium ion. The results for
the free energy change of un-charging the sodium ion with ffG43a1 force
field parameter from q=+e to q=0 in SPC water are the following:

  363.3 +/- 2.4 kJ/molin   GROMACS 4.0.7
  404.7 +/- 1.9 kJ/molin   GROMACS 4.5.3
  405.2 +/- 2.0 kJ/molin   J. Phys. Chem. 1996, 100, 1206-1215, Table 5

   Again there is difference between the results from 4.0.7 and 4.5.3.

   It seems that the problem might be related to the net charge of the
system. In both cases of Cl- and Na+, the system contains 1 charged ion and
certain number of water molecules. Is there any change of the GROMACS codes
dealing with Coulomb interaction in free energy calculation from 4.0.7 to
4.5.3?

   Thanks!

 Yan
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[gmx-users] Fwd: genbox

[leila separdar]

I have .gro and .top of a nanoparticle at temperature 1K and I want to
add the simulation box some other atoms at temperature 300K. is there
any body knows how can I do it. I have  used (genbox -cp
nanoparticle.gro -ci otheratom.gro -p nanoparticle.top -o out) but it
add more than atoms than I expect for example if there is 600 other
atoms in otheratom,gro file this command add 2000 atoms to
simulation box and also nanoparticle.top does not update.
thanks in advance
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