Re: [gmx-users] pbc off

[Justin Lemkul]

On 10/30/13 11:42 AM, jwill...@andrew.cmu.edu wrote:

Hey everyone,

If I ran my simulations with periodic boundary conditions, is there a way
in Gromacs to get a trajectory file tracking the diffusion of the
molecules in the first time frame (i.e. not allow them to exit one side of
the box and reenter the other side)?



trjconv -pbc nojump

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] pbc off

[jwillcox]

Hey everyone,

If I ran my simulations with periodic boundary conditions, is there a way
in Gromacs to get a trajectory file tracking the diffusion of the
molecules in the first time frame (i.e. not allow them to exit one side of
the box and reenter the other side)?

If not, can I specify this in the run parameters before doing the simulation?

Thanks!

Jon

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Re: [gmx-users] pbc problem

[Justin Lemkul]

On 10/29/13 12:02 PM, shahab shariati wrote:

Dear Mark

Very thanks for your reply


To make this clear, center the trajectory on the water and watch the
time evolution in some visualization program.


I did your suggestion (center the trajectory on the water). Again, drug
molecule is in region (1)in some frames and is in region (4) in other
frames.

--
Dear Justin

Very thanks for your attention


As has already been stated several times, there is no problem at all.
The outcome is completely normal, and there are not discrete
regions (1) and (4).
It is a continuous block of water via PBC.  The molecule can freely
diffuse throughout it.


If outcome is completely normal, Can I use this structure for pmf
calculation. I want to calculate potential of mean force, delta G, as a
function of the distance between the centers of mass of drug and the
centers of mass of bilayer.



Given the inherent symmetry of the system, yes.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] pbc problem

[Mark Abraham]

On Tue, Oct 29, 2013 at 5:02 PM, shahab shariati
wrote:

> Dear Mark
>
> Very thanks for your reply
>
> > To make this clear, center the trajectory on the water and watch the
> > time evolution in some visualization program.
>
> I did your suggestion (center the trajectory on the water). Again, drug
> molecule is in region (1)in some frames and is in region (4) in other
> frames.
>

With pbc = xyz, you do not have two chunks of water. You have one chunk of
water. Where you put the box for visualization is irrelevant to the
simulation. You could align one of the box sides with one of the membrane
surfaces, and now you will see only one chunk of membrane, and one chunk of
water. In that chunk of water the drug goes wherever diffusion takes it,
just like it did inside the membrane.

Mark


>
> --
> Dear Justin
>
> Very thanks for your attention
>
> > As has already been stated several times, there is no problem at all.
> > The outcome is completely normal, and there are not discrete
> > regions (1) and (4).
> > It is a continuous block of water via PBC.  The molecule can freely
> > diffuse throughout it.
>
> If outcome is completely normal, Can I use this structure for pmf
> calculation. I want to calculate potential of mean force, delta G, as a
> function of the distance between the centers of mass of drug and the
> centers of mass of bilayer.
>
> Best wishes for you.
> --
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[gmx-users] pbc problem

[shahab shariati]

Dear Mark

Very thanks for your reply

> To make this clear, center the trajectory on the water and watch the
> time evolution in some visualization program.

I did your suggestion (center the trajectory on the water). Again, drug
molecule is in region (1)in some frames and is in region (4) in other
frames.

--
Dear Justin

Very thanks for your attention

> As has already been stated several times, there is no problem at all.
> The outcome is completely normal, and there are not discrete
> regions (1) and (4).
> It is a continuous block of water via PBC.  The molecule can freely
> diffuse throughout it.

If outcome is completely normal, Can I use this structure for pmf
calculation. I want to calculate potential of mean force, delta G, as a
function of the distance between the centers of mass of drug and the
centers of mass of bilayer.

Best wishes for you.
-- 
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Re: [gmx-users] pbc problem

[Mark Abraham]

To make this clear, center the trajectory on the water and watch the time
evolution in some visualization program.

Mark


On Sun, Oct 27, 2013 at 5:08 PM, Justin Lemkul  wrote:

>
>
> On 10/27/13 12:05 PM, shahab shariati wrote:
>
>> Dear Tsjerk Wassenaar
>>
>> Very very thanks for your reply.
>>
>> I used trjconv -pbc mol.
>>
>> pbc problem was solved only for lipid molecules.
>>
>> When I see new trajectory by vmd, there are some problesm about drug
>> molecule.
>>
>> https://www.dropbox.com/s/**xq4s6az17buhvb8/images-2.docx
>>
>> If I show my system as 4 regions, my system before equilibration is as
>> fallows:
>>
>> region (1): water + drug
>> region (2): top leaflet of bilayer
>> region (3): bottom leaflet of bilayer
>> region (4): water
>>
>> After equilibration, drug molecule exits region (1) and enters region (4),
>> alternately.
>>
>> On the other hand, drug molecule is in region (1)in some frames and is
>> in region (4) in other frames.
>>
>> Please tell me how to fix it? Is this issue (about drug molecule) pbc
>> problem?
>>
>>
> As has already been stated several times, there is no problem at all.  The
> outcome is completely normal, and there are not discrete regions (1) and
> (4). It is a continuous block of water via PBC.  The molecule can freely
> diffuse throughout it.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
>
> --
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Re: [gmx-users] pbc problem

[Justin Lemkul]

On 10/27/13 12:05 PM, shahab shariati wrote:

Dear Tsjerk Wassenaar

Very very thanks for your reply.

I used trjconv -pbc mol.

pbc problem was solved only for lipid molecules.

When I see new trajectory by vmd, there are some problesm about drug
molecule.

https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx

If I show my system as 4 regions, my system before equilibration is as
fallows:

region (1): water + drug
region (2): top leaflet of bilayer
region (3): bottom leaflet of bilayer
region (4): water

After equilibration, drug molecule exits region (1) and enters region (4),
alternately.

On the other hand, drug molecule is in region (1)in some frames and is
in region (4) in other frames.

Please tell me how to fix it? Is this issue (about drug molecule) pbc
problem?



As has already been stated several times, there is no problem at all.  The 
outcome is completely normal, and there are not discrete regions (1) and (4). 
It is a continuous block of water via PBC.  The molecule can freely diffuse 
throughout it.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] pbc problem

[shahab shariati]

Dear Tsjerk Wassenaar

Very very thanks for your reply.

I used trjconv -pbc mol.

pbc problem was solved only for lipid molecules.

When I see new trajectory by vmd, there are some problesm about drug
molecule.

https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx

If I show my system as 4 regions, my system before equilibration is as
fallows:

region (1): water + drug
region (2): top leaflet of bilayer
region (3): bottom leaflet of bilayer
region (4): water

After equilibration, drug molecule exits region (1) and enters region (4),
alternately.

On the other hand, drug molecule is in region (1)in some frames and is
in region (4) in other frames.

Please tell me how to fix it? Is this issue (about drug molecule) pbc
problem?

Best wishes
-- 
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Re: [gmx-users] pbc problem

[Tsjerk Wassenaar]

Hi Shahab,

What about running trjconv -pbc mol with a .tpr as input file?

Cheers,

Tsjerk


On Sun, Oct 27, 2013 at 3:24 PM, shahab shariati
wrote:

> Dear Justin
>
> I attached images related to before (em2.gro) and after equilibration.
>
>
> https://www.dropbox.com/s/yjkyj5ycshvp20u/images.docx
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-- 
Tsjerk A. Wassenaar, Ph.D.
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[gmx-users] pbc problem

[shahab shariati]

Dear Justin

I attached images related to before (em2.gro) and after equilibration.


https://www.dropbox.com/s/yjkyj5ycshvp20u/images.docx
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[gmx-users] pbc problem

[shahab shariati]

Dear Justin

Please check this trajectory file (1.xtc) being smaller than 0.xtc.

https://www.dropbox.com/s/9qd2l37qyfqvpox/1.xtc
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Re: [gmx-users] pbc problem

[Justin Lemkul]

On 10/27/13 8:16 AM, shahab shariati wrote:

Dear Justin

I want to study translocation of drug molecule in lipid bilayer.

My gro file after minimization is em2.gro.

After NPT-MD simulation, I obtained npt.gro and 0.xtc files.

When I see trajectory by vmd, there are some things abnormal.

I guess there is pbc problem.

I attached these 3 files. Please after viewing them, tell me is my guess
true.

If yes, please guide me how to fix it. If no, please tell me what is
problem?

https://www.dropbox.com/s/d0hppxdngj7xwst/em2.gro

https://www.dropbox.com/s/gnqf6fuxwwj0zzt/npt.gro

https://www.dropbox.com/s/w899y86mhp0ysbo/0.xtc



Images are better, especially ones that don't have to be downloaded.  I'm not 
going to download a potentially large .xtc file, sorry.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] pbc problem

[shahab shariati]

Dear Justin

I want to study translocation of drug molecule in lipid bilayer.

My gro file after minimization is em2.gro.

After NPT-MD simulation, I obtained npt.gro and 0.xtc files.

When I see trajectory by vmd, there are some things abnormal.

I guess there is pbc problem.

I attached these 3 files. Please after viewing them, tell me is my guess
true.

If yes, please guide me how to fix it. If no, please tell me what is
problem?

https://www.dropbox.com/s/d0hppxdngj7xwst/em2.gro

https://www.dropbox.com/s/gnqf6fuxwwj0zzt/npt.gro

https://www.dropbox.com/s/w899y86mhp0ysbo/0.xtc

Best wishes
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Re: [gmx-users] pbc problem

[Mark Abraham]

As Justin said, there is no actual division between region 1 and 4.
Apparently you got the free diffusion you asked for! :-)

Mark


On Thu, Oct 24, 2013 at 4:57 PM, shahab shariati
wrote:

> Dear Mark
>
> Thank for your reply.
>
> If I show my system as 4 regions, my system before equilibration is as
> fallows:
>
> region (1): water + drug
> region (2): top leaflet of bilayer
> region (3): bottom leaflet of bilayer
> region (4): water
>
> After equilibration, drug molecule exits region (1) and enters region (4).
>
> Please tell me how to fix it? Which options of trjconv are appropriate
> for this problem?
>
> Best wishes
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] pbc problem

[Justin Lemkul]

On 10/24/13 10:57 AM, shahab shariati wrote:

Dear Mark

Thank for your reply.

If I show my system as 4 regions, my system before equilibration is as fallows:

region (1): water + drug
region (2): top leaflet of bilayer
region (3): bottom leaflet of bilayer
region (4): water

After equilibration, drug molecule exits region (1) and enters region (4).

Please tell me how to fix it? Which options of trjconv are appropriate
for this problem?



So the drug diffused within a continuous block of solvent, is that a problem? 
It shouldn't be, since the system is periodic.  In some cases, trjconv magic 
doesn't work because it shouldn't.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] pbc problem

[shahab shariati]

Dear Mark

Thank for your reply.

If I show my system as 4 regions, my system before equilibration is as fallows:

region (1): water + drug
region (2): top leaflet of bilayer
region (3): bottom leaflet of bilayer
region (4): water

After equilibration, drug molecule exits region (1) and enters region (4).

Please tell me how to fix it? Which options of trjconv are appropriate
for this problem?

Best wishes
-- 
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Re: [gmx-users] pbc problem

[Mark Abraham]

On Oct 24, 2013 8:10 AM, "shahab shariati" 
wrote:
>
> Dear jkrieger
>
> I used 2 times trjconv tool:
>
> 1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump
>
> 2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol
-center
>
>
> Dear Mark
>
> I selected all lipid atoms for centering.
>
> With my manner, pbc problem was solved just for lipids and not for drug
> molecule which is put inside water molecules in top leaflet. This pbc
> problem cause to drug molecule be in top and bottom leaflets, while I want
> to study translocation of the drug molecule from water to lipid bilayer.
> I want to solve this problem for drug molecule.

There is only one water region, so "upper" and "lower" don't mean much. If
you just want to see the drug and bilayer in the same PBC cell, then center
on something that is central.

Mark

> If my manner is wrong, please tell me true way.
>
> Best wishes.
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[gmx-users] pbc problem

[shahab shariati]

Dear jkrieger

I used 2 times trjconv tool:

1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump

2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center


Dear Mark

I selected all lipid atoms for centering.

With my manner, pbc problem was solved just for lipids and not for drug
molecule which is put inside water molecules in top leaflet. This pbc
problem cause to drug molecule be in top and bottom leaflets, while I want
to study translocation of the drug molecule from water to lipid bilayer.
I want to solve this problem for drug molecule.

If my manner is wrong, please tell me true way.

Best wishes.
-- 
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Re: [gmx-users] pbc problem

[Mark Abraham]

Center on a particular lipid? Or head group?

Mark
On Oct 23, 2013 6:13 PM, "shahab shariati" 
wrote:

> Dear gromacs users
>
> My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a
> rectangular box.
>
> I put drug molecule in 2 position: a) drug in the center of bilayer
> membrane, b) drug inside water molecules in top leaflet.
>
> For both positions, I did energy minimization successfully with following
> mdp file.
>
> --
> ; Parameters describing what to do, when to stop and what to save
> integrator= steep; Algorithm (steep = steepest descent
> minimization)
> emtol= 1000.0  ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> emstep  = 0.01  ; Energy step size
> nsteps= 5  ; Maximum number of (minimization) steps to
> perform
>
> ; Parameters describing how to find the neighbors of each atom
> nstlist= 1; Frequency to update the neighbor list and
> long range forces
> ns_type= grid; Method to determine neighbor list (simple,
> grid)
> rlist= 1.2; Cut-off for making neighbor list (short range
> forces)
> coulombtype= PME; Treatment of long range electrostatic
> interactions
> rcoulomb= 1.2; Short-range electrostatic cut-off
> rvdw= 1.2; Short-range Van der Waals cut-off
> pbc= xyz ; Periodic Boundary Conditions
>
> ---
> After energy minimization, I saw obtained file (em.gro) by VMD. All things
> were true and intact.
>
> For both positions, I did equilibration in NPT ensemble with following mdp
> file.
>
> ---
> ; Run parameters
> integrator= md; leap-frog integrator
> nsteps= 25; 2 * 50 = 1000 ps (1 ns)
> dt= 0.002; 2 fs
> ; Output control
> nstxout= 100; save coordinates every 0.2 ps
> nstvout= 100; save velocities every 0.2 ps
> nstxtcout   = 100; xtc compressed trajectory output every 2 ps
> nstenergy= 100; save energies every 0.2 ps
> nstlog= 100; update log file every 0.2 ps
> energygrps  = CHOL DOPC drg SOL
> ; Bond parameters
> continuation= no; Restarting after NVT
> constraint_algorithm = lincs; holonomic constraints
> constraints= all-bonds; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter= 1; accuracy of LINCS
> lincs_order= 4; also related to accuracy
> ; Neighborsearching
> ns_type= grid; search neighboring grid cels
> 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
> electrostatics
> pme_order= 4; cubic interpolation
> fourierspacing= 0.16; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl= V-rescale; More accurate thermostat
> tc-grps= CHOL_DOPCdrg SOL; three coupling groups - more
> accurate
> tau_t= 0.50.5   0.5   ; time constant, in ps
> ref_t= 323 323   323 ; reference temperature, one for
> each group, in K
> ; Pressure coupling is on
> pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
> pcoupltype= semiisotropic; uniform scaling of x-y box
> vectors, independent z
> tau_p= 5.0; time constant, in ps
> ref_p= 1.01.0; reference pressure, x-y, z (in
> bar)
> compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1
> ; 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= 323; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the
> solvent/ions
> nstcomm = 1
> comm-mode   = Linear
> comm-grps   = CHOL_DOPC_drg  SOL
> ; Scale COM of reference coordinates
> refcoord_scaling = com
>
>
> ---
> For 2 positions, I chechked tempreture and pressure fluctuation and box
> dimention during equilibration. All things were good. When I saw trajectory
> by VMD (npt.gro and npt xtc), I h

Re: [gmx-users] pbc problem

[jkrieger]

I usually use -pbc nojump for my protein simulations and this works every
time.

> Dear gromacs users
>
> My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a
> rectangular box.
>
> I put drug molecule in 2 position: a) drug in the center of bilayer
> membrane, b) drug inside water molecules in top leaflet.
>
> For both positions, I did energy minimization successfully with following
> mdp file.
> --
> ; Parameters describing what to do, when to stop and what to save
> integrator= steep; Algorithm (steep = steepest descent
> minimization)
> emtol= 1000.0  ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> emstep  = 0.01  ; Energy step size
> nsteps= 5  ; Maximum number of (minimization) steps to
> perform
>
> ; Parameters describing how to find the neighbors of each atom
> nstlist= 1; Frequency to update the neighbor list and
> long range forces
> ns_type= grid; Method to determine neighbor list (simple,
> grid)
> rlist= 1.2; Cut-off for making neighbor list (short range
> forces)
> coulombtype= PME; Treatment of long range electrostatic
> interactions
> rcoulomb= 1.2; Short-range electrostatic cut-off
> rvdw= 1.2; Short-range Van der Waals cut-off
> pbc= xyz ; Periodic Boundary Conditions
> ---
> After energy minimization, I saw obtained file (em.gro) by VMD. All things
> were true and intact.
>
> For both positions, I did equilibration in NPT ensemble with following mdp
> file.
> ---
> ; Run parameters
> integrator= md; leap-frog integrator
> nsteps= 25; 2 * 50 = 1000 ps (1 ns)
> dt= 0.002; 2 fs
> ; Output control
> nstxout= 100; save coordinates every 0.2 ps
> nstvout= 100; save velocities every 0.2 ps
> nstxtcout   = 100; xtc compressed trajectory output every 2 ps
> nstenergy= 100; save energies every 0.2 ps
> nstlog= 100; update log file every 0.2 ps
> energygrps  = CHOL DOPC drg SOL
> ; Bond parameters
> continuation= no; Restarting after NVT
> constraint_algorithm = lincs; holonomic constraints
> constraints= all-bonds; all bonds (even heavy atom-H
> bonds)
> constrained
> lincs_iter= 1; accuracy of LINCS
> lincs_order= 4; also related to accuracy
> ; Neighborsearching
> ns_type= grid; search neighboring grid cels
> 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
> electrostatics
> pme_order= 4; cubic interpolation
> fourierspacing= 0.16; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl= V-rescale; More accurate thermostat
> tc-grps= CHOL_DOPCdrg SOL; three coupling groups - more
> accurate
> tau_t= 0.50.5   0.5   ; time constant, in ps
> ref_t= 323 323   323 ; reference temperature, one for
> each group, in K
> ; Pressure coupling is on
> pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
> pcoupltype= semiisotropic; uniform scaling of x-y box
> vectors, independent z
> tau_p= 5.0; time constant, in ps
> ref_p= 1.01.0; reference pressure, x-y, z (in
> bar)
> compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1
> ; 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= 323; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the
> solvent/ions
> nstcomm = 1
> comm-mode   = Linear
> comm-grps   = CHOL_DOPC_drg  SOL
> ; Scale COM of reference coordinates
> refcoord_scaling = com
>
> ---
> For 2 positions, I chechked tempreture and pressure fluctuation and box
> dimention during equilibration. All things were good. When I saw
> trajectory
> by VMD (npt.gro and npt xtc), I had pbc problem (some atoms

[gmx-users] pbc problem

[shahab shariati]

Dear gromacs users

My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a
rectangular box.

I put drug molecule in 2 position: a) drug in the center of bilayer
membrane, b) drug inside water molecules in top leaflet.

For both positions, I did energy minimization successfully with following
mdp file.
--
; Parameters describing what to do, when to stop and what to save
integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol= 1000.0  ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps= 5  ; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom
nstlist= 1; Frequency to update the neighbor list and
long range forces
ns_type= grid; Method to determine neighbor list (simple,
grid)
rlist= 1.2; Cut-off for making neighbor list (short range
forces)
coulombtype= PME; Treatment of long range electrostatic
interactions
rcoulomb= 1.2; Short-range electrostatic cut-off
rvdw= 1.2; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions
---
After energy minimization, I saw obtained file (em.gro) by VMD. All things
were true and intact.

For both positions, I did equilibration in NPT ensemble with following mdp
file.
---
; Run parameters
integrator= md; leap-frog integrator
nsteps= 25; 2 * 50 = 1000 ps (1 ns)
dt= 0.002; 2 fs
; Output control
nstxout= 100; save coordinates every 0.2 ps
nstvout= 100; save velocities every 0.2 ps
nstxtcout   = 100; xtc compressed trajectory output every 2 ps
nstenergy= 100; save energies every 0.2 ps
nstlog= 100; update log file every 0.2 ps
energygrps  = CHOL DOPC drg SOL
; Bond parameters
continuation= no; Restarting after NVT
constraint_algorithm = lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H bonds)
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cels
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
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
; Temperature coupling is on
tcoupl= V-rescale; More accurate thermostat
tc-grps= CHOL_DOPCdrg SOL; three coupling groups - more
accurate
tau_t= 0.50.5   0.5   ; time constant, in ps
ref_t= 323 323   323 ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
pcoupltype= semiisotropic; uniform scaling of x-y box
vectors, independent z
tau_p= 5.0; time constant, in ps
ref_p= 1.01.0; reference pressure, x-y, z (in
bar)
compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1
; 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= 323; temperature for Maxwell distribution
gen_seed= -1; generate a random seed
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode   = Linear
comm-grps   = CHOL_DOPC_drg  SOL
; Scale COM of reference coordinates
refcoord_scaling = com

---
For 2 positions, I chechked tempreture and pressure fluctuation and box
dimention during equilibration. All things were good. When I saw trajectory
by VMD (npt.gro and npt xtc), I had pbc problem (some atoms leave box and
enter the box in opposit direction).

For position (a): I corrected pbc problem by

trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc mol -center

I selected CHOL_DOPC-drg group for centering. So problem was solved,
approximately.

For position (b) in which drug

Re: [gmx-users] PBC problem

[Tsjerk Wassenaar]

Hi Yutian Yang,

Yes. That is, if the chain is interacting with itself. If it remains curled
up, then it won't be a problem.

Cheers,

Tsjerk


On Thu, Jun 27, 2013 at 10:10 PM, Yutian Yang  wrote:

> Hi all,
>
> I have a question about PBC. If I have a polymer chain that is longer than
> the box length, will the properties of the chain change because the tail of
> the chain may interact with the head of the chain due to PBC? Thank you!
>
> Yutian
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Tsjerk A. Wassenaar, Ph.D.
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[gmx-users] PBC problem

[Yutian Yang]

Hi all, 

I have a question about PBC. If I have a polymer chain that is longer than the 
box length, will the properties of the chain change because the tail of the 
chain may interact with the head of the chain due to PBC? Thank you! 

Yutian
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Re: [gmx-users] pbc problem

[Justin Lemkul]

On 4/14/13 11:21 PM, Kieu Thu Nguyen wrote:

Thank Justin !
I used the command "editconf -center" and i saw my membrane was in center
of the box. I am stupid in that how putting the bilayer in a periodic image
(instead between two periodic images as it was).
Can you give me some instructions ?
Many thanks !



I don't know what it is that you did before, so I can't say.  In principle, one 
could have two leaflets at periodic boundaries along the z-axis and it's exactly 
the same as having an intact membrane in the center of the box from the 
standpoint of dynamics.  For building membrane protein systems, however, that's 
less than convenient.


-Justin



On Fri, Apr 12, 2013 at 6:52 PM, Justin Lemkul  wrote:


On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen 
wrote:



Dear All,

I made a POPC bilayer and carried out embedding a protein into this
membrane. But the fatal error has appeared :
Fatal error:
Something is wrong with your membrane. Max and min z values are 12.342000
and 0.016000. Maybe your membrane is not centered in the box, but located
at the box edge in the z-direction, so that one membrane is distributed
over two periodic box images. Another possibility is that your water

layer

is not thick enough.

I think my bilayer stay at between two periodic images. What should i do

to

put it in corrected position ?



It should be a very simple matter of visualization. Use editconf -center to
place the membrane wherever you want within the unit cell. You can remove
the uncertainty ("I think" is weak compared to "I know") by looking at the
box vectors and then numerically determining the center of the membrane
with g_traj. That should provide you with all the information you need to
determine what's going on.

-Justin

--



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


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--


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


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Re: [gmx-users] pbc problem

[Kieu Thu Nguyen]

Thank Justin !
I used the command "editconf -center" and i saw my membrane was in center
of the box. I am stupid in that how putting the bilayer in a periodic image
(instead between two periodic images as it was).
Can you give me some instructions ?
Many thanks !


On Fri, Apr 12, 2013 at 6:52 PM, Justin Lemkul  wrote:

> On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen  >wrote:
>
> > Dear All,
> >
> > I made a POPC bilayer and carried out embedding a protein into this
> > membrane. But the fatal error has appeared :
> > Fatal error:
> > Something is wrong with your membrane. Max and min z values are 12.342000
> > and 0.016000. Maybe your membrane is not centered in the box, but located
> > at the box edge in the z-direction, so that one membrane is distributed
> > over two periodic box images. Another possibility is that your water
> layer
> > is not thick enough.
> >
> > I think my bilayer stay at between two periodic images. What should i do
> to
> > put it in corrected position ?
> >
> >
> It should be a very simple matter of visualization. Use editconf -center to
> place the membrane wherever you want within the unit cell. You can remove
> the uncertainty ("I think" is weak compared to "I know") by looking at the
> box vectors and then numerically determining the center of the membrane
> with g_traj. That should provide you with all the information you need to
> determine what's going on.
>
> -Justin
>
> --
>
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540)
> 231-9080http://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
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>
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Re: [gmx-users] pbc problem

[Justin Lemkul]

On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen wrote:

> Dear All,
>
> I made a POPC bilayer and carried out embedding a protein into this
> membrane. But the fatal error has appeared :
> Fatal error:
> Something is wrong with your membrane. Max and min z values are 12.342000
> and 0.016000. Maybe your membrane is not centered in the box, but located
> at the box edge in the z-direction, so that one membrane is distributed
> over two periodic box images. Another possibility is that your water layer
> is not thick enough.
>
> I think my bilayer stay at between two periodic images. What should i do to
> put it in corrected position ?
>
>
It should be a very simple matter of visualization. Use editconf -center to
place the membrane wherever you want within the unit cell. You can remove
the uncertainty ("I think" is weak compared to "I know") by looking at the
box vectors and then numerically determining the center of the membrane
with g_traj. That should provide you with all the information you need to
determine what's going on.

-Justin

-- 



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


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[gmx-users] pbc problem

[Kieu Thu Nguyen]

Dear All,

I made a POPC bilayer and carried out embedding a protein into this
membrane. But the fatal error has appeared :
Fatal error:
Something is wrong with your membrane. Max and min z values are 12.342000
and 0.016000. Maybe your membrane is not centered in the box, but located
at the box edge in the z-direction, so that one membrane is distributed
over two periodic box images. Another possibility is that your water layer
is not thick enough.

I think my bilayer stay at between two periodic images. What should i do to
put it in corrected position ?

Thankful for any help !
Regards,

Thu
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[gmx-users] PBC for evaporation of droplets?

[Rasoul Nasiri]

Dear all,

I would like to ask you that using PBC for evaporation of droplets is necessary?

Please note that the MD simulations are to be performed in vacuum.

I checked the relevant references but in some of them PBC has been
taken into account but in others not [for instance please see J.chem.
phys. 125, 154508 (2006) and J. chem. phys. 134, 164309 (2011)].

I would be grateful if you can tell me advantages and disadvantages of
PBC in evaporation of droplets in the vacuum.

Best  regards
Rasoul
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Re: [gmx-users] PBC

[Tsjerk Wassenaar]

Hey Nilesh,

Distance to where? Just think of your PBC in one dimension as being on a circle.

Cheers,

Tsjerk

On Tue, Jun 26, 2012 at 4:26 PM, Nilesh Dhumal  wrote:
> Hello,
>
> I have question about periodic boundary condition. Suppose if one atom is
> going out of the box (x axis distance is more than L/2) and it will come
> inside the box from other side (distance-L).
> Distance before the pbc  should be same or it will be different from center.
>
> Thanks
>
> Nilesh
>
>
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-- 
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
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[gmx-users] PBC

[Nilesh Dhumal]

Hello,

I have question about periodic boundary condition. Suppose if one atom is
going out of the box (x axis distance is more than L/2) and it will come
inside the box from other side (distance-L).
Distance before the pbc  should be same or it will be different from center.

Thanks

Nilesh


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Re: [gmx-users] PBC treatment: need an explanation

[Tsjerk Wassenaar]

Hi Anna,

If there is a representation in which the units are together, then
they're together. Trjconv can't put things together which are, in
fact, separated.

Cheers,

Tsjerk

On Tue, Apr 24, 2012 at 12:51 PM, Anna Marabotti
 wrote:
> Dear gmx-users,
> I know that this is one of the most frequent subjects in the gmx-users list,
> however please let me ask you for a direct answer, since it seems to me that
> this particular question was not treated before.
>
> I'm performing MD simulations on a dimeric protein, using a rhombic
> dodecahedric box. I made 3 simulations in which my system was subjected to
> different isotropic pressures (first simulation: room pressure; second
> simulation: small increase of pressure; third simulation: big increase of
> pressure). I run 50 ns simulation for each system, and at the end of
> simulations I checked for the visualization of the system with VMD and for
> the RMSD against the starting configuration.
> Using g_rms command, I checked for the backbone RMSD against starting
> structure (fullMD.tpr file). The first system stabilized after a few ns of
> simulation, and then the RMSD remained constant. The second system
> stabilized after a few ns of simulation, but with a quantity of "spikes".
> The third system stabilized after a few ns of simulation and then, at about
> 30 ns of simulation, the RMSD value jumped on from approx. 0.4 nm to > 4 nm
> and stayed stable on that new value until the end of simulation.
> I had a look at this trajectory with VMD, and saw that the dimeric protein
> separates into two monomers. This phenomenon is consistent with some
> experimental data about the protein, and it seems to me consistent also with
> the RMSD trend found on the trajectory. However, due to visualization
> problems with my rhombic system, I decided to apply trjconv -pbc nojump:
>
> trjconv -s fullMD.tpr -f fullMD.xtc -o fullMD_noj.xtc -pbc nojump
> (choosing System=0 as option)
>
> After this action, I re-calculated the RMSD of the simulations using the
> same options as before...and found that in the third simultion the RMSD is
> no longer jumping on to > 4 nm. The visualization of the trajectory shows
> the protein in form of a dimer that fluctuates into the zone of "spreaded"
> solvent (no longer a box).
>
> My question is: was the separation into two monomers a simple artifact of
> the simulation, corrected by trjconv, or is trjconv able to affect the
> results of the system in such a way that when monomers truly separate,
> trjconv is able to "force" them together again? How can I check for these
> two possibilities? Finally: in this last case, can you suggest me other ways
> to manage the trajectories in order to remove the spikes related to jump
> across the periodic boundaries?
>
> Thank you very much for help, and best regards
> Anna
> 
> Anna Marabotti, Ph.D.
> Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
>
> "When a man with a gun meets a man with a pen, the man with a gun is a dead
> man"
> (Roberto Benigni, about Roberto Saviano)
>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
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
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Re: [gmx-users] PBC treatment: need an explanation

[Justin A. Lemkul]

On 4/24/12 6:51 AM, Anna Marabotti wrote:

Dear gmx-users,
I know that this is one of the most frequent subjects in the gmx-users list,
however please let me ask you for a direct answer, since it seems to me that
this particular question was not treated before.
I'm performing MD simulations on a dimeric protein, using a rhombic dodecahedric
box. I made 3 simulations in which my system was subjected to different
isotropic pressures (first simulation: room pressure; second simulation: small
increase of pressure; third simulation: big increase of pressure). I run 50 ns
simulation for each system, and at the end of simulations I checked for the
visualization of the system with VMD and for the RMSD against the starting
configuration.
Using g_rms command, I checked for the backbone RMSD against starting structure
(fullMD.tpr file). The first system stabilized after a few ns of simulation, and
then the RMSD remained constant. The second system stabilized after a few ns of
simulation, but with a quantity of "spikes". The third system stabilized after a
few ns of simulation and then, at about 30 ns of simulation, the RMSD value
jumped on from approx. 0.4 nm to > 4 nm and stayed stable on that new value
until the end of simulation.
I had a look at this trajectory with VMD, and saw that the dimeric protein
separates into two monomers. This phenomenon is consistent with some
experimental data about the protein, and it seems to me consistent also with the
RMSD trend found on the trajectory. However, due to visualization problems with
my rhombic system, I decided to apply trjconv -pbc nojump:
trjconv -s fullMD.tpr -f fullMD.xtc -o fullMD_noj.xtc -pbc nojump
(choosing System=0 as option)
After this action, I re-calculated the RMSD of the simulations using the same
options as before...and found that in the third simultion the RMSD is no longer
jumping on to > 4 nm. The visualization of the trajectory shows the protein in
form of a dimer that fluctuates into the zone of "spreaded" solvent (no longer a
box).
My question is: was the separation into two monomers a simple artifact of the
simulation, corrected by trjconv, or is trjconv able to affect the results of
the system in such a way that when monomers truly separate, trjconv is able to
"force" them together again? How can I check for these two possibilities?


The real answer is "neither."  The results you obtained are not an artifact; 
they are normal behavior for a periodic cell.  The visual representation created 
by trjconv was simply a re-wrapping of periodic boundaries so that it was more 
convenient.


If the monomers truly separated, there is no way trjconv (through the simple use 
of -pbc options) can force them back together.  There are many ways in which the 
user can manipulate coordinates; this isn't one of them.


You can check the stability of the dimer interactions in a number of ways - 
hydrogen bonds (g_hbond), distances (g_dist), contacts (g_mindist), etc.


-Justin

--


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


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[gmx-users] PBC treatment: need an explanation

[Anna Marabotti]

Dear gmx-users,
I know that this is one of the most frequent subjects in the gmx-users list,
however please let me ask you for a direct answer, since it seems to me that
this particular question was not treated before.
 
I'm performing MD simulations on a dimeric protein, using a rhombic
dodecahedric box. I made 3 simulations in which my system was subjected to
different isotropic pressures (first simulation: room pressure; second
simulation: small increase of pressure; third simulation: big increase of
pressure). I run 50 ns simulation for each system, and at the end of
simulations I checked for the visualization of the system with VMD and for
the RMSD against the starting configuration.
Using g_rms command, I checked for the backbone RMSD against starting
structure (fullMD.tpr file). The first system stabilized after a few ns of
simulation, and then the RMSD remained constant. The second system
stabilized after a few ns of simulation, but with a quantity of "spikes".
The third system stabilized after a few ns of simulation and then, at about
30 ns of simulation, the RMSD value jumped on from approx. 0.4 nm to > 4 nm
and stayed stable on that new value until the end of simulation.
I had a look at this trajectory with VMD, and saw that the dimeric protein
separates into two monomers. This phenomenon is consistent with some
experimental data about the protein, and it seems to me consistent also with
the RMSD trend found on the trajectory. However, due to visualization
problems with my rhombic system, I decided to apply trjconv -pbc nojump:
 
trjconv -s fullMD.tpr -f fullMD.xtc -o fullMD_noj.xtc -pbc nojump
(choosing System=0 as option)
 
After this action, I re-calculated the RMSD of the simulations using the
same options as before...and found that in the third simultion the RMSD is
no longer jumping on to > 4 nm. The visualization of the trajectory shows
the protein in form of a dimer that fluctuates into the zone of "spreaded"
solvent (no longer a box).
 
My question is: was the separation into two monomers a simple artifact of
the simulation, corrected by trjconv, or is trjconv able to affect the
results of the system in such a way that when monomers truly separate,
trjconv is able to "force" them together again? How can I check for these
two possibilities? Finally: in this last case, can you suggest me other ways
to manage the trajectories in order to remove the spikes related to jump
across the periodic boundaries?
 
Thank you very much for help, and best regards
Anna

Anna Marabotti, Ph.D.
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
 
"When a man with a gun meets a man with a pen, the man with a gun is a dead
man"
(Roberto Benigni, about Roberto Saviano)
 
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Re: [gmx-users] PBC - Protein and Ligands

[Steven Neumann]

Thank you all! That helped a lot!

Steven

On Wed, Feb 29, 2012 at 5:17 PM, Vedat Durmaz  wrote:

> **
> i always did it (successfully) with one single command:
>
> trjconv -f md.trr -s md.tpr -o mdCompact.trr -pbc mol -ur compact -n
> ../../index.ndx
>
>
> regards
> vedat
>
>
> Am 29.02.2012 18:01, schrieb Steven Neumann:
>
> Dear Gmx Users,
>
> I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands.
> The problem I face is PBC which I cannot get rid of. I used:
>
>
> 1.  First make your molecules whole if you want them whole (system).
>
> trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.xtc
>
> 2.  Cluster your molecules/particles if you want them clustered
>
>
>
> 3.  Extract the first frame from the trajectory as reference for
> removing jumps if you want to remove jumps.
>
> trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb
>
> 4.  Remove jumps if you want to have them removed using the first
> frame (system)
>
> trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc
>
>
>
> So the trajecory of my ligands is smooth but they do do bind to the
> different periodic images. As i know it is impossible to obtain the proper
> trajectory of all of them I just want to obtain the realistic final
> positions of my system to extract pdb file for further umbrella sampling.
> Any suggestions?
>
>
>
> Steven
>
>
>
>
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Re: [gmx-users] PBC - Protein and Ligands

[Vedat Durmaz]

i always did it (successfully) with one single command:

trjconv -f md.trr -s md.tpr -o mdCompact.trr -pbc mol -ur compact -n 
../../index.ndx



regards
vedat


Am 29.02.2012 18:01, schrieb Steven Neumann:

Dear Gmx Users,
I am run a simulation with Gromacs 4.5.4. of my protein and 15 
ligands. The problem I face is PBC which I cannot get rid of. I used:


1.First make your molecules whole if you want them whole (system).

trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.xtc

2.Cluster your molecules/particles if you want them clustered

3.Extract the first frame from the trajectory as reference for 
removing jumps if you want to remove jumps.


trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb

4.Remove jumps if you want to have them removed using the first frame 
(system)


trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc

So the trajecory of my ligands is smooth but they do do bind to the 
different periodic images. As i know it is impossible to obtain the 
proper trajectory of all of them I just want to obtain the realistic 
final positions of my system to extract pdb file for further umbrella 
sampling. Any suggestions?


Steven

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Re: [gmx-users] PBC - Protein and Ligands

[lina]

On 1 Mar, 2012, at 1:01, Steven Neumann  wrote:

> Dear Gmx Users,
>  
> I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The 
> problem I face is PBC which I cannot get rid of. I used:
>  
> 1.  First make your molecules whole if you want them whole (system).
> trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.xtc
> 2.  Cluster your molecules/particles if you want them clustered
>  
> 3.  Extract the first frame from the trajectory as reference for removing 
> jumps if you want to remove jumps.
> trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb
> 4.  Remove jumps if you want to have them removed using the first frame 
> (system)
> trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc
>  
> So the trajecory of my ligands is smooth but they do do bind to the different 
> periodic images. As i know it is impossible to obtain the proper trajectory 
> of all of them I just want to obtain the realistic final positions of my 
> system to extract pdb file for further umbrella sampling. Any suggestions?

You may wanna try 

Trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -ur compact -o pdbs.pdb -dt 
1000

Please change dt if necessary. 


>  
> Steven
>  
> -- 
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Re: [gmx-users] PBC - Protein and Ligands

[Justin A. Lemkul]

Steven Neumann wrote:

Dear Gmx Users,
 
I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. 
The problem I face is PBC which I cannot get rid of. I used:
 


1.  First make your molecules whole if you want them whole (system).

trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.xtc

2.  Cluster your molecules/particles if you want them clustered

 

3.  Extract the first frame from the trajectory as reference for 
removing jumps if you want to remove jumps.


trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb

4.  Remove jumps if you want to have them removed using the first 
frame (system)


trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc

 

So the trajecory of my ligands is smooth but they do do bind to the 
different periodic images. As i know it is impossible to obtain the 
proper trajectory of all of them I just want to obtain the realistic 
final positions of my system to extract pdb file for further umbrella 
sampling. Any suggestions?


 


If you have a single protein to which all the molecules bind, you can simply:

trjconv -s md298.tpr -f md298SKIP4.xtc -o center.xtc -center (center on protein, 
output system)


trjconv -s md298.tpr -f center.xtc -o fit.xtc -fit rot+trans

The protein will stay in the center of the box, with its rotational and 
translational motions fitted.  It should produce a very smooth trajectory.


-Justin

--


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


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[gmx-users] pbc visualization advice

[Peter C. Lai]

Hi all:

I'm running a diffusion simulation involving a membrane protein and may be 
having a problem with the trjconv workflow.

I have some molecules I'd like to study the diffusion of across the membrane
(if it happens) and/or see if they interact with the membrane protein inside
the membrane.

So I trjconv -pbc whole, then trjconv -pbc nojump. After this, the trajectory
is continuous but of course the water and some of the ligands are leaving
the box.

What's the next step I should perform to make a good visualization so that
the box looks intact and the protein remains centered? If I try to use
something like -pbc mol -center it forms a nice box but now I have molecules
that diffuse into the mirror and makes it look like they have diffused
into the intracellular space (bottom of the mirror) which does not look good.

Will clustering help me? 


-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] -pbc nojump

[mohammad agha]

Thank you very much from your reply.

Best Regards
Sara



 From: Tsjerk Wassenaar 
To: mohammad agha ; Discussion list for GROMACS users 
 
Sent: Thursday, December 29, 2011 1:56 AM
Subject: Re: [gmx-users] -pbc nojump
 
Hi Sara,

Please keep discussions on the list. I'm not your private tutor.

Whether you can do your analysis depends on the analysis you want to
do. But if your aim is analyzing the formation of the micelle, you're
probably better of reversing the trajectory.

> 1- trjconv -f md.trr -o md1.xtc -n index.ndx -pbc whole -s md.tpr

This makes molecules whole, which is fine. Clustering should make
molecules whole too, though, making this step redundant.

> 2- trjconv -f md1.xtc -s md.tpr -o cluster1.gro -e 60 -pbc cluster

Fine, you get a cluster

> 3- trjconv -f cluster1.gro -s md.tpr -dump 150 -o cluster2.gro

This does nothing special. Just because you have a reference clustered
doesn't mean the output frame will turn out clustered.

> 4- grompp -f md.mdp -c cluster2.gro -o cluster1.tpr -n index.ndx
> 5- trjconv -f cluster1.gro -o cluster1.xtc -s cluster1.tpr -pbc nojump

This screws up everything. You can only use -pbc nojump with a
reference structure that is sufficiently close to the first frame of
the trajectory. Your reference is a snapshot at t=600 ns.

> 6- trjconv -f cluster1.xtc -s cluster1.tpr -pbc mol -ur compact -center -o
> cluster3.xtc

This would probably be fine if the trajectory was okay there.

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-- 
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Re: [gmx-users] -pbc nojump

[Tsjerk Wassenaar]

Hi Sara,

Please keep discussions on the list. I'm not your private tutor.

Whether you can do your analysis depends on the analysis you want to
do. But if your aim is analyzing the formation of the micelle, you're
probably better of reversing the trajectory.

> 1- trjconv -f md.trr -o md1.xtc -n index.ndx -pbc whole -s md.tpr

This makes molecules whole, which is fine. Clustering should make
molecules whole too, though, making this step redundant.

> 2- trjconv -f md1.xtc -s md.tpr -o cluster1.gro -e 60 -pbc cluster

Fine, you get a cluster

> 3- trjconv -f cluster1.gro -s md.tpr -dump 150 -o cluster2.gro

This does nothing special. Just because you have a reference clustered
doesn't mean the output frame will turn out clustered.

> 4- grompp -f md.mdp -c cluster2.gro -o cluster1.tpr -n index.ndx
> 5- trjconv -f cluster1.gro -o cluster1.xtc -s cluster1.tpr -pbc nojump

This screws up everything. You can only use -pbc nojump with a
reference structure that is sufficiently close to the first frame of
the trajectory. Your reference is a snapshot at t=600 ns.

> 6- trjconv -f cluster1.xtc -s cluster1.tpr -pbc mol -ur compact -center -o
> cluster3.xtc

This would probably be fine if the trajectory was okay there.

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
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Re: [gmx-users] -pbc nojump

[Tsjerk Wassenaar]

Hi Sara,

The problem is that your micelle is formed at the end of the
trajectory. To get what you want, you need to mirror the trajectory,
follow the procedure you followed, and mirror the resulting
trajectory. I posted a piece of python code for mirroring a trajectory
a while back: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061443.html

Hope it helps,

Tsjerk


On Wed, Dec 28, 2011 at 5:25 PM, mohammad agha  wrote:
> Dear GROMACS users,
>
> I have a problem about trjconv -pbc nojump, I have 2 micelles in the end of
> my simulation. For analysis I should do three steps for micelle clustering
> at
> http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering?highlight=micelle+clustering
> Steps 1 and 2 work good and when I view my trajectory after step2 by :
> ngmx -f a_cluster.gro -s a_cluster.tpr
> is viewed 2 micelles, but when I did step 3 (trjconv -nojump) and after do :
> ngmx -f a_cluster.xtc -s a_cluster.tpr
> has been created 1 micelle and reminder of monomers have been collected as
> some groups at different places.
> May I ask you to help me, please?
> Thank you
>
> Best Regards
> Sara
>
>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
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
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[gmx-users] -pbc nojump

[mohammad agha]

Dear GROMACS users,

I have a problem 
about trjconv -pbc nojump, I have 2 micelles in the end of my simulation. 
For analysis I should do three steps for micelle clustering at
http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering?highlight=micelle+clustering 
Steps 1 and 2 work good and when I view my trajectory after step2 by :
ngmx -f a_cluster.gro -s a_cluster.tpr
is viewed 2 micelles, but when I did step 3 (trjconv -nojump) and after do : 
ngmx -f a_cluster.xtc -s a_cluster.tpr
has been created 1 micelle and reminder of monomers have been collected as some 
groups at different places.
May I ask you to help me, please?
Thank you

Best Regards
Sara-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] PBC - Protein - ligand

[Mark Abraham]

On 8/11/2011 3:17 AM, Steven Neumann wrote:



On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul > wrote:




Steven Neumann wrote:

Dear Gmx Users,
 I know that this problem has been discussed may times but I
cannot find the solution to get rid of pbc in my system:
protein and ligand. I followed the workflow:

1.  First make your molecules whole if you want them whole

trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc

2.  Cluster your molecules/particles if you want them
clustered

3.  Extract the first frame from the trajectory as
reference for removing jumps if you want to remove jumps.

trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb

4.  Remove jumps if you want to have them removed using
the first frame

trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o
mdwholeNOjump.xtc

5.  Center your system using some criterion. Doing so
shifts the system, so don't use |trjconv -|pbc| nojump| after
this step.


trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc

6.  Put everything in some box.

trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o
mdwholeNOjumpCENTERbox.xtc

7.  Fit if desired and don't use any PBC related option
afterwards.

trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit
rot+trans -o mdfinal.xtc


I used SYSTEM everywhere as output orinput. However, my ligand
is still jumping like a fly around the stable protein. Do you
have any suggestions?



Center on either the protein, the ligand, or some custom index
group of residues surrounding the ligand.  Centering on the whole
system usually doesn't do anything useful.

-Justin

Thank you guys but...
I am trying and it does not work... my ligand is jumping like an idiot 
outside the box changing its position even two dimensions of box in 
one frame.


I have no idea what you mean by this.

I removed -ur compact from the first line and I tried centering on 
ligand or protein (centering group: LIG or Protein, output: SYSTEM). 
No results...
My ligand at the begining of the simualtion is not within the protein. 
Please, help : I tried this workflow with many ligands and same 
protein - it worked! Now it does not...


Sure. So far you've given us no understanding of what your ligand is 
doing during the simulation. If you don't know either, go and look at 
it. Then go and look at the trajectory from each stage of your work flow 
and see what it looks like and how things are changing. Then when 
something looks wrong you have a single step you can trouble shoot... 
maybe the operation is not sensible, maybe the way you did it is wrong, 
maybe the code is wrong.


You cannot expect to transfer work flows from another simulation without 
considering what is happening in this one. Scenarios where your ligand 
is diffusing away from your protein and reassociating to another side 
require different work flows from one where the ligand stays nearby a 
binding pocket. In the latter, you should probably use -pbc cluster in 
step 2, though some of the time it won't matter. In the former, using 
-nojump to allow diffusion out of the box, and then step 6 to put 
everything back in the box doesn't make sense. Just doing operations and 
selecting groups without considering the nature of the operation will 
get a garbage result. There's a good reason mdrun doesn't attempt to 
second-guess how you would like all of this done!


Mark


Here is my workflow:

1.First make your molecules whole if you want them whole.

trjconv -f md.trr -s md.tpr -pbc whole -o mdwhole.xtc

2.Cluster your molecules/particles if you want them clustered

3.Extract the first frame from the trajectory as reference for 
removing jumps if you want to remove jumps.


trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb

4.Remove jumps if you want to have them removed using the first frame 
(system)


trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc

5.Center your system using some criterion. Doing so shifts the system, 
so don't use |trjconv -|pbc|nojump|after this step (tried centering on 
LIG or PROTEIN)


trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -center -o 
mdwholeNOjumpCENTER.xtc


6.Put everything in some box.

trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o 
mdwholeNOjumpCENTERbox.xtc


7.Fit if desired and don't use any PBC related option afterwards.

trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans 
-o mdfinal.xtc


With point three, the issue is that trjconv 
 
removes the jumps from the first frame using the reference structure 
provided with |-s|. If the reference structure (run input file) is not 
clustered/whole, |trjconv -|

Re: [gmx-users] PBC - Protein - ligand

[Tsjerk Wassenaar]

Hi Steven,

Step 2: Cluster your molecules.
This is where you have to forge a reference frame that you can use to
remove jumps from your trajectory. If the ligand is not with the
protein at the start, you'll have to shift it so that it is. Maybe
-pbc cluster is your friend there. I do assume that the ligand is
really with the protein and not in the solvent...

Cheers,

Tsjerk

On Mon, Nov 7, 2011 at 5:17 PM, Steven Neumann  wrote:
>
>
> On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul  wrote:
>>
>>
>> Steven Neumann wrote:
>>>
>>> Dear Gmx Users,
>>>  I know that this problem has been discussed may times but I cannot find
>>> the solution to get rid of pbc in my system: protein and ligand. I followed
>>> the workflow:
>>>
>>> 1.      First make your molecules whole if you want them whole
>>>
>>> trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc
>>>
>>> 2.      Cluster your molecules/particles if you want them clustered
>>>
>>> 3.      Extract the first frame from the trajectory as reference for
>>> removing jumps if you want to remove jumps.
>>>
>>> trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb
>>>
>>> 4.      Remove jumps if you want to have them removed using the first
>>> frame
>>>
>>> trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc
>>>
>>> 5.      Center your system using some criterion. Doing so shifts the
>>> system, so don't use |trjconv -|pbc| nojump| after this step.
>>>
>>> trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc
>>>
>>> 6.      Put everything in some box.
>>>
>>> trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o
>>> mdwholeNOjumpCENTERbox.xtc
>>>
>>> 7.      Fit if desired and don't use any PBC related option afterwards.
>>>
>>> trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o
>>> mdfinal.xtc
>>>
>>>
>>> I used SYSTEM everywhere as output orinput. However, my ligand is still
>>> jumping like a fly around the stable protein. Do you have any suggestions?
>>>
>>>
>>
>> Center on either the protein, the ligand, or some custom index group of
>> residues surrounding the ligand.  Centering on the whole system usually
>> doesn't do anything useful.
>>
>> -Justin
>>
>
> Thank you guys but...
>
> I am trying and it does not work... my ligand is jumping like an idiot
> outside the box changing its position even two dimensions of box in one
> frame. I removed -ur compact from the first line and I tried centering on
> ligand or protein (centering group: LIG or Protein, output: SYSTEM). No
> results...
> My ligand at the begining of the simualtion is not within the protein.
> Please, help : I tried this workflow with many ligands and same protein
> - it worked! Now it does not...
> Here is my workflow:
>
>
> 1.  First make your molecules whole if you want them whole.
>
> trjconv -f md.trr -s md.tpr -pbc whole -o mdwhole.xtc
>
> 2.  Cluster your molecules/particles if you want them clustered
>
> 3.  Extract the first frame from the trajectory as reference for
> removing jumps if you want to remove jumps.
>
> trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb
>
> 4.  Remove jumps if you want to have them removed using the first frame
> (system)
>
> trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc
>
> 5.  Center your system using some criterion. Doing so shifts the system,
> so don't use trjconv -pbc nojump after this step (tried centering on LIG or
> PROTEIN)
>
> trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -center -o
> mdwholeNOjumpCENTER.xtc
>
> 6.  Put everything in some box.
>
> trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc
>
> 7.  Fit if desired and don't use any PBC related option afterwards.
>
> trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o
> mdfinal.xtc
>
> With point three, the issue is that trjconv removes the jumps from the first
> frame using the reference structure provided with -s. If the reference
> structure (run input file) is not clustered/whole, trjconv -pbc nojump will
> undo steps 1 and
>
> Steven
>
>
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>>
>> --
>> gmx-users mailing list    gmx-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
>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://ww

Re: [gmx-users] PBC - Protein - ligand

[Steven Neumann]

On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>> Dear Gmx Users,
>>  I know that this problem has been discussed may times but I cannot find
>> the solution to get rid of pbc in my system: protein and ligand. I followed
>> the workflow:
>>
>> 1.  First make your molecules whole if you want them whole
>>
>> trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc
>>
>> 2.  Cluster your molecules/particles if you want them clustered
>>
>> 3.  Extract the first frame from the trajectory as reference for
>> removing jumps if you want to remove jumps.
>>
>> trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb
>>
>> 4.  Remove jumps if you want to have them removed using the first
>> frame
>>
>> trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc
>>
>> 5.  Center your system using some criterion. Doing so shifts the
>> system, so don't use |trjconv -|pbc| nojump| after this step.
>>
>>
>> trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc
>>
>> 6.  Put everything in some box.
>>
>> trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o
>> mdwholeNOjumpCENTERbox.xtc
>>
>> 7.  Fit if desired and don't use any PBC related option afterwards.
>>
>> trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o
>> mdfinal.xtc
>>
>>
>> I used SYSTEM everywhere as output orinput. However, my ligand is still
>> jumping like a fly around the stable protein. Do you have any suggestions?
>>
>>
>>
>
> Center on either the protein, the ligand, or some custom index group of
> residues surrounding the ligand.  Centering on the whole system usually
> doesn't do anything useful.
>
> -Justin
>
>
Thank you guys but...

I am trying and it does not work... my ligand is jumping like an idiot
outside the box changing its position even two dimensions of box in one
frame. I removed -ur compact from the first line and I tried centering on
ligand or protein (centering group: LIG or Protein, output: SYSTEM). No
results...
My ligand at the begining of the simualtion is not within the protein.
Please, help : I tried this workflow with many ligands and same protein
- it worked! Now it does not...
Here is my workflow:


1.  First make your molecules whole if you want them whole.

trjconv -f md.trr -s md.tpr -pbc whole -o mdwhole.xtc

2.  Cluster your molecules/particles if you want them clustered

3.  Extract the first frame from the trajectory as reference for
removing jumps if you want to remove jumps.

trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb

4.  Remove jumps if you want to have them removed using the first frame
(system)

trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc

5.  Center your system using some criterion. Doing so shifts the
system, so don't use trjconv -pbc nojump after this step (tried centering
on LIG or PROTEIN)

trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -center -o
mdwholeNOjumpCENTER.xtc

6.  Put everything in some box.

trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc

7.  Fit if desired and don't use any PBC related option afterwards.

trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o
mdfinal.xtc
With point three, the issue is that
trjconvremoves
the jumps from the first frame using the reference structure
provided with -s. If the reference structure (run input file) is not
clustered/whole, trjconv -pbc nojump will undo steps 1 and

Steven


==**==

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

==**==

>
> --
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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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> Can't post? Read 
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Re: [gmx-users] PBC - Protein - ligand

[Justin A. Lemkul]

Steven Neumann wrote:

Dear Gmx Users,
 
I know that this problem has been discussed may times but I cannot find 
the solution to get rid of pbc in my system: protein and ligand. I 
followed the workflow:
 


1.  First make your molecules whole if you want them whole

trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc

2.  Cluster your molecules/particles if you want them clustered

3.  Extract the first frame from the trajectory as reference for 
removing jumps if you want to remove jumps.


trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb

4.  Remove jumps if you want to have them removed using the first frame

trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc

5.  Center your system using some criterion. Doing so shifts the 
system, so don't use |trjconv -|pbc| nojump| after this step.


trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc

6.  Put everything in some box.

trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc

7.  Fit if desired and don't use any PBC related option afterwards.

trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o 
mdfinal.xtc


 

I used SYSTEM everywhere as output orinput. However, my ligand is still 
jumping like a fly around the stable protein. Do you have any suggestions?


 


Center on either the protein, the ligand, or some custom index group of residues 
surrounding the ligand.  Centering on the whole system usually doesn't do 
anything useful.


-Justin



Steven



--


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


--
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Re: [gmx-users] PBC - Protein - ligand

[Tsjerk Wassenaar]

Hi Steven,

Don't use -ur compact in the first step and see if that solves the problem.

Oh, and be sure that the thing is not just diffusing. There was a
thread lately where a diffusing ligand drove someone mad trying to
remove the 'jumps'.

Cheers,

Tsjerk

On Mon, Nov 7, 2011 at 3:08 PM, Steven Neumann  wrote:
> Dear Gmx Users,
>
> I know that this problem has been discussed may times but I cannot find the
> solution to get rid of pbc in my system: protein and ligand. I followed the
> workflow:
>
>
> 1.  First make your molecules whole if you want them whole
>
> trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc
>
> 2.  Cluster your molecules/particles if you want them clustered
>
> 3.  Extract the first frame from the trajectory as reference for
> removing jumps if you want to remove jumps.
>
> trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb
>
> 4.  Remove jumps if you want to have them removed using the first frame
>
> trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc
>
> 5.  Center your system using some criterion. Doing so shifts the system,
> so don't use trjconv -pbc nojump after this step.
>
> trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc
>
> 6.  Put everything in some box.
>
> trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc
>
> 7.  Fit if desired and don't use any PBC related option afterwards.
>
> trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o
> mdfinal.xtc
>
>
>
> I used SYSTEM everywhere as output orinput. However, my ligand is still
> jumping like a fly around the stable protein. Do you have any suggestions?
>
>
>
> Steven
>
> --
> 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
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[gmx-users] PBC - Protein - ligand

[Steven Neumann]

Dear Gmx Users,

I know that this problem has been discussed may times but I cannot find the
solution to get rid of pbc in my system: protein and ligand. I followed the
workflow:


1.  First make your molecules whole if you want them whole

trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc

2.  Cluster your molecules/particles if you want them clustered

3.  Extract the first frame from the trajectory as reference for
removing jumps if you want to remove jumps.

trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb

4.  Remove jumps if you want to have them removed using the first frame

trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc

5.  Center your system using some criterion. Doing so shifts the
system, so don't use trjconv -pbc nojump after this step.

trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc

6.  Put everything in some box.

trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc

7.  Fit if desired and don't use any PBC related option afterwards.

trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o
mdfinal.xtc



I used SYSTEM everywhere as output orinput. However, my ligand is still
jumping like a fly around the stable protein. Do you have any suggestions?



Steven
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Re: [gmx-users] PBC

[Carla Jamous]

Thank you Justin,

indeed it's pbc = xyz in my md.log file.

Carla

On Fri, Feb 25, 2011 at 3:20 PM, Justin A. Lemkul  wrote:

>
>
> Carla Jamous wrote:
>
>> Hi everyone,
>>
>> In my .mdp MD file, I didn't put "pbc =xyz". Then, I used tpbconv and
>> mdrun to continue my simulation.
>>
>> My question is: did I run my simulation using periodic boundary conditions
>> because I have the impression that I did but I'm not sure if not using the
>> mention "pbc" in my mdp file  means that I didn't use PBC?
>>
>
> pbc=xyz is the default if not specified.  Check your mdout.mdp and md.log
> files to be sure.
>
> -Justin
>
>
>> Thanks
>>
>> Carla
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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Re: [gmx-users] PBC

[Justin A. Lemkul]

Carla Jamous wrote:

Hi everyone,

In my .mdp MD file, I didn't put "pbc =xyz". Then, I used tpbconv and 
mdrun to continue my simulation.


My question is: did I run my simulation using periodic boundary 
conditions because I have the impression that I did but I'm not sure if 
not using the mention "pbc" in my mdp file  means that I didn't use PBC?


pbc=xyz is the default if not specified.  Check your mdout.mdp and md.log files 
to be sure.


-Justin



Thanks

Carla



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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] PBC

[Carla Jamous]

Hi everyone,

In my .mdp MD file, I didn't put "pbc =xyz". Then, I used tpbconv and mdrun
to continue my simulation.

My question is: did I run my simulation using periodic boundary conditions
because I have the impression that I did but I'm not sure if not using the
mention "pbc" in my mdp file  means that I didn't use PBC?

Thanks

Carla
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Re: [gmx-users] -pbc nojump

[Mark Abraham]

On 20/10/2010 10:26 PM, shahab shariati wrote:


Dear Mark

you said in answer to -pbc nojump that using of new xtc file for 
analysis section depends what one wants to observe.


what observations is relevant to periodicity?



Anything that measures where something is relative to another. Normally 
one is only interested in the nearest periodic image. IIRC, some of the 
GROMACS tools are PBC-aware and determine the nearest suitable for 
themselves, other times they treat the trajectory as if there were no 
periodicity. In the latter case, if your results will be sensitive to 
the actual locations of atoms with respect to the periodic cell, then 
you'll wish to use trjconv to choose the configuration best suited to 
your needs. In the analysis desired the original post, the waters should 
all be in the same cell as the DNA+protein interstice, hence centering 
the cell on that group, and putting all waters into the cell.


Mark
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[gmx-users] -pbc nojump

[shahab shariati]

Dear Mark



you said in answer to -pbc nojump that using of new xtc file for analysis
section depends what one wants to observe.



what observations is relevant to periodicity?
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Re: [gmx-users] -pbc nojump

[Mark Abraham]

On 20/10/2010 9:55 PM, leila karami wrote:

Dear Mark
my mean of [when I used trjconv -pbc nojump, I made one group (protein and dna) 
in index file and I selected that as centering group.] is that

the problem (nonentity of water molecules in interface of protein and dna) was 
not solved.

what is your mean of [You might need two passes with trjconv]?
You might need to use trjconv once to center, and then again to put all 
the molecules in the box (or similar). trjconv can't always do 
everything you want in one invocation.


Mark
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[gmx-users] -pbc nojump

[leila karami]

Dear Mark

my mean of [when I used trjconv -pbc nojump, I made one group (protein
and dna) in index file and I selected that as centering group.] is
that
the problem (nonentity of water molecules in interface of protein and
dna) was not solved.

what is your mean of [You might need two passes with trjconv]?
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Re: [gmx-users] -pbc nojump

[Mark Abraham]

On 20/10/2010 9:24 PM, leila karami wrote:

Dear Mark

thanks for your attention

when I used trjconv -pbc nojump, I made one group (protein and dna) in 
index file and I selected that as centering group.


What is the problem? :-) You might need two passes with trjconv.

Mark
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[gmx-users] -pbc nojump

[leila karami]

Dear Mark

thanks for your attention

when I used trjconv -pbc nojump, I made one group (protein and dna) in index
file and I selected that as centering group.
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Re: [gmx-users] -pbc nojump

[Mark Abraham]

On 20/10/2010 9:07 PM, leila karami wrote:


Hi gromacs users


I study simulation of protein-dna interaction using gromacs. After 
full md simulation, because of diffusion of one strand of dna to edge 
of box, I used trjconv -f old.xtc –o new.xtc –s *.tpr -pbc nojump -ur 
compact –center. By this way my first problem is solved.


1)Should I use new xtc file for analysis section?

That depends what you want to observe, and whether periodicity is 
relevant to that observation.


2)When I see new xtc file, there isn’t any water molecule in interface 
between protein and dna(where as there were water molecules interface 
between protein and dna, before full md simulation). I want to survey 
water mediated hydrogen bond between protein and dna. Do –pbc nojump 
cause to this problem?


Probably. Probably what you want is to center on the combined 
protein+DNA group (need to make an index group) and then put the COM of 
all residues in the box. That will mean your water region and surrounds 
of interest are contiguous.


Mark

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[gmx-users] -pbc nojump

[leila karami]

Hi gromacs users


I study simulation of protein-dna interaction using gromacs. After full md
simulation, because of diffusion of one strand of dna to edge of box, I used
trjconv -f old.xtc –o new.xtc –s *.tpr -pbc nojump -ur compact –center. By
this way my first problem is solved.

1) Should I use new xtc file for analysis section?

2)When I see new xtc file, there isn’t any water molecule in interface
between protein and dna(where as there were water molecules interface
between protein and dna, before full md simulation). I want to survey water
mediated hydrogen bond between protein and dna. Do –pbc nojump cause to this
problem?
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[gmx-users] pbc in one direction only for analysis?

[chris . neale]

It's a messy solution, but you could

1. run trjconv so that your cylinder is in the unit cell
2. convert your trajectory to .gro files
3. massively expand the x and y dimensions of each .gro
4. join the .gros to a .xtc
5. g_rdf

You could also use template.c to write a program that does this  
directly to a .xtc file.



Chris.

-- original message --


Dear gromacs users

I have surface groups anchored on a cylindrical pore wall (similar to
a carbon nanotube). The pore runs along the z direction. I am trying
to determine to what extent my surface groups are clustered together
and was thinking of using g_mindist and/or g_rdf for this analysis.

I usually work with periodic boundary conditions in all 3 directions
for MD runs.

The problem I have is that I want to use periodic boundaries only in
the z direction and not the x and y for the anaysis. I.e I dont want
the surface groups in my pore to see other surface groups in
neighbouring cells in the x or y direction.

 From what I can see, the options with g_rdf is either to have pbc in
all 3 directions or not at all. Does anyone know a way around this?

I am analyzing one pdb file and not a trajectory.

I am using gromacs 4.0.7

Thanks



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[gmx-users] pbc in one direction only for analysis?

[Jennifer Williams]

Dear gromacs users

I have surface groups anchored on a cylindrical pore wall (similar to  
a carbon nanotube). The pore runs along the z direction. I am trying  
to determine to what extent my surface groups are clustered together  
and was thinking of using g_mindist and/or g_rdf for this analysis.


I usually work with periodic boundary conditions in all 3 directions  
for MD runs.


The problem I have is that I want to use periodic boundaries only in  
the z direction and not the x and y for the anaysis. I.e I dont want  
the surface groups in my pore to see other surface groups in  
neighbouring cells in the x or y direction.


From what I can see, the options with g_rdf is either to have pbc in  
all 3 directions or not at all. Does anyone know a way around this?


I am analyzing one pdb file and not a trajectory.

I am using gromacs 4.0.7

Thanks



--
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Scotland, with registration number SC005336.


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[gmx-users] pbc atom

[chris . neale]

velocities are not taken from the .gro as far as I know. You can get  
them from the .trr if you also use a .edr.


If you want to check, then do a run for only 1 ps and save your .edr  
every timestep. Then run g_energy and look at the temperature.


I am not sure that a constant energy simulation in vacuum is a good  
idea. When I say the initial forces become the initial velocities, I  
mean this: you start with no thermal noise, your system is momentarily  
at zero kinetic energy. After the first time step, you get some  
velocities from the initial forces. It is quite likely that these will  
be concerted motions more than random oscillations, especially if you  
are using the pull code. But the kinetic energies are still quite  
small, so your thermostat scales them up massively and you get a  
"flying ice cube" problem (again, read about this please).


I think that you will get farther if you try to test some of these  
yourself: e.g. if you think that you get initial velocities, then  
think of a way to test if you really do (here you have the method I  
suggested above, but it's just an analogy).


Chris.

-- original message --

Thanks for all your help. I am actually considering removing the
thermostat all together seeing as my system is quite small.
I have also started using gen_vel = yes (no matter how much I think my
system is in equilibrium). One quick question (perhaps its silly). When
you say the initial forces become the initial velocities; I thought the
initial velocities were taken from the velocities in the initial
configuration (taking into account that I do have velocities in the
initial configurations from previous simulations).

Cheers

Gavin



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Re: [gmx-users] pbc atom

[Gavin Melaugh]

O.K Chris

Thanks for all your help. I am actually considering removing the
thermostat all together seeing as my system is quite small.
I have also started using gen_vel = yes (no matter how much I think my
system is in equilibrium). One quick question (perhaps its silly). When
you say the initial forces become the initial velocities; I thought the
initial velocities were taken from the velocities in the initial
configuration (taking into account that I do have velocities in the
initial configurations from previous simulations).

Cheers

Gavin

chris.ne...@utoronto.ca wrote:
> Gavin, I recall mentioning gen_vel=no with temperature coupling as a
> possible problem a while ago (the problem is that the initial forces
> become initial velocities and then those get scaled up and what you
> have are velocities and not temperatures -- read about the flying ice
> cube problem). Do you have any idea why it would only cause you
> problems at a distance of greater than 2 nm?
>
> Also, Justin seemed to intuit this was a thermostat. I suspect that if
> you switch to the sd integrator things will all be ok. I don't really
> do anything in vacuum so it was harder to pick this up.
>
> If you're tied to your md/NH settings, then you probably need to
> reduce the timestep -- but you will probaby run into problem
> eventually here too so I don't advise it.
>
> Chris.
>
> -- original message --
>
> Dear Chris and Justin
>
> I ran a simulation for two water molecules (100 ns). It only took 5
> minutes. Firstly I ran the simulation with ref distance 2.35 nm, genvel
> =yes, and gen temp =600 (using Nose Hoover). This produced a histogram
> with one main peak. I then took the final configuration from that
> simulation and ran the simulation again for the exact same duration and
> parameters etc, with the only exception that I set gen_vel = no. The
> resulting histogram did indeed have two main peaks. I am now currently
> running the simulation of my two cage molecules using berensden
> thermostat to see if there is a difference.
>
> Many Thanks
>
> Gavin
>
>
>

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[gmx-users] pbc atom

[chris . neale]

Gavin, I recall mentioning gen_vel=no with temperature coupling as a  
possible problem a while ago (the problem is that the initial forces  
become initial velocities and then those get scaled up and what you  
have are velocities and not temperatures -- read about the flying ice  
cube problem). Do you have any idea why it would only cause you  
problems at a distance of greater than 2 nm?


Also, Justin seemed to intuit this was a thermostat. I suspect that if  
you switch to the sd integrator things will all be ok. I don't really  
do anything in vacuum so it was harder to pick this up.


If you're tied to your md/NH settings, then you probably need to  
reduce the timestep -- but you will probaby run into problem  
eventually here too so I don't advise it.


Chris.

-- original message --

Dear Chris and Justin

I ran a simulation for two water molecules (100 ns). It only took 5
minutes. Firstly I ran the simulation with ref distance 2.35 nm, genvel
=yes, and gen temp =600 (using Nose Hoover). This produced a histogram
with one main peak. I then took the final configuration from that
simulation and ran the simulation again for the exact same duration and
parameters etc, with the only exception that I set gen_vel = no. The
resulting histogram did indeed have two main peaks. I am now currently
running the simulation of my two cage molecules using berensden
thermostat to see if there is a difference.

Many Thanks

Gavin



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Re: [gmx-users] pbc atom

[Gavin Melaugh]

Dear Chris and Justin

I ran a simulation for two water molecules (100 ns). It only took 5
minutes. Firstly I ran the simulation with ref distance 2.35 nm, genvel
=yes, and gen temp =600 (using Nose Hoover). This produced a histogram
with one main peak. I then took the final configuration from that
simulation and ran the simulation again for the exact same duration and
parameters etc, with the only exception that I set gen_vel = no. The
resulting histogram did indeed have two main peaks. I am now currently
running the simulation of my two cage molecules using berensden
thermostat to see if there is a difference.

Many Thanks

Gavin

chris.ne...@utoronto.ca wrote:
> Dear Gavin:
>
> What happens if you replace your reference group by a single water
> molecule and your pulled group by a single water molecule and run the
> 2.35 nm simulation again. Do you get the same two-peaked histogram?
> What about if you use a system with a single water for the reference
> and your regular pulled group?
>
> You should not need to run 100 ns to get an idea about the shape of
> that histogram so it should be a quick test. This is usually how I
> figure things out -- see how much I can reduce the complexity and
> maintain the problem.
>
> Chris.
>
>
> -- original message --
>
> Hi Chris
>
> I have generated a histogram from the my.data file and i get a histogram
> with the exact same profile as that generated from g_wham. Also on
> comparison of the dx, dy, dz values in the g_dist file with the vaules
> in the pullx.xvg file I notice that the magnitudes of the vectors are
> identical but their signs are opposite. e.g.
> g_dist file
> -2.2756047   -0.03699810.3126130
>
> pullx.xvg file
> 2.2756  0.036998-0.312613
>
> Cheers
>
> Gavin
>
> Please note that there is a significantly more interaction between the
> molecules below 2 nm whereas above they interact very weakly (from
> viewing the trajectories)
>
>
>

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[gmx-users] pbc atom

[chris . neale]

Tsjerk,

Two reasons. First, I simply don't understand awk as well as you do.  
Second, I think that breaking it down into simpler commands linked by  
pipes is better for teaching. If somebody needs help to combine 3 cols  
into a vector distance, then they may copy and paste your solution to  
good effect, but may not learn how to apply that technique to another  
problem as easily as they could when seeing the individual actions  
split by pipes. I could easily be wrong on that, but I'm trying to  
provide an answer to your "why" in case you were asking in earnest.


Aside, thanks again for the awk tips, I appreciate them always and  
they are useful to me.


Chris.


directly. I think you want this (assuming that cols 5,6,7 give you the
dx,dy,dz, which I believe that they do):

cat pullx.xvg | grep -v '[#|@]' | awk '{print $1,sqrt($5*$5+$6*$6+$7*$7)}' >
my.data


Nothing directly harmful of course, but why using three programs for
this? awk will do fine:

awk '/^...@]/{print $1,sqrt($5*$5+$6*$6+$7*$7)}' > my.data

Tsjerk

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Re: [gmx-users] pbc atom

[Tsjerk Wassenaar]

Hey,

> directly. I think you want this (assuming that cols 5,6,7 give you the
> dx,dy,dz, which I believe that they do):
>
> cat pullx.xvg | grep -v '[#|@]' | awk '{print $1,sqrt($5*$5+$6*$6+$7*$7)}' >
> my.data

Nothing directly harmful of course, but why using three programs for
this? awk will do fine:

awk '/^...@]/{print $1,sqrt($5*$5+$6*$6+$7*$7)}' > my.data

Tsjerk

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post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands
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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

There are 168 atom types in my system, 2 molecules comprising of 84
atoms each. The average temperature is 600 K but there are large
fluctuations ca ~100 K, which I assume is expected with such a smal
system. Ill check the energies



I would think it possible, even likely, that the thermostat is driving the 
behavior of your system, since it contains so few atoms.  Do check to see if 
temperature spikes correlate with movement of your pull_group to one side of the 
sampling window.  If it is the problem, try a different thermostat (or at least 
longer tau_t with N-H), and/or a substantially stronger pull_k1 if you're sure 
you need/want N-H as your thermostat.


I certainly agree with Chris' proposed test with two water molecules.  If you 
see the same thing, I'm even more confident that I'm right :)


-Justin


Gavin

Justin A. Lemkul wrote:


Gavin Melaugh wrote:

O.K Thanks

My apologies for not stating earlier that I had the box dimensions set
to zero but I thought that when you set pbc = no and ns_type = simple
that "ignore the box" (from manual) was implemented.


Indeed.

How many atoms are in your system?  How well-conserved is the
temperature?  I imagine that if you only have a few atoms (relative to
a normal condensed-phase system), the species involved would be fairly
strongly impacted by the (potentially) wide oscillations of the
Nose-Hoover thermostat.  Maybe the thermostat is kicking your system
around?  Check the relevant energies and see if they sync up with the
configurations moving back and forth.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Justin

In regard to my query regarding the cut-offs at zero with no pbc. I
assume its is fine to have box dimensions (0 0 0) to comply with the
definition of a vacuum simulation. I am just worried that there may be
some default cut-off that I am not aware of.


You have a box of zero size?  That doesn't make any sense to me, and I
doubt that such a setup plays nice with the MD code.  Frankly, I don't
see how it worked at all.

What if you place your system in a big box, no PBC, cutoffs = 0,
etc? Does that give you a sensible result?


Cheers

P.S I have plotted the pullx.xvg files for the distances between the
COMs of the molecules in the problematic windows. As was the case with
plotting with g_dist there is significant population of the at the
extremities of the window compared to that around the average r0.


Then technically, the average is probably fine, so the pull code is
satisfied. The sampling is clearly messed up for some reason.  Keep
digging :)

-Justin


Justin A. Lemkul wrote:

chris.ne...@utoronto.ca wrote:

I have seen this before, and there are a few possible reasons, but
I'm still waiting to see that histogram with two peaks
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).


It's really hard to help you when we have to guess what the problem
looks like... or perhaps you posted it and I missed it?

The histogram was posted several days ago:

http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html

The attachment link is:

http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin




-Justin


-- original message --

O.K thanks anyway


Justin A. Lemkul
wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html




Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the
pmf I
would get two peaks in the histograms above a distance of 2 nm,
but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.








--


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] pbc atom

[chris . neale]

Dear Gavin:

What happens if you replace your reference group by a single water  
molecule and your pulled group by a single water molecule and run the  
2.35 nm simulation again. Do you get the same two-peaked histogram?  
What about if you use a system with a single water for the reference  
and your regular pulled group?


You should not need to run 100 ns to get an idea about the shape of  
that histogram so it should be a quick test. This is usually how I  
figure things out -- see how much I can reduce the complexity and  
maintain the problem.


Chris.


-- original message --

Hi Chris

I have generated a histogram from the my.data file and i get a histogram
with the exact same profile as that generated from g_wham. Also on
comparison of the dx, dy, dz values in the g_dist file with the vaules
in the pullx.xvg file I notice that the magnitudes of the vectors are
identical but their signs are opposite. e.g.
g_dist file
-2.2756047   -0.03699810.3126130

pullx.xvg file
2.2756  0.036998-0.312613

Cheers

Gavin

Please note that there is a significantly more interaction between the
molecules below 2 nm whereas above they interact very weakly (from
viewing the trajectories)



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Re: [gmx-users] pbc atom

[Gavin Melaugh]

Hi Chris

I have generated a histogram from the my.data file and i get a histogram
with the exact same profile as that generated from g_wham. Also on
comparison of the dx, dy, dz values in the g_dist file with the vaules
in the pullx.xvg file I notice that the magnitudes of the vectors are
identical but their signs are opposite. e.g.
g_dist file
-2.2756047   -0.03699810.3126130

pullx.xvg file
2.2756  0.036998-0.312613

Cheers

Gavin

Please note that there is a significantly more interaction between the
molecules below 2 nm whereas above they interact very weakly (from
viewing the trajectories)


chris.ne...@utoronto.ca wrote:
> Yup, just got the link. Thank you for posting, and sorry that I missed
> it. It seems possible that Justin is correct and you'll get good data
> if you take it out of the pullx.xvg file (perhaps the g_dist tool is
> wrapping pbc for you).
>
> 1. How big is your box definition in your .gro file?
>
> You are right that you need the actual distance, which is not provided
> directly. I think you want this (assuming that cols 5,6,7 give you the
> dx,dy,dz, which I believe that they do):
>
> cat pullx.xvg | grep -v '[#|@]' | awk '{print
> $1,sqrt($5*$5+$6*$6+$7*$7)}' > my.data
>
> 2. If you do this to a window > 2.0 nm and generate a histogram, do
> you still get two peaks?
>
> A quick look at the src/tools/gmx_dist.c file indicates that it should
> only apply periodicity if you give it a .tpr where PBC was applied --
> you can check this by comparing the dx, dy, dz out of g_dist with the
> values in pullx.xvg
>
> If the problem is not solved here, then you can send me off-list all
> the files needed to run a window around 2.5 nm plus all the output
> that you have obtained from a single run and I'll take a look if you
> wish. If you'd rather not do that and there are still problems, then
> perhaps you can post a step by step from the beginning where you copy
> and paste absolutely all of your commands (e.g. paste the *exact*
> grompp, mdrun, g_dist, etc. commands) and the complete .mdp file and
> the last line in your starting .gro file.
>
> Chris.
>
> -- original message --
>
> [gmx-users] pbc atom
> Gavin Melaugh gmelaugh01 at qub.ac.uk
> Tue Aug 24 17:19:45 CEST 2010
>
> * Previous message: [gmx-users] pbc atom
> * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>
> Hi Chris
>
> Yeah I posted the histograms a few days ago as Justin said. Did you get
> the link?
>
> Gavin
> chris.neale at utoronto.ca wrote:
>> I have seen this before, and there are a few possible reasons, but I'm
>> still waiting to see that histogram with two peaks
>> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
>> It's really hard to help you when we have to guess what the problem
>> looks like... or perhaps you posted it and I missed it?
>>
>> -- original message --
>>
>> O.K thanks anyway
>>
>>
>> Justin A. Lemkul
>> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html
>>
>>
>>>
>>>
>>> Gavin Melaugh wrote:
>>>> Thanks Justin
>>>>
>>>> Have you any idea why when generating umbrella histograms for the
>>>> pmf I
>>>> would get two peaks in the histograms above a distance of 2 nm, but
>>>> below 2 nm I get well behaved histograms that lead to a very
>>>> good profile in the pmf. To the best of my knowledge the
>>>> configurations
>>>> are all very well equilibrated at their respective COM distances.
>>>> Umbrella sampling is performed on all windows using a force
>>>> constant of
>>>> 1000 kj/mol at 600 K.
>>>>
>
>

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Re: [gmx-users] pbc atom

[Gavin Melaugh]

Chris

The box dimensions that I type at the bottom of the .gro file are
0.0 0.0 0.0

In regards to the other points you made I'll get back to you as soon as
I can

Many Thanks

Gavin
chris.ne...@utoronto.ca wrote:
> Yup, just got the link. Thank you for posting, and sorry that I missed
> it. It seems possible that Justin is correct and you'll get good data
> if you take it out of the pullx.xvg file (perhaps the g_dist tool is
> wrapping pbc for you).
>
> 1. How big is your box definition in your .gro file?
>
> You are right that you need the actual distance, which is not provided
> directly. I think you want this (assuming that cols 5,6,7 give you the
> dx,dy,dz, which I believe that they do):
>
> cat pullx.xvg | grep -v '[#|@]' | awk '{print
> $1,sqrt($5*$5+$6*$6+$7*$7)}' > my.data
>
> 2. If you do this to a window > 2.0 nm and generate a histogram, do
> you still get two peaks?
>
> A quick look at the src/tools/gmx_dist.c file indicates that it should
> only apply periodicity if you give it a .tpr where PBC was applied --
> you can check this by comparing the dx, dy, dz out of g_dist with the
> values in pullx.xvg
>
> If the problem is not solved here, then you can send me off-list all
> the files needed to run a window around 2.5 nm plus all the output
> that you have obtained from a single run and I'll take a look if you
> wish. If you'd rather not do that and there are still problems, then
> perhaps you can post a step by step from the beginning where you copy
> and paste absolutely all of your commands (e.g. paste the *exact*
> grompp, mdrun, g_dist, etc. commands) and the complete .mdp file and
> the last line in your starting .gro file.
>
> Chris.
>
> -- original message --
>
> [gmx-users] pbc atom
> Gavin Melaugh gmelaugh01 at qub.ac.uk
> Tue Aug 24 17:19:45 CEST 2010
>
> * Previous message: [gmx-users] pbc atom
> * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>
> Hi Chris
>
> Yeah I posted the histograms a few days ago as Justin said. Did you get
> the link?
>
> Gavin
> chris.neale at utoronto.ca wrote:
>> I have seen this before, and there are a few possible reasons, but I'm
>> still waiting to see that histogram with two peaks
>> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
>> It's really hard to help you when we have to guess what the problem
>> looks like... or perhaps you posted it and I missed it?
>>
>> -- original message --
>>
>> O.K thanks anyway
>>
>>
>> Justin A. Lemkul
>> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html
>>
>>
>>>
>>>
>>> Gavin Melaugh wrote:
>>>> Thanks Justin
>>>>
>>>> Have you any idea why when generating umbrella histograms for the
>>>> pmf I
>>>> would get two peaks in the histograms above a distance of 2 nm, but
>>>> below 2 nm I get well behaved histograms that lead to a very
>>>> good profile in the pmf. To the best of my knowledge the
>>>> configurations
>>>> are all very well equilibrated at their respective COM distances.
>>>> Umbrella sampling is performed on all windows using a force
>>>> constant of
>>>> 1000 kj/mol at 600 K.
>>>>
>
>

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Re: [gmx-users] pbc atom

[Gavin Melaugh]

There are 168 atom types in my system, 2 molecules comprising of 84
atoms each. The average temperature is 600 K but there are large
fluctuations ca ~100 K, which I assume is expected with such a smal
system. Ill check the energies

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> O.K Thanks
>>
>> My apologies for not stating earlier that I had the box dimensions set
>> to zero but I thought that when you set pbc = no and ns_type = simple
>> that "ignore the box" (from manual) was implemented.
>>
>
> Indeed.
>
> How many atoms are in your system?  How well-conserved is the
> temperature?  I imagine that if you only have a few atoms (relative to
> a normal condensed-phase system), the species involved would be fairly
> strongly impacted by the (potentially) wide oscillations of the
> Nose-Hoover thermostat.  Maybe the thermostat is kicking your system
> around?  Check the relevant energies and see if they sync up with the
> configurations moving back and forth.
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 Justin

 In regard to my query regarding the cut-offs at zero with no pbc. I
 assume its is fine to have box dimensions (0 0 0) to comply with the
 definition of a vacuum simulation. I am just worried that there may be
 some default cut-off that I am not aware of.

>>> You have a box of zero size?  That doesn't make any sense to me, and I
>>> doubt that such a setup plays nice with the MD code.  Frankly, I don't
>>> see how it worked at all.
>>>
>>> What if you place your system in a big box, no PBC, cutoffs = 0,
>>> etc? Does that give you a sensible result?
>>>
 Cheers

 P.S I have plotted the pullx.xvg files for the distances between the
 COMs of the molecules in the problematic windows. As was the case with
 plotting with g_dist there is significant population of the at the
 extremities of the window compared to that around the average r0.

>>> Then technically, the average is probably fine, so the pull code is
>>> satisfied. The sampling is clearly messed up for some reason.  Keep
>>> digging :)
>>>
>>> -Justin
>>>
 Justin A. Lemkul wrote:
> chris.ne...@utoronto.ca wrote:
>> I have seen this before, and there are a few possible reasons, but
>> I'm still waiting to see that histogram with two peaks
>> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
>>
>>
>> It's really hard to help you when we have to guess what the problem
>> looks like... or perhaps you posted it and I missed it?
> The histogram was posted several days ago:
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html
>
> The attachment link is:
>
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin
>
>
>
>
> -Justin
>
>> -- original message --
>>
>> O.K thanks anyway
>>
>>
>> Justin A. Lemkul
>> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html
>>
>>
>>
>>> Gavin Melaugh wrote:
 Thanks Justin

 Have you any idea why when generating umbrella histograms for the
 pmf I
 would get two peaks in the histograms above a distance of 2 nm,
 but
 below 2 nm I get well behaved histograms that lead to a very
 good profile in the pmf. To the best of my knowledge the
 configurations
 are all very well equilibrated at their respective COM distances.
 Umbrella sampling is performed on all windows using a force
 constant of
 1000 kj/mol at 600 K.

>>> Sorry, no clue.
>>>

>>
>>
>

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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

O.K Thanks

My apologies for not stating earlier that I had the box dimensions set
to zero but I thought that when you set pbc = no and ns_type = simple
that "ignore the box" (from manual) was implemented.



Indeed.

How many atoms are in your system?  How well-conserved is the temperature?  I 
imagine that if you only have a few atoms (relative to a normal condensed-phase 
system), the species involved would be fairly strongly impacted by the 
(potentially) wide oscillations of the Nose-Hoover thermostat.  Maybe the 
thermostat is kicking your system around?  Check the relevant energies and see 
if they sync up with the configurations moving back and forth.


-Justin


Gavin

Justin A. Lemkul wrote:


Gavin Melaugh wrote:

Justin

In regard to my query regarding the cut-offs at zero with no pbc. I
assume its is fine to have box dimensions (0 0 0) to comply with the
definition of a vacuum simulation. I am just worried that there may be
some default cut-off that I am not aware of.


You have a box of zero size?  That doesn't make any sense to me, and I
doubt that such a setup plays nice with the MD code.  Frankly, I don't
see how it worked at all.

What if you place your system in a big box, no PBC, cutoffs = 0, etc? 
Does that give you a sensible result?



Cheers

P.S I have plotted the pullx.xvg files for the distances between the
COMs of the molecules in the problematic windows. As was the case with
plotting with g_dist there is significant population of the at the
extremities of the window compared to that around the average r0.


Then technically, the average is probably fine, so the pull code is
satisfied. The sampling is clearly messed up for some reason.  Keep
digging :)

-Justin


Justin A. Lemkul wrote:

chris.ne...@utoronto.ca wrote:

I have seen this before, and there are a few possible reasons, but
I'm still waiting to see that histogram with two peaks
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).

It's really hard to help you when we have to guess what the problem
looks like... or perhaps you posted it and I missed it?

The histogram was posted several days ago:

http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html

The attachment link is:

http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin



-Justin


-- original message --

O.K thanks anyway


Justin A. Lemkul
wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html



Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the
pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.








--


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] pbc atom

[chris . neale]

Yup, just got the link. Thank you for posting, and sorry that I missed  
it. It seems possible that Justin is correct and you'll get good data  
if you take it out of the pullx.xvg file (perhaps the g_dist tool is  
wrapping pbc for you).


1. How big is your box definition in your .gro file?

You are right that you need the actual distance, which is not provided  
directly. I think you want this (assuming that cols 5,6,7 give you the  
dx,dy,dz, which I believe that they do):


cat pullx.xvg | grep -v '[#|@]' | awk '{print  
$1,sqrt($5*$5+$6*$6+$7*$7)}' > my.data


2. If you do this to a window > 2.0 nm and generate a histogram, do  
you still get two peaks?


A quick look at the src/tools/gmx_dist.c file indicates that it should  
only apply periodicity if you give it a .tpr where PBC was applied --  
you can check this by comparing the dx, dy, dz out of g_dist with the  
values in pullx.xvg


If the problem is not solved here, then you can send me off-list all  
the files needed to run a window around 2.5 nm plus all the output  
that you have obtained from a single run and I'll take a look if you  
wish. If you'd rather not do that and there are still problems, then  
perhaps you can post a step by step from the beginning where you copy  
and paste absolutely all of your commands (e.g. paste the *exact*  
grompp, mdrun, g_dist, etc. commands) and the complete .mdp file and  
the last line in your starting .gro file.


Chris.

-- original message --

[gmx-users] pbc atom
Gavin Melaugh gmelaugh01 at qub.ac.uk
Tue Aug 24 17:19:45 CEST 2010

* Previous message: [gmx-users] pbc atom
* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

Hi Chris

Yeah I posted the histograms a few days ago as Justin said. Did you get
the link?

Gavin
chris.neale at utoronto.ca wrote:

I have seen this before, and there are a few possible reasons, but I'm
still waiting to see that histogram with two peaks
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
It's really hard to help you when we have to guess what the problem
looks like... or perhaps you posted it and I missed it?

-- original message --

O.K thanks anyway


Justin A. Lemkul
wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html




Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force constant of
1000 kj/mol at 600 K.




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Re: [gmx-users] pbc atom

[Gavin Melaugh]

O.K Thanks

My apologies for not stating earlier that I had the box dimensions set
to zero but I thought that when you set pbc = no and ns_type = simple
that "ignore the box" (from manual) was implemented.

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Justin
>>
>> In regard to my query regarding the cut-offs at zero with no pbc. I
>> assume its is fine to have box dimensions (0 0 0) to comply with the
>> definition of a vacuum simulation. I am just worried that there may be
>> some default cut-off that I am not aware of.
>>
>
> You have a box of zero size?  That doesn't make any sense to me, and I
> doubt that such a setup plays nice with the MD code.  Frankly, I don't
> see how it worked at all.
>
> What if you place your system in a big box, no PBC, cutoffs = 0, etc? 
> Does that give you a sensible result?
>
>> Cheers
>>
>> P.S I have plotted the pullx.xvg files for the distances between the
>> COMs of the molecules in the problematic windows. As was the case with
>> plotting with g_dist there is significant population of the at the
>> extremities of the window compared to that around the average r0.
>>
>
> Then technically, the average is probably fine, so the pull code is
> satisfied. The sampling is clearly messed up for some reason.  Keep
> digging :)
>
> -Justin
>
>> Justin A. Lemkul wrote:
>>>
>>> chris.ne...@utoronto.ca wrote:
 I have seen this before, and there are a few possible reasons, but
 I'm still waiting to see that histogram with two peaks
 (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).

 It's really hard to help you when we have to guess what the problem
 looks like... or perhaps you posted it and I missed it?
>>> The histogram was posted several days ago:
>>>
>>> http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html
>>>
>>> The attachment link is:
>>>
>>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin
>>>
>>>
>>>
>>> -Justin
>>>
 -- original message --

 O.K thanks anyway


 Justin A. Lemkul
 wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html


>
> Gavin Melaugh wrote:
>> Thanks Justin
>>
>> Have you any idea why when generating umbrella histograms for the
>> pmf I
>> would get two peaks in the histograms above a distance of 2 nm, but
>> below 2 nm I get well behaved histograms that lead to a very
>> good profile in the pmf. To the best of my knowledge the
>> configurations
>> are all very well equilibrated at their respective COM distances.
>> Umbrella sampling is performed on all windows using a force
>> constant of
>> 1000 kj/mol at 600 K.
>>
> Sorry, no clue.
>

>>
>>
>

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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

Justin

In regard to my query regarding the cut-offs at zero with no pbc. I
assume its is fine to have box dimensions (0 0 0) to comply with the
definition of a vacuum simulation. I am just worried that there may be
some default cut-off that I am not aware of.



You have a box of zero size?  That doesn't make any sense to me, and I doubt 
that such a setup plays nice with the MD code.  Frankly, I don't see how it 
worked at all.


What if you place your system in a big box, no PBC, cutoffs = 0, etc?  Does that 
give you a sensible result?



Cheers

P.S I have plotted the pullx.xvg files for the distances between the
COMs of the molecules in the problematic windows. As was the case with
plotting with g_dist there is significant population of the at the
extremities of the window compared to that around the average r0.



Then technically, the average is probably fine, so the pull code is satisfied. 
The sampling is clearly messed up for some reason.  Keep digging :)


-Justin


Justin A. Lemkul wrote:


chris.ne...@utoronto.ca wrote:

I have seen this before, and there are a few possible reasons, but
I'm still waiting to see that histogram with two peaks
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
It's really hard to help you when we have to guess what the problem
looks like... or perhaps you posted it and I missed it?

The histogram was posted several days ago:

http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html

The attachment link is:

http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin


-Justin


-- original message --

O.K thanks anyway


Justin A. Lemkul
wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html



Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the
pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.








--


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


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Re: [gmx-users] pbc atom

[Gavin Melaugh]

Justin

In regard to my query regarding the cut-offs at zero with no pbc. I
assume its is fine to have box dimensions (0 0 0) to comply with the
definition of a vacuum simulation. I am just worried that there may be
some default cut-off that I am not aware of.

Cheers

P.S I have plotted the pullx.xvg files for the distances between the
COMs of the molecules in the problematic windows. As was the case with
plotting with g_dist there is significant population of the at the
extremities of the window compared to that around the average r0.

Justin A. Lemkul wrote:
>
>
> chris.ne...@utoronto.ca wrote:
>> I have seen this before, and there are a few possible reasons, but
>> I'm still waiting to see that histogram with two peaks
>> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
>> It's really hard to help you when we have to guess what the problem
>> looks like... or perhaps you posted it and I missed it?
>
> The histogram was posted several days ago:
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html
>
> The attachment link is:
>
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin
>
>
> -Justin
>
>>
>> -- original message --
>>
>> O.K thanks anyway
>>
>>
>> Justin A. Lemkul
>> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html
>>
>>>
>>>
>>> Gavin Melaugh wrote:
 Thanks Justin

 Have you any idea why when generating umbrella histograms for the
 pmf I
 would get two peaks in the histograms above a distance of 2 nm, but
 below 2 nm I get well behaved histograms that lead to a very
 good profile in the pmf. To the best of my knowledge the
 configurations
 are all very well equilibrated at their respective COM distances.
 Umbrella sampling is performed on all windows using a force
 constant of
 1000 kj/mol at 600 K.

>>>
>>> Sorry, no clue.
>>>
>>
>>
>

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Re: [gmx-users] pbc atom

[Gavin Melaugh]

Hi Chris

Yeah I posted the histograms a few days ago as Justin said. Did you get
the link?

Gavin
chris.ne...@utoronto.ca wrote:
> I have seen this before, and there are a few possible reasons, but I'm
> still waiting to see that histogram with two peaks
> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
> It's really hard to help you when we have to guess what the problem
> looks like... or perhaps you posted it and I missed it?
>
> -- original message --
>
> O.K thanks anyway
>
>
> Justin A. Lemkul
> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html
>
>>
>>
>> Gavin Melaugh wrote:
>>> Thanks Justin
>>>
>>> Have you any idea why when generating umbrella histograms for the pmf I
>>> would get two peaks in the histograms above a distance of 2 nm, but
>>> below 2 nm I get well behaved histograms that lead to a very
>>> good profile in the pmf. To the best of my knowledge the configurations
>>> are all very well equilibrated at their respective COM distances.
>>> Umbrella sampling is performed on all windows using a force constant of
>>> 1000 kj/mol at 600 K.
>>>
>>
>> Sorry, no clue.
>>
>
>

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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

chris.ne...@utoronto.ca wrote:
I have seen this before, and there are a few possible reasons, but I'm 
still waiting to see that histogram with two peaks 
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html). 
It's really hard to help you when we have to guess what the problem 
looks like... or perhaps you posted it and I missed it?


The histogram was posted several days ago:

http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html

The attachment link is:

http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin

-Justin



-- original message --

O.K thanks anyway


Justin A. Lemkul 
wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html



Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force constant of
1000 kj/mol at 600 K.



Sorry, no clue.






--


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] pbc atom

[chris . neale]

I have seen this before, and there are a few possible reasons, but I'm  
still waiting to see that histogram with two peaks  
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html). It's  
really hard to help you when we have to guess what the problem looks  
like... or perhaps you posted it and I missed it?


-- original message --

O.K thanks anyway


Justin A. Lemkul  
wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html



Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force constant of
1000 kj/mol at 600 K.



Sorry, no clue.




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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

O.K thanks Justine I'll look at these files and see if there is any
weirdness.
Just to make sure that there are no cut-off artefacts. If I  set the
cut-offs to zero as in the following mdp file; that does mean that I am
considering all electrostatic and LJ interactions between the molecules?
and not including them at all. I assume the former given that there are
both electrostatic and LJ energy values in the log and energy files.



Correct.

-Justin


Gavin

title   = Pull test
cpp =
include =
define  =
integrator  = md
nsteps  = 5000
dt  = 0.002
nstxout = 25
nstvout = 25
nstlog  = 25
nstenergy   = 5000
nstfout = 25
pbc = no
nstlist = 10
ns_type = simple
vdwtype = cut-off
rlist   = 0
rvdw_switch = 0
rvdw= 0
coulombtype = cut-off
rcoulomb= 0
tcoupl  = nose-hoover
tc_grps = system
tau_t   = 0.1
ref_t   = 600
gen_vel = no
gen_temp=
constraints = none
comm_mode   = angular
pull= umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = no
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_init1 = 2.59
pull_rate1 = 0.0
pull_k1 = 1000
pull_nstxout = 1000
pull_nstfout = 1000


Justin A. Lemkul wrote:


Gavin Melaugh wrote:

For the umbrella sampling I am not pulling in any direction I am just
applying the umbrella potential so that two molecules can sample space
about a give value of r0 (COM distance). Maybe I am confused but should
I not plot the absolute value of the displacement (modulus) as supposed
to the displacement along a given vector component?


For diagnosing weird behavior, I would always start with the primary
data, not any post-processed interpretation of it.  Use the pullx.xvg
file.  Any weird changes in sign or sudden changes in magnitude would
indicate problems.  If you start manipulating the data, you may be
hiding the real reason for the problem.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

I always used g_dist to plot the COM distances because the pullx.xvg
files doesn't give this value directly. Can you access the COM
distance
from the pullx.xvg file


That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference
group, then displacement (dX,dY,dZ) of the pull group relative to the
reference.  Not all terms may be present, depending on the axis along
which you're pulling, i.e. if you only pull along Z, there will be two
terms in pullx.xvg - Z and dZ.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Justin

I have looked at the movies but it's very hard to tell what's
going on
as I save teh trajectories every 25 steps for every 5000
step
simulation (100 ns). Ill look at them  again in more detail and post
back.


Plotting the pullx.xvg file(s) may be useful, too, to indicate where
any weird jumps or sudden changes in position might occur.  Mapping
that information back onto the trajectory could help focus your
attention.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

O.K thanks anyway


I saw the plots you posted during a conversation with Chris, but
I'll
ask the obvious anyway: have you watched the trajectories for
any of
the problematic windows?  It didn't seem like you had two
metastable
states, but maybe having a look at the movie would shed some
light on
what's going on.  I know that's the first thing I'd do.

-Justin


Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for
the
pmf I
would get two peaks in the histograms above a distance of 2 nm,
but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM
distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.

-Justin


Cheers

Gavin

Justin A. Lemkul wrote:

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull
code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the
output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start   
reference at

t=0
   07236
   172   360   4.290 4.290

why is this so?


grompp always assigns the numerical middle atom of a group as
the
PBC 

...unless over-ridden by providing a different value for
pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin







--


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

=

Re: [gmx-users] pbc atom

[Gavin Melaugh]

O.K thanks Justine I'll look at these files and see if there is any
weirdness.
Just to make sure that there are no cut-off artefacts. If I  set the
cut-offs to zero as in the following mdp file; that does mean that I am
considering all electrostatic and LJ interactions between the molecules?
and not including them at all. I assume the former given that there are
both electrostatic and LJ energy values in the log and energy files.

Gavin

title   = Pull test
cpp =
include =
define  =
integrator  = md
nsteps  = 5000
dt  = 0.002
nstxout = 25
nstvout = 25
nstlog  = 25
nstenergy   = 5000
nstfout = 25
pbc = no
nstlist = 10
ns_type = simple
vdwtype = cut-off
rlist   = 0
rvdw_switch = 0
rvdw= 0
coulombtype = cut-off
rcoulomb= 0
tcoupl  = nose-hoover
tc_grps = system
tau_t   = 0.1
ref_t   = 600
gen_vel = no
gen_temp=
constraints = none
comm_mode   = angular
pull= umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = no
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_init1 = 2.59
pull_rate1 = 0.0
pull_k1 = 1000
pull_nstxout = 1000
pull_nstfout = 1000


Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> For the umbrella sampling I am not pulling in any direction I am just
>> applying the umbrella potential so that two molecules can sample space
>> about a give value of r0 (COM distance). Maybe I am confused but should
>> I not plot the absolute value of the displacement (modulus) as supposed
>> to the displacement along a given vector component?
>>
>
> For diagnosing weird behavior, I would always start with the primary
> data, not any post-processed interpretation of it.  Use the pullx.xvg
> file.  Any weird changes in sign or sudden changes in magnitude would
> indicate problems.  If you start manipulating the data, you may be
> hiding the real reason for the problem.
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 I always used g_dist to plot the COM distances because the pullx.xvg
 files doesn't give this value directly. Can you access the COM
 distance
 from the pullx.xvg file

>>> That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference
>>> group, then displacement (dX,dY,dZ) of the pull group relative to the
>>> reference.  Not all terms may be present, depending on the axis along
>>> which you're pulling, i.e. if you only pull along Z, there will be two
>>> terms in pullx.xvg - Z and dZ.
>>>
>>> -Justin
>>>
 Gavin

 Justin A. Lemkul wrote:
> Gavin Melaugh wrote:
>> Justin
>>
>> I have looked at the movies but it's very hard to tell what's
>> going on
>> as I save teh trajectories every 25 steps for every 5000
>> step
>> simulation (100 ns). Ill look at them  again in more detail and post
>> back.
>>
> Plotting the pullx.xvg file(s) may be useful, too, to indicate where
> any weird jumps or sudden changes in position might occur.  Mapping
> that information back onto the trajectory could help focus your
> attention.
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>> Gavin Melaugh wrote:
 O.K thanks anyway

>>> I saw the plots you posted during a conversation with Chris, but
>>> I'll
>>> ask the obvious anyway: have you watched the trajectories for
>>> any of
>>> the problematic windows?  It didn't seem like you had two
>>> metastable
>>> states, but maybe having a look at the movie would shed some
>>> light on
>>> what's going on.  I know that's the first thing I'd do.
>>>
>>> -Justin
>>>
 Justin A. Lemkul wrote:
> Gavin Melaugh wrote:
>> Thanks Justin
>>
>> Have you any idea why when generating umbrella histograms for
>> the
>> pmf I
>> would get two peaks in the histograms above a distance of 2 nm,
>> but
>> below 2 nm I get well behaved histograms that lead to a very
>> good profile in the pmf. To the best of my knowledge the
>> configurations
>> are all very well equilibrated at their respective COM
>> distances.
>> Umbrella sampling is performed on all windows using a force
>> constant of
>> 1000 kj/mol at 600 K.
>>
> Sorry, no clue.
>
> -Justin
>
>> Cheers
>>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>> Justin A. Lemkul wrote:
 Gavin Melaugh wrote:
> Hi all
>
> I am generating a series of configurations using the pull
> code to
> calculate the pmf. I am using no pbc i.e. pbc =no, howver the
> output
> from grommp gives me info on pbc atom.
>
> Pull group  natoms  pbc atom  

Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

For the umbrella sampling I am not pulling in any direction I am just
applying the umbrella potential so that two molecules can sample space
about a give value of r0 (COM distance). Maybe I am confused but should
I not plot the absolute value of the displacement (modulus) as supposed
to the displacement along a given vector component?



For diagnosing weird behavior, I would always start with the primary data, not 
any post-processed interpretation of it.  Use the pullx.xvg file.  Any weird 
changes in sign or sudden changes in magnitude would indicate problems.  If you 
start manipulating the data, you may be hiding the real reason for the problem.


-Justin


Gavin

Justin A. Lemkul wrote:


Gavin Melaugh wrote:

I always used g_dist to plot the COM distances because the pullx.xvg
files doesn't give this value directly. Can you access the COM distance
from the pullx.xvg file


That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference
group, then displacement (dX,dY,dZ) of the pull group relative to the
reference.  Not all terms may be present, depending on the axis along
which you're pulling, i.e. if you only pull along Z, there will be two
terms in pullx.xvg - Z and dZ.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Justin

I have looked at the movies but it's very hard to tell what's going on
as I save teh trajectories every 25 steps for every 5000 step
simulation (100 ns). Ill look at them  again in more detail and post
back.


Plotting the pullx.xvg file(s) may be useful, too, to indicate where
any weird jumps or sudden changes in position might occur.  Mapping
that information back onto the trajectory could help focus your
attention.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

O.K thanks anyway


I saw the plots you posted during a conversation with Chris, but I'll
ask the obvious anyway: have you watched the trajectories for any of
the problematic windows?  It didn't seem like you had two metastable
states, but maybe having a look at the movie would shed some light on
what's going on.  I know that's the first thing I'd do.

-Justin


Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the
pmf I
would get two peaks in the histograms above a distance of 2 nm,
but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.

-Justin


Cheers

Gavin

Justin A. Lemkul wrote:

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull
code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the
output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start
reference at

t=0
   07236
   172   360   4.290 4.290

why is this so?


grompp always assigns the numerical middle atom of a group as
the
PBC 

...unless over-ridden by providing a different value for
pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin







--


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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Please search the archive at http://www.gromacs.org/search before posting!
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www interface or send it to gmx-users-requ...@gromacs.org.

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Re: [gmx-users] pbc atom

[Gavin Melaugh]

For the umbrella sampling I am not pulling in any direction I am just
applying the umbrella potential so that two molecules can sample space
about a give value of r0 (COM distance). Maybe I am confused but should
I not plot the absolute value of the displacement (modulus) as supposed
to the displacement along a given vector component?

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> I always used g_dist to plot the COM distances because the pullx.xvg
>> files doesn't give this value directly. Can you access the COM distance
>> from the pullx.xvg file
>>
>
> That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference
> group, then displacement (dX,dY,dZ) of the pull group relative to the
> reference.  Not all terms may be present, depending on the axis along
> which you're pulling, i.e. if you only pull along Z, there will be two
> terms in pullx.xvg - Z and dZ.
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 Justin

 I have looked at the movies but it's very hard to tell what's going on
 as I save teh trajectories every 25 steps for every 5000 step
 simulation (100 ns). Ill look at them  again in more detail and post
 back.

>>> Plotting the pullx.xvg file(s) may be useful, too, to indicate where
>>> any weird jumps or sudden changes in position might occur.  Mapping
>>> that information back onto the trajectory could help focus your
>>> attention.
>>>
>>> -Justin
>>>
 Gavin

 Justin A. Lemkul wrote:
> Gavin Melaugh wrote:
>> O.K thanks anyway
>>
> I saw the plots you posted during a conversation with Chris, but I'll
> ask the obvious anyway: have you watched the trajectories for any of
> the problematic windows?  It didn't seem like you had two metastable
> states, but maybe having a look at the movie would shed some light on
> what's going on.  I know that's the first thing I'd do.
>
> -Justin
>
>> Justin A. Lemkul wrote:
>>> Gavin Melaugh wrote:
 Thanks Justin

 Have you any idea why when generating umbrella histograms for the
 pmf I
 would get two peaks in the histograms above a distance of 2 nm,
 but
 below 2 nm I get well behaved histograms that lead to a very
 good profile in the pmf. To the best of my knowledge the
 configurations
 are all very well equilibrated at their respective COM distances.
 Umbrella sampling is performed on all windows using a force
 constant of
 1000 kj/mol at 600 K.

>>> Sorry, no clue.
>>>
>>> -Justin
>>>
 Cheers

 Gavin

 Justin A. Lemkul wrote:
> Justin A. Lemkul wrote:
>> Gavin Melaugh wrote:
>>> Hi all
>>>
>>> I am generating a series of configurations using the pull
>>> code to
>>> calculate the pmf. I am using no pbc i.e. pbc =no, howver the
>>> output
>>> from grommp gives me info on pbc atom.
>>>
>>> Pull group  natoms  pbc atom  distance at start
>>> reference at
>>> t=0
>>>07236
>>>172   360   4.290 4.290
>>>
>>> why is this so?
>>>
>> grompp always assigns the numerical middle atom of a group as
>> the
>> PBC 
> ...unless over-ridden by providing a different value for
> pbc_pullatom1.
>
> -Justin
>
>> reference point.  In the case of pbc=no, it shouldn't matter.
>>
>> http://manual.gromacs.org/current/online/mdp_opt.html#pull
>>
>> -Justin
>>
>>> Cheers
>>>
>>> Gavin

>>
>>
>

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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

I always used g_dist to plot the COM distances because the pullx.xvg
files doesn't give this value directly. Can you access the COM distance
from the pullx.xvg file



That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference group, then 
displacement (dX,dY,dZ) of the pull group relative to the reference.  Not all 
terms may be present, depending on the axis along which you're pulling, i.e. if 
you only pull along Z, there will be two terms in pullx.xvg - Z and dZ.


-Justin


Gavin

Justin A. Lemkul wrote:


Gavin Melaugh wrote:

Justin

I have looked at the movies but it's very hard to tell what's going on
as I save teh trajectories every 25 steps for every 5000 step
simulation (100 ns). Ill look at them  again in more detail and post
back.


Plotting the pullx.xvg file(s) may be useful, too, to indicate where
any weird jumps or sudden changes in position might occur.  Mapping
that information back onto the trajectory could help focus your
attention.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

O.K thanks anyway


I saw the plots you posted during a conversation with Chris, but I'll
ask the obvious anyway: have you watched the trajectories for any of
the problematic windows?  It didn't seem like you had two metastable
states, but maybe having a look at the movie would shed some light on
what's going on.  I know that's the first thing I'd do.

-Justin


Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the
pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.

-Justin


Cheers

Gavin

Justin A. Lemkul wrote:

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the
output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at
t=0
   07236
   172   360   4.290 4.290

why is this so?


grompp always assigns the numerical middle atom of a group as the
PBC 

...unless over-ridden by providing a different value for
pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin







--


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


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Re: [gmx-users] pbc atom

[Gavin Melaugh]

I always used g_dist to plot the COM distances because the pullx.xvg
files doesn't give this value directly. Can you access the COM distance
from the pullx.xvg file

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Justin
>>
>> I have looked at the movies but it's very hard to tell what's going on
>> as I save teh trajectories every 25 steps for every 5000 step
>> simulation (100 ns). Ill look at them  again in more detail and post
>> back.
>>
>
> Plotting the pullx.xvg file(s) may be useful, too, to indicate where
> any weird jumps or sudden changes in position might occur.  Mapping
> that information back onto the trajectory could help focus your
> attention.
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 O.K thanks anyway

>>> I saw the plots you posted during a conversation with Chris, but I'll
>>> ask the obvious anyway: have you watched the trajectories for any of
>>> the problematic windows?  It didn't seem like you had two metastable
>>> states, but maybe having a look at the movie would shed some light on
>>> what's going on.  I know that's the first thing I'd do.
>>>
>>> -Justin
>>>
 Justin A. Lemkul wrote:
> Gavin Melaugh wrote:
>> Thanks Justin
>>
>> Have you any idea why when generating umbrella histograms for the
>> pmf I
>> would get two peaks in the histograms above a distance of 2 nm, but
>> below 2 nm I get well behaved histograms that lead to a very
>> good profile in the pmf. To the best of my knowledge the
>> configurations
>> are all very well equilibrated at their respective COM distances.
>> Umbrella sampling is performed on all windows using a force
>> constant of
>> 1000 kj/mol at 600 K.
>>
> Sorry, no clue.
>
> -Justin
>
>> Cheers
>>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>> Justin A. Lemkul wrote:
 Gavin Melaugh wrote:
> Hi all
>
> I am generating a series of configurations using the pull code to
> calculate the pmf. I am using no pbc i.e. pbc =no, howver the
> output
> from grommp gives me info on pbc atom.
>
> Pull group  natoms  pbc atom  distance at start reference at
> t=0
>07236
>172   360   4.290 4.290
>
> why is this so?
>
 grompp always assigns the numerical middle atom of a group as the
 PBC 
>>> ...unless over-ridden by providing a different value for
>>> pbc_pullatom1.
>>>
>>> -Justin
>>>
 reference point.  In the case of pbc=no, it shouldn't matter.

 http://manual.gromacs.org/current/online/mdp_opt.html#pull

 -Justin

> Cheers
>
> Gavin

>>
>>
>

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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

Justin

I have looked at the movies but it's very hard to tell what's going on
as I save teh trajectories every 25 steps for every 5000 step
simulation (100 ns). Ill look at them  again in more detail and post back.



Plotting the pullx.xvg file(s) may be useful, too, to indicate where any weird 
jumps or sudden changes in position might occur.  Mapping that information back 
onto the trajectory could help focus your attention.


-Justin


Gavin

Justin A. Lemkul wrote:


Gavin Melaugh wrote:

O.K thanks anyway


I saw the plots you posted during a conversation with Chris, but I'll
ask the obvious anyway: have you watched the trajectories for any of
the problematic windows?  It didn't seem like you had two metastable
states, but maybe having a look at the movie would shed some light on
what's going on.  I know that's the first thing I'd do.

-Justin


Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the
pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.

-Justin


Cheers

Gavin

Justin A. Lemkul wrote:

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the
output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at
t=0
   07236
   172   360   4.290 4.290

why is this so?


grompp always assigns the numerical middle atom of a group as the
PBC 

...unless over-ridden by providing a different value for
pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin







--


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


--
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Re: [gmx-users] pbc atom

[Gavin Melaugh]

Justin

I have looked at the movies but it's very hard to tell what's going on
as I save teh trajectories every 25 steps for every 5000 step
simulation (100 ns). Ill look at them  again in more detail and post back.

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> O.K thanks anyway
>>
>
> I saw the plots you posted during a conversation with Chris, but I'll
> ask the obvious anyway: have you watched the trajectories for any of
> the problematic windows?  It didn't seem like you had two metastable
> states, but maybe having a look at the movie would shed some light on
> what's going on.  I know that's the first thing I'd do.
>
> -Justin
>
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 Thanks Justin

 Have you any idea why when generating umbrella histograms for the
 pmf I
 would get two peaks in the histograms above a distance of 2 nm, but
 below 2 nm I get well behaved histograms that lead to a very
 good profile in the pmf. To the best of my knowledge the
 configurations
 are all very well equilibrated at their respective COM distances.
 Umbrella sampling is performed on all windows using a force
 constant of
 1000 kj/mol at 600 K.

>>> Sorry, no clue.
>>>
>>> -Justin
>>>
 Cheers

 Gavin

 Justin A. Lemkul wrote:
> Justin A. Lemkul wrote:
>> Gavin Melaugh wrote:
>>> Hi all
>>>
>>> I am generating a series of configurations using the pull code to
>>> calculate the pmf. I am using no pbc i.e. pbc =no, howver the
>>> output
>>> from grommp gives me info on pbc atom.
>>>
>>> Pull group  natoms  pbc atom  distance at start reference at
>>> t=0
>>>07236
>>>172   360   4.290 4.290
>>>
>>> why is this so?
>>>
>> grompp always assigns the numerical middle atom of a group as the
>> PBC 
> ...unless over-ridden by providing a different value for
> pbc_pullatom1.
>
> -Justin
>
>> reference point.  In the case of pbc=no, it shouldn't matter.
>>
>> http://manual.gromacs.org/current/online/mdp_opt.html#pull
>>
>> -Justin
>>
>>> Cheers
>>>
>>> Gavin

>>
>>
>

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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

O.K thanks anyway



I saw the plots you posted during a conversation with Chris, but I'll ask the 
obvious anyway: have you watched the trajectories for any of the problematic 
windows?  It didn't seem like you had two metastable states, but maybe having a 
look at the movie would shed some light on what's going on.  I know that's the 
first thing I'd do.


-Justin



Justin A. Lemkul wrote:


Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force constant of
1000 kj/mol at 600 K.


Sorry, no clue.

-Justin


Cheers

Gavin

Justin A. Lemkul wrote:

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at t=0
   07236
   172   360   4.290 4.290

why is this so?

grompp always assigns the numerical middle atom of a group as the PBC 

...unless over-ridden by providing a different value for pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin







--


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


--
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Re: [gmx-users] pbc atom

[Gavin Melaugh]

O.K thanks anyway


Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Thanks Justin
>>
>> Have you any idea why when generating umbrella histograms for the pmf I
>> would get two peaks in the histograms above a distance of 2 nm, but
>> below 2 nm I get well behaved histograms that lead to a very
>> good profile in the pmf. To the best of my knowledge the configurations
>> are all very well equilibrated at their respective COM distances.
>> Umbrella sampling is performed on all windows using a force constant of
>> 1000 kj/mol at 600 K.
>>
>
> Sorry, no clue.
>
> -Justin
>
>> Cheers
>>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Justin A. Lemkul wrote:

 Gavin Melaugh wrote:
> Hi all
>
> I am generating a series of configurations using the pull code to
> calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
> from grommp gives me info on pbc atom.
>
> Pull group  natoms  pbc atom  distance at start reference at t=0
>07236
>172   360   4.290 4.290
>
> why is this so?
>
 grompp always assigns the numerical middle atom of a group as the PBC 
>>> ...unless over-ridden by providing a different value for pbc_pullatom1.
>>>
>>> -Justin
>>>
 reference point.  In the case of pbc=no, it shouldn't matter.

 http://manual.gromacs.org/current/online/mdp_opt.html#pull

 -Justin

> Cheers
>
> Gavin
>>
>>
>

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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force constant of
1000 kj/mol at 600 K.



Sorry, no clue.

-Justin


Cheers

Gavin

Justin A. Lemkul wrote:


Justin A. Lemkul wrote:


Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at t=0
   07236
   172   360   4.290 4.290

why is this so?

grompp always assigns the numerical middle atom of a group as the PBC 

...unless over-ridden by providing a different value for pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin





--


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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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] pbc atom

[Gavin Melaugh]

Thanks Justin

Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force constant of
1000 kj/mol at 600 K.

Cheers

Gavin

Justin A. Lemkul wrote:
>
>
> Justin A. Lemkul wrote:
>>
>>
>> Gavin Melaugh wrote:
>>> Hi all
>>>
>>> I am generating a series of configurations using the pull code to
>>> calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
>>> from grommp gives me info on pbc atom.
>>>
>>> Pull group  natoms  pbc atom  distance at start reference at t=0
>>>07236
>>>172   360   4.290 4.290
>>>
>>> why is this so?
>>>
>>
>> grompp always assigns the numerical middle atom of a group as the PBC 
>
> ...unless over-ridden by providing a different value for pbc_pullatom1.
>
> -Justin
>
>> reference point.  In the case of pbc=no, it shouldn't matter.
>>
>> http://manual.gromacs.org/current/online/mdp_opt.html#pull
>>
>> -Justin
>>
>>> Cheers
>>>
>>> Gavin
>>
>

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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Justin A. Lemkul wrote:



Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at t=0
   07236
   172   360   4.290 4.290

why is this so?



grompp always assigns the numerical middle atom of a group as the PBC 


...unless over-ridden by providing a different value for pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin




--


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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Please search the archive at http://www.gromacs.org/search before posting!
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at t=0
   07236
   172   360   4.290 4.290

why is this so?



grompp always assigns the numerical middle atom of a group as the PBC reference 
point.  In the case of pbc=no, it shouldn't matter.


http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin


--


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] pbc atom

[Gavin Melaugh]

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at t=0
   07236
   172   360   4.290 4.290

why is this so?

Cheers

Gavin
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Re: [gmx-users] PBC

[Sai Kumar Ramadugu]

Hi Morteza,
  I had this problem when I was running a trimeric protein attached to an
oligosaccharide.

*I have used the following command:*

* *

*trjconv  -s .tpr -f .xtc -o   -boxcenter tric -pbc mol*

* *

*but it is not working.*


Do the following. It worked for me.


In the first round, run

trjconv -f *.xtc -s *.tpr -center -boxcenter tric -pbc mol -o 1.xtc

and choose backbone (which is usually 4 from the index) for centring.


In the second round,

use 1.xtc obtained from the first step and run the command as follows


trjconv -f 1.xtc -s *.tpr -center -boxcenter tric -pbc a -o 2.xtc

and this time also choose the backbone for centring.


This should bring back the dimeric protein system in the box. Sometimes the
water molecules around the edge are broken. Hope this is not a big worry.


By the way is your box cubic or truncated octahedron?

My case was a cubic box.


Hope this helps.


Regards

Sai


On Tue, Jun 8, 2010 at 2:23 AM, shahab shariati
wrote:

> Morteza Khabiri wrote:
>
>
>
> Dear users
>
>
>
> I have a dimer protein in the water box. It was run for 30ns.
>
> during the simulation dimer split to two monomer. This things happen bc of
>
> PBC. ( I checked it by vmd pbc option )
>
> to have a two monomer together during trajectories (for visualization)
>
> I have used the following command:
>
>
>
> trjconv  -s .tpr -f .xtc -o   -boxcenter tric -pbc mol
>
>
>
> but it is not working.
>
> Is there any other method or command which I could implement pbc in
>
> trajectory.
>
>
>
> Thanks in advance
>
>
>
> Morteza
>
>
>
>
>
>
>
> Shahab Shariati wrote:
>
>
>
> You can use other flags of trjconv command as follows:
>
>
>
> Trjconv –f *.xtc –s **.tpr –o ***.xtc –pbc nojump –ur compact -center
>
>
>
>
>
>
>
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[gmx-users] PBC

[shahab shariati]

Morteza Khabiri wrote:



Dear users



I have a dimer protein in the water box. It was run for 30ns.

during the simulation dimer split to two monomer. This things happen bc of

PBC. ( I checked it by vmd pbc option )

to have a two monomer together during trajectories (for visualization)

I have used the following command:



trjconv  -s .tpr -f .xtc -o   -boxcenter tric -pbc mol



but it is not working.

Is there any other method or command which I could implement pbc in

trajectory.



Thanks in advance



Morteza







Shahab Shariati wrote:



You can use other flags of trjconv command as follows:



Trjconv –f *.xtc –s **.tpr –o ***.xtc –pbc nojump –ur compact -center
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Re: [gmx-users] PBC

[ms]

On 02/06/10 18:48, Morteza Khabiri wrote:

Dear users

I have a dimer protein in the water box. It was run for 30ns.
during the simulation dimer split to two monomer. This things happen bc of
PBC. ( I checked it by vmd pbc option )
to have a two monomer together during trajectories (for visualization)
I have used the following command:

trjconv  -s .tpr -f .xtc -o   -boxcenter tric -pbc mol

but it is not working.


Not working *how*? that is, what is output? .tpr and .xtc don't look 
like sensible file parameters.



Is there any other method or command which I could implement pbc in
trajectory.

Thanks in advance

Morteza



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[gmx-users] PBC

[Morteza Khabiri]

Dear users

I have a dimer protein in the water box. It was run for 30ns.
during the simulation dimer split to two monomer. This things happen bc of
PBC. ( I checked it by vmd pbc option )
to have a two monomer together during trajectories (for visualization)
I have used the following command:

trjconv  -s .tpr -f .xtc -o   -boxcenter tric -pbc mol

but it is not working.
Is there any other method or command which I could implement pbc in
trajectory.

Thanks in advance

Morteza

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Re: [gmx-users] pbc whole

[Carla Jamous]

Hi Justin and Tsjerk,
Thank you for your answers, but I found a command that worked for me:)

First, I concatenated the ensemble of my trajectory.
& then, I did the following:

trjconv -s a.tpr -f traj.xtc -o traj1.xtc -pbc nojump -n b.ndx

Cheers,
Carla

On Thu, Feb 18, 2010 at 12:47 PM, Justin A. Lemkul  wrote:

>
>
> Carla Jamous wrote:
>
>>
>> Hi Tsjerk,
>> sorry I didn't understand this part of your explanation:"Can you make an
>> image of the last frame and send a link
>> to it?"
>>
>
> Render an image of your system from the end of your trajectory and post it
> somewhere online (like photobucket); do not send it as an attachment to your
> email.
>
> -Justin
>
>  But anyhow, please can you send me the version of trjconv that does the
>> trick?
>>
>> Thanks,
>> Carla
>>
>> On Thu, Feb 18, 2010 at 11:42 AM, Tsjerk Wassenaar > tsje...@gmail.com>> wrote:
>>
>>Hi Carla,
>>
>> > I checked with genconf & now I'm certain that my ATP molecule is
>>still with
>> > the protein
>>
>>That's good to know :)
>>
>> >>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol
>> >>> (centering on "Protein")
>>
>>So what did come out of this then? It should have given you a compact
>>representation of your system with the protein in the center. But if
>>the protein's in the center and everything is put as close to that
>>center as possible, which is what "compact" does, then the ATP should
>>be there too. Can you make an image of the last frame and send a link
>>to it? Alternatively, I have a patched version of trjconv that you can
>>use to do the trick. I can send it if you want.
>>
>>Cheers,
>>
>>Tsjerk
>>
>>
>>--
>>Tsjerk A. Wassenaar, Ph.D.
>>
>>Computational Chemist
>>Medicinal Chemist
>>Neuropharmacologist
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>>gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>posting!
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>>.
>>
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>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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