[gmx-users] Whether my simulation is conserved?

[Seera Suryanarayana]

Dear gromacs users,

I have done simulations for 100ns. To know whether my simulation is
conserved, I have preferred to do simulated annealing. I have set the
highest temperature as 350K at 25ns and allowed it go down to room
temperature 300K at 50ns. And eventually I executed the mdrun for 50ns at
300K(you can find SA parameters below). From this simulated annealing
trajectory how can I find global minima of protein?

;simulated annealing
annealing  = single single
annealing-npoints = 3 3
annealing-time = 0 25000 5 0 25000 5
annealing-temp = 300 350 300 300 350 300

Surya
Graduate student
India.
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[gmx-users] Regarding calculation of Lennard-Jones potential

[Dilip H N]

Hello,
I have a simulation mixture of aminoacid (eg., glycine) with water and
cosolvent. I want to calculate Lennard-Jones Parameters of the all atom
types. How can i calculate it...??

Can it be done with commands, or any other method..??
Any suggestions are appreciated...

Thank you..

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



 Sent with Mailtrack

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Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

[Vidya R]

Thank you for your reply.

When I try to run my job in a single processor through qsub command, (by
feeding the gromacs mdrun command in script file), it says SEGMENTATION
FAULT, CORE DUMPED...


But, when I run my job in login node (which we are not supposed to do), it
works very well...


Can you comment on this?


Thanks,
Vidya.R

On Mon, Sep 18, 2017 at 2:50 AM, Mark Abraham 
wrote:

> Hi,
>
> You're running a thread-MPI version of GROMACS, which is probably not what
> you want to do if you're running mpirun. It should work even so, but
> whatever quirks exist with SGE are unfortunately between you, its docs and
> your cluster's docs and admins :-(
>
> Mark
>
> On Sun, Sep 17, 2017 at 7:23 AM Vidya R  wrote:
>
> > My log file is provided in the link below
> >
> > Can you please look into it and let me know why the error arises?
> >
> > I am feeding my commands in SGE cluster.   When I run it in my login
> node,
> > gmx mdrun -v -deffnm eql runs well
> >
> >
> > But, through qsub command, (with 8 processors) It says,
> >
> > mpirun noticed that process rank 7 with PID 19160 on node
> > compute-0-28.local exited on signal 11 (Segmentation fault).
> >
> > Please help me.
> >
> > I am unable to figure out, as to whether the problem is with the version
> of
> > gromacs or the method of compiling.
> >
> >
> >
> > https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU/
> view?usp=sharing
> > --
> > Gromacs Users mailing list
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> > posting!
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Changes in the simulation box after the production run

[Dallas Warren]

These two images will help you see what is going on:

https://twitter.com/dr_dbw/status/909559339366572032 - shows a
molecule that appears to be outside the box.

https://twitter.com/dr_dbw/status/909559783291723776 - however, that
molecule actually enters through the opposite face of the box.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 18 September 2017 at 09:22, Mahsa E  wrote:
> Thank you for you quick reply, Justin and Dallas! Very good point!
>
> Best regards,
> Mahsa
>
>
>
>
>
> On Mon, Sep 18, 2017 at 1:00 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 9/17/17 6:57 PM, Mahsa E wrote:
>>
>>> Could you please see the link below for the input and output simulation
>>> box:
>>>
>>> https://www.dropbox.com/sh/kb36ake7mj5iovh/AABPF4_FUfvSPZxdO5WN3JnEa?dl=0
>>>
>>>
>>> Actually, I thought since some of the chains went out of the simulation
>>> box, then density have been changed. In my previous experience with
>>> another
>>> polymer, I didn't see this difference in the systems after the production
>>> run, so I'm wondering if this is related to the stability of the system?
>>>
>>>
>> As Dallas said, this is just a periodicity/visualization effect - there's
>> no such thing as "outside" a periodic cell.
>>
>> Your "before MD" has "broken" molecules, i.e. all the atoms are visualized
>> as being in the central image.  Your "after MD" is just those molecules
>> made whole.  If you make the initial frame whole (trjconv -pbc whole), you
>> will see a similar configuration.
>>
>> -Justin
>>
>>
>> Best regards,
>>> Mahsa
>>>
>>>
>>>
>>>
>>>
>>> On Mon, Sep 18, 2017 at 12:10 AM, Dallas Warren >> >
>>> wrote:
>>>
>>> Because that is how the system changed within the simulation time?

 What exactly is the problem as you see it, and why do you think it is a
 problem?

 And remember, you have a periodic boundary condition that means the
 one edge of the box wraps around to the opposite one.  So "out of the
 box" is a visualisation artefact, not a "problem".
 http://www.gromacs.org/Documentation/Terminology/
 Periodic_Boundary_Conditions
 Catch ya,

 Dr. Dallas Warren
 Drug Delivery, Disposition and Dynamics
 Monash Institute of Pharmaceutical Sciences, Monash University
 381 Royal Parade, Parkville VIC 3052
 dallas.war...@monash.edu
 -
 When the only tool you own is a hammer, every problem begins to resemble
 a
 nail.


 On 18 September 2017 at 06:31, Mahsa E  wrote:

> Dear gmx-users,
>
> I did a 200 ns production md run in NVT ensemble for a simulation box of
> polymer chains. Before this step, I did the energy minimisation, NVT and
> NPT equilibration on the system. The problem is after the production
>
 run, I

> don't get the initial equilibrated packed box of polymer and it seems
>
 more

> like a circular shape with some parts of the chains out of the box. What
>
 is

> the reason for getting this result?
> For the MD run I used the mdp file below:
>
> ; 7.3.2 Preprocessing
>
> ;define  =   ; defines to pass to the preprocessor
>
>
> ; 7.3.3 Run Control
>
> integrator  = md; md integrator
>
> tinit   = 0 ; [ps] starting time for
>
 run

>
> dt  = 0.002 ; [ps] time step for
> integration
>
> nsteps  = 1; maximum number of
> steps to integrate, 0.002 * 1 = 20 ps
>
> comm_mode   = Linear; remove center of mass
> translation
>
> nstcomm = 100 ; [steps] frequency of
> mass motion removal
>
> ;comm_grps   = Protein Non-Protein   ; group(s) for center
> of
> mass motion removal
>
>
> ; 7.3.8 Output Control
>
> nstxout = 0 ; [steps] freq to write coordinates
>
 to

> trajectory
>
> nstvout = 0 ; [steps] freq to write velocities
> to
> trajectory
>
> nstfout = 0 ; [steps] freq to write forces to
> trajectory
>
> nstlog  = 1000   ; [steps] freq to write
> energies
> to log file
>
> nstenergy   = 1000   ; [steps] freq to write
> energies
> to energy file
>
> nstxtcout   = 1000  

Re: [gmx-users] Changes in the simulation box after the production run

[Mahsa E]

Thank you for you quick reply, Justin and Dallas! Very good point!

Best regards,
Mahsa





On Mon, Sep 18, 2017 at 1:00 AM, Justin Lemkul  wrote:

>
>
> On 9/17/17 6:57 PM, Mahsa E wrote:
>
>> Could you please see the link below for the input and output simulation
>> box:
>>
>> https://www.dropbox.com/sh/kb36ake7mj5iovh/AABPF4_FUfvSPZxdO5WN3JnEa?dl=0
>>
>>
>> Actually, I thought since some of the chains went out of the simulation
>> box, then density have been changed. In my previous experience with
>> another
>> polymer, I didn't see this difference in the systems after the production
>> run, so I'm wondering if this is related to the stability of the system?
>>
>>
> As Dallas said, this is just a periodicity/visualization effect - there's
> no such thing as "outside" a periodic cell.
>
> Your "before MD" has "broken" molecules, i.e. all the atoms are visualized
> as being in the central image.  Your "after MD" is just those molecules
> made whole.  If you make the initial frame whole (trjconv -pbc whole), you
> will see a similar configuration.
>
> -Justin
>
>
> Best regards,
>> Mahsa
>>
>>
>>
>>
>>
>> On Mon, Sep 18, 2017 at 12:10 AM, Dallas Warren > >
>> wrote:
>>
>> Because that is how the system changed within the simulation time?
>>>
>>> What exactly is the problem as you see it, and why do you think it is a
>>> problem?
>>>
>>> And remember, you have a periodic boundary condition that means the
>>> one edge of the box wraps around to the opposite one.  So "out of the
>>> box" is a visualisation artefact, not a "problem".
>>> http://www.gromacs.org/Documentation/Terminology/
>>> Periodic_Boundary_Conditions
>>> Catch ya,
>>>
>>> Dr. Dallas Warren
>>> Drug Delivery, Disposition and Dynamics
>>> Monash Institute of Pharmaceutical Sciences, Monash University
>>> 381 Royal Parade, Parkville VIC 3052
>>> dallas.war...@monash.edu
>>> -
>>> When the only tool you own is a hammer, every problem begins to resemble
>>> a
>>> nail.
>>>
>>>
>>> On 18 September 2017 at 06:31, Mahsa E  wrote:
>>>
 Dear gmx-users,

 I did a 200 ns production md run in NVT ensemble for a simulation box of
 polymer chains. Before this step, I did the energy minimisation, NVT and
 NPT equilibration on the system. The problem is after the production

>>> run, I
>>>
 don't get the initial equilibrated packed box of polymer and it seems

>>> more
>>>
 like a circular shape with some parts of the chains out of the box. What

>>> is
>>>
 the reason for getting this result?
 For the MD run I used the mdp file below:

 ; 7.3.2 Preprocessing

 ;define  =   ; defines to pass to the preprocessor


 ; 7.3.3 Run Control

 integrator  = md; md integrator

 tinit   = 0 ; [ps] starting time for

>>> run
>>>

 dt  = 0.002 ; [ps] time step for
 integration

 nsteps  = 1; maximum number of
 steps to integrate, 0.002 * 1 = 20 ps

 comm_mode   = Linear; remove center of mass
 translation

 nstcomm = 100 ; [steps] frequency of
 mass motion removal

 ;comm_grps   = Protein Non-Protein   ; group(s) for center
 of
 mass motion removal


 ; 7.3.8 Output Control

 nstxout = 0 ; [steps] freq to write coordinates

>>> to
>>>
 trajectory

 nstvout = 0 ; [steps] freq to write velocities
 to
 trajectory

 nstfout = 0 ; [steps] freq to write forces to
 trajectory

 nstlog  = 1000   ; [steps] freq to write
 energies
 to log file

 nstenergy   = 1000   ; [steps] freq to write
 energies
 to energy file

 nstxtcout   = 1000   ; [steps] freq to write
 coordinates to xtc trajectory

 xtc_precision   = 1000  ; [real] precision to write xtc
 trajectory

 xtc_grps= System; group(s) to write to xtc
 trajectory

 energygrps  = System; group(s) to write to energy

>>> file
>>>

 cutoff-scheme= verlet

 ; 7.3.9 Neighbor Searching

 nstlist = 20 ; [steps] freq to update

>>> neighbor
>>>
 list

 ns_type = grid  ; method of updating neighbor

>>> list
>>>

 pbc = xyz   ; periodic boundary conditions
 in
 all directions

 rlist   = 0.8   ; [nm] cut-off distance for the

[gmx-users] Cloud based molecular simulations

[michael mwangi]

Hello,



We have been hard at work and are now ready to let the public test our intial 
product offering. Please check our web based molecular simulations platform

at https://ioniclabs.io.



At Ionic Labs you can run your simulations in two ways:

1. By creating a workstation which has a ssh terminal accessible right from 
the web browser

2. By submitting a simulation job to our backend infrastructure.



We would love to get feedback from the Gromacs commnunity.



Thanks.


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Re: [gmx-users] Changes in the simulation box after the production run

[Justin Lemkul]

On 9/17/17 6:57 PM, Mahsa E wrote:

Could you please see the link below for the input and output simulation box:

https://www.dropbox.com/sh/kb36ake7mj5iovh/AABPF4_FUfvSPZxdO5WN3JnEa?dl=0


Actually, I thought since some of the chains went out of the simulation
box, then density have been changed. In my previous experience with another
polymer, I didn't see this difference in the systems after the production
run, so I'm wondering if this is related to the stability of the system?



As Dallas said, this is just a periodicity/visualization effect - there's no 
such thing as "outside" a periodic cell.


Your "before MD" has "broken" molecules, i.e. all the atoms are visualized as 
being in the central image.  Your "after MD" is just those molecules made whole. 
 If you make the initial frame whole (trjconv -pbc whole), you will see a 
similar configuration.


-Justin


Best regards,
Mahsa





On Mon, Sep 18, 2017 at 12:10 AM, Dallas Warren 
wrote:


Because that is how the system changed within the simulation time?

What exactly is the problem as you see it, and why do you think it is a
problem?

And remember, you have a periodic boundary condition that means the
one edge of the box wraps around to the opposite one.  So "out of the
box" is a visualisation artefact, not a "problem".
http://www.gromacs.org/Documentation/Terminology/
Periodic_Boundary_Conditions
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On 18 September 2017 at 06:31, Mahsa E  wrote:

Dear gmx-users,

I did a 200 ns production md run in NVT ensemble for a simulation box of
polymer chains. Before this step, I did the energy minimisation, NVT and
NPT equilibration on the system. The problem is after the production

run, I

don't get the initial equilibrated packed box of polymer and it seems

more

like a circular shape with some parts of the chains out of the box. What

is

the reason for getting this result?
For the MD run I used the mdp file below:

; 7.3.2 Preprocessing

;define  =   ; defines to pass to the preprocessor


; 7.3.3 Run Control

integrator  = md; md integrator

tinit   = 0 ; [ps] starting time for

run


dt  = 0.002 ; [ps] time step for
integration

nsteps  = 1; maximum number of
steps to integrate, 0.002 * 1 = 20 ps

comm_mode   = Linear; remove center of mass
translation

nstcomm = 100 ; [steps] frequency of
mass motion removal

;comm_grps   = Protein Non-Protein   ; group(s) for center of
mass motion removal


; 7.3.8 Output Control

nstxout = 0 ; [steps] freq to write coordinates

to

trajectory

nstvout = 0 ; [steps] freq to write velocities to
trajectory

nstfout = 0 ; [steps] freq to write forces to
trajectory

nstlog  = 1000   ; [steps] freq to write energies
to log file

nstenergy   = 1000   ; [steps] freq to write energies
to energy file

nstxtcout   = 1000   ; [steps] freq to write
coordinates to xtc trajectory

xtc_precision   = 1000  ; [real] precision to write xtc
trajectory

xtc_grps= System; group(s) to write to xtc
trajectory

energygrps  = System; group(s) to write to energy

file


cutoff-scheme= verlet

; 7.3.9 Neighbor Searching

nstlist = 20 ; [steps] freq to update

neighbor

list

ns_type = grid  ; method of updating neighbor

list


pbc = xyz   ; periodic boundary conditions in
all directions

rlist   = 0.8   ; [nm] cut-off distance for the
short-range neighbor list


; 7.3.10 Electrostatics

coulombtype = PME   ; Particle-Mesh Ewald

electrostatics


rcoulomb= 1.2   ; [nm] distance for Coulomb

cut-off



; 7.3.11 VdW

vdwtype = cut-off   ; twin-range cut-off with rlist
where rvdw >= rlist

vdw-modifier = potential-switch

rvdw-switch  = 1.1

rvdw= 1.2   ; [nm] distance for LJ cut-off

DispCorr= EnerPres  ; apply long range dispersion
corrections


; 7.3.13 Ewald

fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
when using PME

pme_order   = 4 ; interpolation order for PME, 4

=

cubic

ewald_rtol  = 1e-6  ; relative strength of

Re: [gmx-users] Changes in the simulation box after the production run

[Mahsa E]

Could you please see the link below for the input and output simulation box:

https://www.dropbox.com/sh/kb36ake7mj5iovh/AABPF4_FUfvSPZxdO5WN3JnEa?dl=0


Actually, I thought since some of the chains went out of the simulation
box, then density have been changed. In my previous experience with another
polymer, I didn't see this difference in the systems after the production
run, so I'm wondering if this is related to the stability of the system?

Best regards,
Mahsa





On Mon, Sep 18, 2017 at 12:10 AM, Dallas Warren 
wrote:

> Because that is how the system changed within the simulation time?
>
> What exactly is the problem as you see it, and why do you think it is a
> problem?
>
> And remember, you have a periodic boundary condition that means the
> one edge of the box wraps around to the opposite one.  So "out of the
> box" is a visualisation artefact, not a "problem".
> http://www.gromacs.org/Documentation/Terminology/
> Periodic_Boundary_Conditions
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 18 September 2017 at 06:31, Mahsa E  wrote:
> > Dear gmx-users,
> >
> > I did a 200 ns production md run in NVT ensemble for a simulation box of
> > polymer chains. Before this step, I did the energy minimisation, NVT and
> > NPT equilibration on the system. The problem is after the production
> run, I
> > don't get the initial equilibrated packed box of polymer and it seems
> more
> > like a circular shape with some parts of the chains out of the box. What
> is
> > the reason for getting this result?
> > For the MD run I used the mdp file below:
> >
> > ; 7.3.2 Preprocessing
> >
> > ;define  =   ; defines to pass to the preprocessor
> >
> >
> > ; 7.3.3 Run Control
> >
> > integrator  = md; md integrator
> >
> > tinit   = 0 ; [ps] starting time for
> run
> >
> > dt  = 0.002 ; [ps] time step for
> > integration
> >
> > nsteps  = 1; maximum number of
> > steps to integrate, 0.002 * 1 = 20 ps
> >
> > comm_mode   = Linear; remove center of mass
> > translation
> >
> > nstcomm = 100 ; [steps] frequency of
> > mass motion removal
> >
> > ;comm_grps   = Protein Non-Protein   ; group(s) for center of
> > mass motion removal
> >
> >
> > ; 7.3.8 Output Control
> >
> > nstxout = 0 ; [steps] freq to write coordinates
> to
> > trajectory
> >
> > nstvout = 0 ; [steps] freq to write velocities to
> > trajectory
> >
> > nstfout = 0 ; [steps] freq to write forces to
> > trajectory
> >
> > nstlog  = 1000   ; [steps] freq to write energies
> > to log file
> >
> > nstenergy   = 1000   ; [steps] freq to write energies
> > to energy file
> >
> > nstxtcout   = 1000   ; [steps] freq to write
> > coordinates to xtc trajectory
> >
> > xtc_precision   = 1000  ; [real] precision to write xtc
> > trajectory
> >
> > xtc_grps= System; group(s) to write to xtc
> > trajectory
> >
> > energygrps  = System; group(s) to write to energy
> file
> >
> > cutoff-scheme= verlet
> >
> > ; 7.3.9 Neighbor Searching
> >
> > nstlist = 20 ; [steps] freq to update
> neighbor
> > list
> >
> > ns_type = grid  ; method of updating neighbor
> list
> >
> > pbc = xyz   ; periodic boundary conditions in
> > all directions
> >
> > rlist   = 0.8   ; [nm] cut-off distance for the
> > short-range neighbor list
> >
> >
> > ; 7.3.10 Electrostatics
> >
> > coulombtype = PME   ; Particle-Mesh Ewald
> electrostatics
> >
> > rcoulomb= 1.2   ; [nm] distance for Coulomb
> cut-off
> >
> >
> > ; 7.3.11 VdW
> >
> > vdwtype = cut-off   ; twin-range cut-off with rlist
> > where rvdw >= rlist
> >
> > vdw-modifier = potential-switch
> >
> > rvdw-switch  = 1.1
> >
> > rvdw= 1.2   ; [nm] distance for LJ cut-off
> >
> > DispCorr= EnerPres  ; apply long range dispersion
> > corrections
> >
> >
> > ; 7.3.13 Ewald
> >
> > fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
> > when using PME
> >
> > pme_order   = 4 ; interpolation order for PME, 4
> =
> > cubic
> >
> > ewald_rtol  = 1e-6  ; relative 

Re: [gmx-users] Diffusion coefficient

[Justin Lemkul]

On 9/17/17 6:05 PM, Dallas Warren wrote:

http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html

Don't know exactly how to do it myself, but there will be an option
there where you can specify the z coordinate as a way to break it up
into groups.


And herein lies the challenge.  The selections themselves will give index groups 
per frame, may vary in size, and the individual molecules themselves will likely 
occupy each slice discontinuously with respect to time.  So a lot of effort 
would have to be made to make per-molecule sub-trajectories to compute a 
diffusion coefficient for a given time frame in which the molecule continuously 
satisfies the criterion, then calculated again over another period of time if 
the molecule moves out and comes back (otherwise one would get a spurious 
contribution to the MSD if a molecule seems to jump around).  I suppose it can 
be done, but only very tediously in reassembling frames to make 
sub-trajectories, then looping over every molecule individually in doing so.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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Re: [gmx-users] Changes in the simulation box after the production run

[Dallas Warren]

Because that is how the system changed within the simulation time?

What exactly is the problem as you see it, and why do you think it is a problem?

And remember, you have a periodic boundary condition that means the
one edge of the box wraps around to the opposite one.  So "out of the
box" is a visualisation artefact, not a "problem".
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 18 September 2017 at 06:31, Mahsa E  wrote:
> Dear gmx-users,
>
> I did a 200 ns production md run in NVT ensemble for a simulation box of
> polymer chains. Before this step, I did the energy minimisation, NVT and
> NPT equilibration on the system. The problem is after the production run, I
> don't get the initial equilibrated packed box of polymer and it seems more
> like a circular shape with some parts of the chains out of the box. What is
> the reason for getting this result?
> For the MD run I used the mdp file below:
>
> ; 7.3.2 Preprocessing
>
> ;define  =   ; defines to pass to the preprocessor
>
>
> ; 7.3.3 Run Control
>
> integrator  = md; md integrator
>
> tinit   = 0 ; [ps] starting time for run
>
> dt  = 0.002 ; [ps] time step for
> integration
>
> nsteps  = 1; maximum number of
> steps to integrate, 0.002 * 1 = 20 ps
>
> comm_mode   = Linear; remove center of mass
> translation
>
> nstcomm = 100 ; [steps] frequency of
> mass motion removal
>
> ;comm_grps   = Protein Non-Protein   ; group(s) for center of
> mass motion removal
>
>
> ; 7.3.8 Output Control
>
> nstxout = 0 ; [steps] freq to write coordinates to
> trajectory
>
> nstvout = 0 ; [steps] freq to write velocities to
> trajectory
>
> nstfout = 0 ; [steps] freq to write forces to
> trajectory
>
> nstlog  = 1000   ; [steps] freq to write energies
> to log file
>
> nstenergy   = 1000   ; [steps] freq to write energies
> to energy file
>
> nstxtcout   = 1000   ; [steps] freq to write
> coordinates to xtc trajectory
>
> xtc_precision   = 1000  ; [real] precision to write xtc
> trajectory
>
> xtc_grps= System; group(s) to write to xtc
> trajectory
>
> energygrps  = System; group(s) to write to energy file
>
> cutoff-scheme= verlet
>
> ; 7.3.9 Neighbor Searching
>
> nstlist = 20 ; [steps] freq to update neighbor
> list
>
> ns_type = grid  ; method of updating neighbor list
>
> pbc = xyz   ; periodic boundary conditions in
> all directions
>
> rlist   = 0.8   ; [nm] cut-off distance for the
> short-range neighbor list
>
>
> ; 7.3.10 Electrostatics
>
> coulombtype = PME   ; Particle-Mesh Ewald electrostatics
>
> rcoulomb= 1.2   ; [nm] distance for Coulomb cut-off
>
>
> ; 7.3.11 VdW
>
> vdwtype = cut-off   ; twin-range cut-off with rlist
> where rvdw >= rlist
>
> vdw-modifier = potential-switch
>
> rvdw-switch  = 1.1
>
> rvdw= 1.2   ; [nm] distance for LJ cut-off
>
> DispCorr= EnerPres  ; apply long range dispersion
> corrections
>
>
> ; 7.3.13 Ewald
>
> fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
> when using PME
>
> pme_order   = 4 ; interpolation order for PME, 4 =
> cubic
>
> ewald_rtol  = 1e-6  ; relative strength of
> Ewald-shifted potential at rcoulomb
>
> ewald-rtol-lj= 0.001
>
> lj-pme-comb-rule = Geometric
>
> ewald-geometry   = 3d
>
> epsilon_surface  = 0
>
>
> ; 7.3.14 Temperature Coupling
>
> tcoupl  = v-rescale; temperature
> coupling with
>
> tc_grps = system; groups to couple seperately to
> temperature bath
>
> tau_t   = 0.1; [ps] time constant
> for coupling
>
> ref_t   = 303; [K] reference
> temperature for coupling
>
>
> ; 7.3.17 Velocity Generation
>
> gen_vel = no   ; generate velocities according to
> Maxwell distribution of temperature
>
> gen_temp= 303   ; [K] temperature for Maxwell
> distribution
>
> 

Re: [gmx-users] Diffusion coefficient

[Dallas Warren]

http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html

Don't know exactly how to do it myself, but there will be an option
there where you can specify the z coordinate as a way to break it up
into groups.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 17 September 2017 at 06:05, Sohaib. Mohammed
 wrote:
> Any help!
>
> On Saturday, September 16, 2017, Sohaib. Mohammed <
> sohaibmohamme...@gmail.com> wrote:
>
>> Hey Users,
>>
>> I want to calculate the diffusion coefficient using gmx msd. I want to
>> divide the box into slices of 5 A parallel to z axis and calculate the
>> diffusion coefficient for each slice. My question is how to make these
>> slices, I've tried gmx trajconv but didn't work with me. I believe it's
>> quite simple and provided by gromacs, but I am struggling with it.
>> Appreciate any idea on how to make these slices.
>>
>> Thank you,
>>
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Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

[Mark Abraham]

Hi,

You're running a thread-MPI version of GROMACS, which is probably not what
you want to do if you're running mpirun. It should work even so, but
whatever quirks exist with SGE are unfortunately between you, its docs and
your cluster's docs and admins :-(

Mark

On Sun, Sep 17, 2017 at 7:23 AM Vidya R  wrote:

> My log file is provided in the link below
>
> Can you please look into it and let me know why the error arises?
>
> I am feeding my commands in SGE cluster.   When I run it in my login node,
> gmx mdrun -v -deffnm eql runs well
>
>
> But, through qsub command, (with 8 processors) It says,
>
> mpirun noticed that process rank 7 with PID 19160 on node
> compute-0-28.local exited on signal 11 (Segmentation fault).
>
> Please help me.
>
> I am unable to figure out, as to whether the problem is with the version of
> gromacs or the method of compiling.
>
>
>
> https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU/view?usp=sharing
> --
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[gmx-users] Changes in the simulation box after the production run

[Mahsa E]

Dear gmx-users,

I did a 200 ns production md run in NVT ensemble for a simulation box of
polymer chains. Before this step, I did the energy minimisation, NVT and
NPT equilibration on the system. The problem is after the production run, I
don't get the initial equilibrated packed box of polymer and it seems more
like a circular shape with some parts of the chains out of the box. What is
the reason for getting this result?
For the MD run I used the mdp file below:

; 7.3.2 Preprocessing

;define  =   ; defines to pass to the preprocessor


; 7.3.3 Run Control

integrator  = md; md integrator

tinit   = 0 ; [ps] starting time for run

dt  = 0.002 ; [ps] time step for
integration

nsteps  = 1; maximum number of
steps to integrate, 0.002 * 1 = 20 ps

comm_mode   = Linear; remove center of mass
translation

nstcomm = 100 ; [steps] frequency of
mass motion removal

;comm_grps   = Protein Non-Protein   ; group(s) for center of
mass motion removal


; 7.3.8 Output Control

nstxout = 0 ; [steps] freq to write coordinates to
trajectory

nstvout = 0 ; [steps] freq to write velocities to
trajectory

nstfout = 0 ; [steps] freq to write forces to
trajectory

nstlog  = 1000   ; [steps] freq to write energies
to log file

nstenergy   = 1000   ; [steps] freq to write energies
to energy file

nstxtcout   = 1000   ; [steps] freq to write
coordinates to xtc trajectory

xtc_precision   = 1000  ; [real] precision to write xtc
trajectory

xtc_grps= System; group(s) to write to xtc
trajectory

energygrps  = System; group(s) to write to energy file

cutoff-scheme= verlet

; 7.3.9 Neighbor Searching

nstlist = 20 ; [steps] freq to update neighbor
list

ns_type = grid  ; method of updating neighbor list

pbc = xyz   ; periodic boundary conditions in
all directions

rlist   = 0.8   ; [nm] cut-off distance for the
short-range neighbor list


; 7.3.10 Electrostatics

coulombtype = PME   ; Particle-Mesh Ewald electrostatics

rcoulomb= 1.2   ; [nm] distance for Coulomb cut-off


; 7.3.11 VdW

vdwtype = cut-off   ; twin-range cut-off with rlist
where rvdw >= rlist

vdw-modifier = potential-switch

rvdw-switch  = 1.1

rvdw= 1.2   ; [nm] distance for LJ cut-off

DispCorr= EnerPres  ; apply long range dispersion
corrections


; 7.3.13 Ewald

fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
when using PME

pme_order   = 4 ; interpolation order for PME, 4 =
cubic

ewald_rtol  = 1e-6  ; relative strength of
Ewald-shifted potential at rcoulomb

ewald-rtol-lj= 0.001

lj-pme-comb-rule = Geometric

ewald-geometry   = 3d

epsilon_surface  = 0


; 7.3.14 Temperature Coupling

tcoupl  = v-rescale; temperature
coupling with

tc_grps = system; groups to couple seperately to
temperature bath

tau_t   = 0.1; [ps] time constant
for coupling

ref_t   = 303; [K] reference
temperature for coupling


; 7.3.17 Velocity Generation

gen_vel = no   ; generate velocities according to
Maxwell distribution of temperature

gen_temp= 303   ; [K] temperature for Maxwell
distribution

gen_seed= -1; [integer] used to initialize
random generator for random velocities


; 7.3.18 Bonds

constraints = h-bonds

constraint_algorithm= LINCS ; LINear Constraint Solver

continuation= no; no = apply constraints to the
start configuration

lincs_order = 4 ; highest order in the expansion of
the contraint coupling matrix

lincs_iter  = 1 ; number of iterations to correct
for rotational lengthening

lincs_warnangle = 30; [degrees] maximum angle that a
bond can rotate before LINCS will complain

Best regards,

Mahsa
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Re: [gmx-users] how to generate a trr file

[Subhomoi Borkotoky]

Hi,

You can use "trjconv" command and specify "-e 5".


Hope it helps!!

Regards,

Subhomoi B.

On 17 Sep 2017 8:34 pm, "marzieh dehghan"  wrote:

> Dear all
> Hi
>
> I performed molecular dynamics simulation during 100 ns, but now I want to
> create a trr or xtc file including 50 ns. how I can generate trajectory
> file containing 50 ns from 100 ns of MD run?
>
> thanks a lot
> best wishes
>
> --
>
>
>
>
> *Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
> (IBB)University of Tehran, Tehran- Iran.*
> --
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[gmx-users] unsatisfactory result for kinetic energy using trj ekt and ekr

[Tushar Ranjan Moharana]

Hi Everyone,
I want to calculate the kinetic energy  of a particular group. I use gmx
trj ekt and ekr to calculate translational and rotational kinetic energy.
But the result I obtained doesn't look correct. As I choose larger groups
(even the smaller group is a subset of larger group) total translational
kinetic energy is decreasing while rotational kinetic energy remain almost
the same (from the visual observation as well as averaging the  .xvg
output) . I am using GROMACS 5.0. Anybody familiar with the problem kindly
help me. Or if there is any other way to calculate the kinetic energy also
let me know.


Thanks a lot.


"A society with free knowledge is better than a society with free food"
-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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[gmx-users] how to generate a trr file

[marzieh dehghan]

Dear all
Hi

I performed molecular dynamics simulation during 100 ns, but now I want to
create a trr or xtc file including 50 ns. how I can generate trajectory
file containing 50 ns from 100 ns of MD run?

thanks a lot
best wishes

-- 




*Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
(IBB)University of Tehran, Tehran- Iran.*
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Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

[Vidya R]

https://drive.google.com/file/d/0BxGqxeGwTDLbLWJ5SExDblVhRFU
/view?usp=sharing=59be86ad

On Sun, Sep 17, 2017 at 6:35 PM, Justin Lemkul  wrote:

>
>
> On 9/17/17 1:22 AM, Vidya R wrote:
>
>> My log file is provided in the link below
>>
>> Can you please look into it and let me know why the error arises?
>>
>> I am feeding my commands in SGE cluster.   When I run it in my login node,
>> gmx mdrun -v -deffnm eql runs well
>>
>>
>> But, through qsub command, (with 8 processors) It says,
>>
>> mpirun noticed that process rank 7 with PID 19160 on node
>> compute-0-28.local exited on signal 11 (Segmentation fault).
>>
>> Please help me.
>>
>> I am unable to figure out, as to whether the problem is with the version
>> of
>> gromacs or the method of compiling.
>>
>>
>> https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU
>> /view?usp=sharing
>>
>>
> I am unable to view the file, as it says I do not have permission.  Please
> change the access restrictions on it.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
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[gmx-users] gromacs-error.docx

[Vidya R (via Google Drive)]

I've shared an item with you:

gromacs-error.docx
https://drive.google.com/file/d/0BxGqxeGwTDLbLWJ5SExDblVhRFU/view?usp=sharing=59be86ad

It's not an attachment -- it's stored online. To open this item, just click  
the link above.

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Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

[Justin Lemkul]

On 9/17/17 1:22 AM, Vidya R wrote:

My log file is provided in the link below

Can you please look into it and let me know why the error arises?

I am feeding my commands in SGE cluster.   When I run it in my login node,
gmx mdrun -v -deffnm eql runs well


But, through qsub command, (with 8 processors) It says,

mpirun noticed that process rank 7 with PID 19160 on node
compute-0-28.local exited on signal 11 (Segmentation fault).

Please help me.

I am unable to figure out, as to whether the problem is with the version of
gromacs or the method of compiling.


https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU/view?usp=sharing



I am unable to view the file, as it says I do not have permission.  Please 
change the access restrictions on it.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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