Re: Aw: [gmx-users] Umbrella sampling- force vs time plots

[rookie417]

Thanks Justin and Stephan, 

One more question, while pulling from the interior of a multiple monomer
micelle structure, I used higher force  constants (5000 kJ/mol/nm^2) for
position restraints on the reference group to keep the system intact. I am
assuming that I have to use different pull_k1 for inside and outside the
structure, due to the nature of interactions. Is that correct? I was also
wondering how g_wham evaluates the PMF for the multiple interactions inside
the system considering the position restraints and pull force constant.

Thanks again!! 



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[gmx-users] How to apply trjconv -nojump to a part of a system

[Bin Liu]

Hi All,

For the convenience of visualization, I need to remove the jump of one
component (say a protein) of the system at the boundary. I don't need to,
or say I need not to remove the jump of the other components (say a lipid
bilayer), since otherwise the system will look falling apart. I noticed I
can cluster a part of a system, then output all the atoms in the system in
which only the part is clustered, and the other components unchanged. Does
GROMACS have similar function when *-nojump* is used?

If this can not be accomplished directly, is there a way to circumvent it?
I figured out a way, but haven't implemented it. I can plug the coordinates
of the protein treated with *-nojump* into the trajectory of the whole
system which is not treated with *-nojump*. It is kind of substituting the
coordinates of one component in one trajectory with the coordinates of the
same component in another trajectory. Is there anyone aware of a tool or a
script to do this job?

Thank you very much.

Regards

Bin
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[gmx-users] Re: gInstallation Problems with Gromacs4.6

[Éric Germaneau]

Dear all,

I call cmake the following way and get the error bellow:

   CC=mpicc CXX=mpicxx
   CMAKE_PREFIX_PATH=$FFTW3DIR:$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin
   \
  /lustre/utility/bin/cmake \
   -DCMAKE_CXX_COMPILER=/xxx/xxx/intel/impi/4.1.1.036/intel64/bin/mpicxx \
   -DCMAKE_C_COMPILER=/xxx/xxx/intel/impi/4.1.1.036/intel64/bin/mpicc \
   -DFFTW_INCLUDE_DIR=$FFTW3DIR/include \
   -DFFTW_LIBRARY=$FFTW3DIR/lib/ \
   -DGMX_MPI=ON \
   -DGMX_GPU=OFF [-DCUDA_TOOLKIT_ROOT_DIR=$CUDAPATH] \
   -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
   -DGMX_X11=OFF ../$APP

   -- Looking for fftwf_plan_r2r_1d in
   /lustre/software/fftw3/fftw-3.3.3_impi/FLOAT/lib/libfftw3f.so - not
   found
   CMake Error at cmake/FindFFTW.cmake:97 (message):
  Could not find fftwf_plan_r2r_1d in
  /lustre/software/fftw3/fftw-3.3.3_impi/FLOAT/lib/libfftw3f.so,
   take a look
  at the error message in
   
/lustre/home/hpceric/soft/science/opensource/gromacs/build-4.6.3/CMakeFiles/CMakeError.log
  to find out what went wrong.  If you are using a static lib (.a)
   make sure
  you have specified all dependencies of fftw3f in FFTWF_LIBRARY by
   hand
  (e.g.  -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
   Call Stack (most recent call first):
  CMakeLists.txt:948 (find_package)

Can you please shed some light on this?
Thanks in advance,

'Eric.

--
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Éric Germaneau 

Shanghai Jiao Tong University
Network & Information Center
room 205
Minhang Campus
800 Dongchuan Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn 



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Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/

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[gmx-users] Re: Problem with Amber99SB-ILDN ff

[Melchor S.]

Sorry for the misunderstanding. I should had explained it better.

I know that is a zwitterionic residue, I have run several simulations with
the same PDB and with other forcefields. ACPYPE does not work, I tried it
yesterday, but I have to check it. Antechamber I don't know, I have to try
it.

Also I will try to find other related parameters, but I was searching
without succes. Could you suggest me something?

Thanks for all your answers



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Aw: [gmx-users] Umbrella sampling- force vs time plots

[lloyd riggs]

 

From running a bunch of these your pullf.xvg should look like a curve and taper off at the end (go down) or you didnt reach the maximum...with the force I had to play around and started with published work for similar proteins, but had to increase the force from 1000 (published) to 2000, so a large pull force (say 2500) and then looking at the pullf.xvg gives you the max peak, which you just set it slightly over this, mine was higher than published as the protein had more affinity, if you set it too low it just acts like a horminic oscillator...with the rate, I found if there is no force, only rate, it doesn't do anything pulling apart something with a high affinity, with a small molecule the pull rate worked (I only tried this a couple times)...somone may have better suggestions,

 

Stephan Watkins


Gesendet: Dienstag, 09. Juli 2013 um 18:56 Uhr
Von: rookie417 
An: gmx-users@gromacs.org
Betreff: [gmx-users] Umbrella sampling- force vs time plots

Hello all,

I am trying to understand the force vs time plots using Gromacs' umbrella
sampling method. I am trying to pull a short polymer chain from the interior
of a micelle and see what the PMF looks like. I use the following parameters
to run the pulling simulation for 500ps to pull the polymer over a distance
of 5nm:

pull=umbrella
pull_geometry=direction
pull_vec1=1 0 0
pull_start=yes
pull_ngroups=1
pull_group0=surf
pull_group1=poly
pull_rate1=0.01
pull_k1=1000

After the simulation, pullf.xvg plot I obtained is a linearly increasing
plot with time and similar result when pull_rate1=0.001 nm per ps. I am not
sure if this is right. My question is, on what basis do we select the
optimum pull_rate1 and pull_k1 for a particular system? Or is it just a
choice of parameters as long as the system does not deform? How does an
ideal force-time plot look like and does the choice of pull_k1 affect the
histogram? It appears, the entire procedure depends on the choice of input
of these two variables. I would greatly appreciate if someone can explain
this concept.

Thanks a lot.
Andy




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Re: [gmx-users] Umbrella sampling- force vs time plots

[Justin Lemkul]

On 7/9/13 12:56 PM, rookie417 wrote:

Hello all,

I am trying to understand the force vs time plots using Gromacs' umbrella
sampling method. I am trying to pull a short polymer chain from the interior
of a micelle and see what the PMF looks like. I use the following parameters
to run the pulling simulation for 500ps to pull the polymer over a distance
of 5nm:

pull=umbrella
pull_geometry=direction
pull_vec1=1 0 0
pull_start=yes
pull_ngroups=1
pull_group0=surf
pull_group1=poly
pull_rate1=0.01
pull_k1=1000



Note that what you're doing is not umbrella sampling, but steered MD, which is a 
nonequilibrium process.  The "umbrella" pulling method is unfortunately named, 
as it is just a harmonic potential.  Umbrella sampling is a separate procedure, 
one that uses the "umbrella" method and zero pull rate.



After the simulation, pullf.xvg plot I obtained is a linearly increasing
plot with time and similar result when pull_rate1=0.001 nm per ps. I am not
sure if this is right. My question is, on what basis do we select the
optimum pull_rate1 and pull_k1 for a particular system? Or is it just a
choice of parameters as long as the system does not deform? How does an


Basically, yes.  No one (to my knowledge) has done a systematic study of such 
parameters.  I suspect that is because they are largely dependent upon the 
system and the interactions you are trying to disrupt.



ideal force-time plot look like and does the choice of pull_k1 affect the
histogram?  It appears, the entire procedure depends on the choice of input
of these two variables. I would greatly appreciate if someone can explain
this concept.



There will be an initial increase in force until restoring forces are overcome, 
at which point forces decrease and level off.  I don't know about a comparison 
of force constants, but I suspect the result should be similar to varying the 
pull rate.  The progression will be steeper with faster pulling or a harder 
force constant, more shallow with slow pulling or a soft constant.  We addressed 
this topic in the supporting information for 
http://pubs.acs.org/doi/abs/10.1021/jp9110794.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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] the principle of pulling

[Justin Lemkul]

On 7/9/13 8:09 AM, wanghua wrote:

Dear,  i am doing some simulation about pulling alkane into my micelle in
umbrella sampling. i want to ask somethin about the output result in the
pullf.xvg file. In the file, there are two lines data, one is time and the
other is force.  I want to know how the force come? or is there any formula
about calculating the force? And, I do not understant the principle about


Hooke's law.


the pulling in GMX after I learing the manual. Is there any literature or
book about the pulling. Thanks in advance!



Google "steered molecular dynamics" and you'll get a ton.

-Justin

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==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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] Re: Problem with Amber99SB-ILDN ff

[Justin Lemkul]

On 7/9/13 11:23 AM, Melchor S. wrote:

I am using gromacs 4.5.5, I didn't  tell you yesterday. I have been tried a
lot of things, but without any success.

One of that I think has to work fine, is with the NGLU nomenclature, but
when I use it, I obtain this
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Edit a .n.tdb and/or
.c.tdb file.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I am really sure about the structure of the Ligand ( Glu is in a separate
chain like a ligand) so I don't know what to do.

My PDB file looks like this

...
[...]
ATOM   1896  OXT ALA A 258  -5.158  76.455 109.444  1.00 26.88  A
TER
HETATM 1932  N   NGLU B   1  18.161  74.498 104.017  1.00 24.96
HETATM 1933  CA  NGLU B   1  18.483  73.747 105.315  1.00 22.94
HETATM 1934  C   NGLU B   1  19.769  73.978 105.618  1.00 27.29
HETATM 1945  O   NGLU B   1  20.258  74.226 106.781  1.00 28.71
HETATM 1936  CB  NGLU B   1  18.262  72.255 105.280  1.00 19.40
HETATM 1937  CG  NGLU B   1  18.556  71.574 106.686  1.00 19.32
HETATM 1938  CD  NGLU B   1  17.462  71.977 107.666  1.00 21.73
HETATM 1939  OE1 NGLU B   1  16.330  72.460 107.490  1.00 22.44
HETATM 1940  OE2 NGLU B   1  17.965  71.816 108.815  1.00 30.0
HETATM 1941  OXT NGLU B   1  20.862  74.195 104.777  1.00 27.10
END



This is a very different situation, one that pdb2gmx is not equipped to cope 
with.  You don't actually have another protein chain, which your original posts 
seemed to imply.  Instead, you have a zwitterionic form of Glu, which is not 
present in your chosen force field.  You will have to derive its parameters in 
some other manner (other published parameters, acpype, antechamber, etc).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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

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Re: [gmx-users] Multiple LINCS Warnings in NVT Equillibration

[Justin Lemkul]

On 7/9/13 10:22 AM, ashish24294 wrote:

I am simulating one urea molecule in water and am struggling with it nvt.log




*The .mdp for energy minimization is*

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 100.0 ; 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
energygrps  = URE

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and 
long range forces
ns_type = grid  ; Method to determine neighbor list (simple, 
grid)
rlist   = 1.0   ; Cut-off for making neighbor list (short range 
forces)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)




/*And the nvt.mdp is:
*/
title   = UREA_in_WATER NVT equillibration

; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
energygrps  = URE
; Bond parameters
continuation= no; first dynamics run
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 cells
nstlist = 5 ; 10 fs
rlist   = 0.75   ; short-range neighborlist cutoff (in nm)
rcoulomb= 0.75   ; short-range electrostatic cutoff (in nm)
rvdw= 0.75   ; short-range van der Waals cutoff (in nm)


These cutoffs don't make sense for any of the force fields within Gromacs.  This 
is the most likely source of instability outside the topology itself.


-Justin


; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = URE_Water; two coupling groups - more accurate
tau_t   = 0.1 ; time constant, in ps
ref_t   = 300   ; reference temperature, one for
each group, in K
; Pressure coupling
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

*The resultant nvt.log has been attached*



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==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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] Frozen covalent bound atoms

[Nash, Anthony]

Hi all,

I would imagine this has been covered before, yet I don't think I have 
unearthed the right search inquiry yet.

I want to make a dihedral angle along the length of a helical protein using the 
vectors (A, B, C), (B, C, D), where B is a C-alpha on the helix backbone, and A 
, C and D are fake atoms. I need the fake atom A to be covalently 
bound/attached to C-alpha atom B, maintaining the constant angle A-B-C. I then 
need to keep a totally frozen position of fake atoms C and D, which are 
covalently bound in the order B-C-D.

All fake atoms must not interact with any atoms at all.

I don't want someone to tell me how to do it, I would just rather someone told 
me a key word/link/section in the gromacs manual.

Many thanks
Anthony
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[gmx-users] Umbrella sampling- force vs time plots

[rookie417]

Hello all,

I am trying to understand the force vs time plots using Gromacs' umbrella
sampling method. I am trying to pull a short polymer chain from the interior
of a micelle and see what the PMF looks like. I use the following parameters
to run the pulling simulation for 500ps to pull the polymer over a distance
of 5nm:

pull=umbrella
pull_geometry=direction
pull_vec1=1 0 0
pull_start=yes
pull_ngroups=1
pull_group0=surf
pull_group1=poly
pull_rate1=0.01
pull_k1=1000

After the simulation, pullf.xvg plot I obtained is a linearly increasing
plot with time and similar result when pull_rate1=0.001 nm per ps. I am not
sure if this is right. My question is, on what basis do we select the
optimum pull_rate1 and pull_k1 for a particular system? Or is it just a
choice of parameters as long as the system does not deform? How does an
ideal force-time plot look like and does the choice of pull_k1 affect the
histogram?  It appears, the entire procedure depends on the choice of input
of these two variables. I would greatly appreciate if someone can explain
this concept.

Thanks a lot.
Andy




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[gmx-users] why DGbind=0 ?

[Albert]

Hello:

 I am using glie to evaluate my ligand binding affinity with command:

g_lie_d -f md.edr -o lie.xvg -ligand LIG

but I obtained the following results:

Opened md.edr as single precision energy file
Using the following energy terms:
LJ:
Coul:
DGbind = 0.000 (0.000)

@title "LIE free energy estimate"
@xaxis  label "Time (ps)"
@yaxis  label "DGbind (kJ/mol)"
@TYPE xy
 0   0
  1000   0
  2000   0
  3000   0
  4000   0
  5000   0
  6000   0
  7000   0
  8000   0
  9000   0
 1   0
 11000   0
 12000   0
 13000   0
 14000   0
 15000   0
 16000   0
 17000   0
 18000   0
 19000   0
 2   0
 21000   0
 22000   0
 23000   0
 24000   0


I am just wondering why the result is zero?

thank you very much

Albert

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[gmx-users] Problem with running REMD in Gromacs 4.6.3

[gigo]

Dear GMXers,
With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were 
separate MPI jobs of course (OpenMPI 1.6.4). Each replica I run on 4 
cores with OpenMP. There is Torque installed on the cluster build of 
12-cores nodes, so I used the following script:


#!/bin/tcsh -f
#PBS -S /bin/tcsh
#PBS -N test
#PBS -l nodes=48:ppn=12
#PBS -l walltime=300:00:00
#PBS -l mem=288Gb
#PBS -r n
cd $PBS_O_WORKDIR
mpiexec -np 144 --loadbalance mdrun_mpi -v -cpt 20 -multi 144 -ntomp 4 
-replex 2000


It was working just great with 4.6.2. It does not work with 4.6.3. The 
new version was compiled with the same options in the same environment. 
Mpiexec spreads the replicas evenly over the cluster. Each replica forks 
4 threads, but only one of them uses any cpu. Logs end at the citations. 
Some empty energy and trajectory files are created, nothing is written 
to them.
Please let me know if you have any immediate suggestion on how to make 
it work (maybe based on some differences between versions), or if I 
should fill the bug report with all the technical details.

Best Regards,

Grzegorz Wieczorek

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[gmx-users] Re: Problem with Amber99SB-ILDN ff

[Melchor S.]

I am using gromacs 4.5.5, I didn't  tell you yesterday. I have been tried a
lot of things, but without any success.

One of that I think has to work fine, is with the NGLU nomenclature, but
when I use it, I obtain this
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Edit a .n.tdb and/or
.c.tdb file.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I am really sure about the structure of the Ligand ( Glu is in a separate
chain like a ligand) so I don't know what to do.

My PDB file looks like this 

...
[...]
ATOM   1896  OXT ALA A 258  -5.158  76.455 109.444  1.00 26.88  A 
TER
HETATM 1932  N   NGLU B   1  18.161  74.498 104.017  1.00 24.96
HETATM 1933  CA  NGLU B   1  18.483  73.747 105.315  1.00 22.94
HETATM 1934  C   NGLU B   1  19.769  73.978 105.618  1.00 27.29
HETATM 1945  O   NGLU B   1  20.258  74.226 106.781  1.00 28.71
HETATM 1936  CB  NGLU B   1  18.262  72.255 105.280  1.00 19.40
HETATM 1937  CG  NGLU B   1  18.556  71.574 106.686  1.00 19.32
HETATM 1938  CD  NGLU B   1  17.462  71.977 107.666  1.00 21.73
HETATM 1939  OE1 NGLU B   1  16.330  72.460 107.490  1.00 22.44
HETATM 1940  OE2 NGLU B   1  17.965  71.816 108.815  1.00 30.0
HETATM 1941  OXT NGLU B   1  20.862  74.195 104.777  1.00 27.10
END



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[gmx-users] Issue with g_lie

[Sainitin Donakonda]

Hi Everybody,

I want to use g_lie for my protein-drug complex to get binding energy ..i
read some information that we need take care some issues if we used PME
electrostatics..

Indeed i have used PME in my simulation..

Can any body explain which parameters to be taken care while running g_LIE
and what is the isssue with PME ..

Regards,
Sainitin
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Re: [gmx-users] Multiple LINCS Warnings in NVT Equillibration

[Matthew Zwier]

Try using -DFLEXIBLE in your minimization prior to running NVT.

MZ


On Tue, Jul 9, 2013 at 10:22 AM, ashish24294 wrote:

> I am simulating one urea molecule in water and am struggling with it
> nvt.log
> 
>
>
>
> *The .mdp for energy minimization is*
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator  = steep ; Algorithm (steep = steepest descent
> minimization)
> emtol   = 100.0 ; 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
> energygrps  = URE
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list
> and long range forces
> ns_type = grid  ; Method to determine neighbor list
> (simple, grid)
> rlist   = 1.0   ; Cut-off for making neighbor list (short
> range forces)
> coulombtype = PME   ; Treatment of long range electrostatic
> interactions
> rcoulomb= 1.0   ; Short-range electrostatic cut-off
> rvdw= 1.0   ; Short-range Van der Waals cut-off
> pbc = xyz   ; Periodic Boundary Conditions (yes/no)
>
>
>
>
> /*And the nvt.mdp is:
> */
> title   = UREA_in_WATER NVT equillibration
>
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 5 ; 2 * 5 = 100 ps
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 100   ; save coordinates every 0.2 ps
> nstvout = 100   ; save velocities every 0.2 ps
> nstenergy   = 100   ; save energies every 0.2 ps
> nstlog  = 100   ; update log file every 0.2 ps
> energygrps  = URE
> ; Bond parameters
> continuation= no; first dynamics run
> 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 cells
> nstlist = 5 ; 10 fs
> rlist   = 0.75   ; short-range neighborlist cutoff (in nm)
> rcoulomb= 0.75   ; short-range electrostatic cutoff (in nm)
> rvdw= 0.75   ; 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
> tcoupl  = V-rescale ; modified Berendsen thermostat
> tc-grps = URE_Water; two coupling groups - more accurate
> tau_t   = 0.1 ; time constant, in
> ps
> ref_t   = 300   ; reference temperature, one for
> each group, in K
> ; Pressure coupling
> pcoupl  = no; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc = xyz   ; 3-D PBC
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = yes   ; assign velocities from Maxwell distribution
> gen_temp= 300   ; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
>
> *The resultant nvt.log has been attached*
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Multiple-LINCS-Warnings-in-NVT-Equillibration-tp5009701.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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RE: [gmx-users] Re: Re: Which/What is the adequate overlap using g_BAR

[Ullmann, Thomas]

Hi Mike,

Your confusion might stem from a very simple issue.
To see the overlap of the forward and backward distributions,
you have to plot

 N(+Delta H(lambda=x) | lambda=y) and
 N(-Delta H(lambda=y) | lambda=x).

That is, you have to plot the histogram for the negative of the energy 
difference samples in the backward direction.

See also the original paper of Charles Bennett for an explanation of the 
overlap and how it is measured.

Best,
Thomas.

-
R. Thomas Ullmann, PhD 
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
-


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Mike Nemec [mike.ne...@stud.uni-due.de]
Sent: Tuesday, July 09, 2013 4:01 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: Re: Which/What is the adequate overlap using   g_BAR

>> Dear Gromacs People,
>>
>> I want to calculate free energy differences between two states A and B
>> using g_BAR.
>>
>> For this I read many papers concerning the overlap between neighboring
>> sample windows (Delta H) but I am still wondering about the following
>> issue:
>>
>> I know, that there has to be an adequate overlap to get accurate free
>> energy differences, but I am not sure, which neighboring sample
>> distributions have to overlap in the gromacs nomenclature.
>>
>> Do the neighboring distributions N(Delta H(lambda=0.05) | lambda=0) AND
>> N(Delta H(lambda=0) | lambda=0.05) have to overlap? Or shall there be an
>> overlap between neighboring distributions calculated from the left side
>>
>> N(Delta H(lambda=0.05) | lambda=0) ; N(Delta H(lambda=0.10) |
>> lambda=0.05) ; N(Delta H(lambda=0.15) | lambda=0.10) ...
>>
>> and then neighboring from the right side
>>
>> N(Delta H(lambda=0) | lambda=0.05) ; N(Delta H(lambda=0.05) |
>> lambda=0.10) ; N(Delta H(lambda=0.10) | lambda=0.15) ... ?
>>
>> I am puzzled, because if one takes a hypothetic stepsize of "1", then
>> one only gets two distributions
>>
>> N(Delta H(lambda=1) | lambda=0) AND N(Delta H(lambda=0) | lambda=1)
>>
>> which then should overlap to get a right free energy difference
>> estimation. Am I right?
>
> Perhaps I'm a bit confused on how you're presenting the question. Are you
> asking about "forward" and "reverse" transformations giving an equivalent
> result?  Keep in mind that there is no such directionality in these
> types of
> transformations, as long as you're not using a slow-growth method.
> Otherwise, I
> don't see how one can have left-handed overlap but not right-handed
> overlap in
> adjacent distributions.
Sorry for the misunderstanding. What I was asking is the following:

 From the histogram, one gets distributions, e.g. N(Delta H(lambda=0.15)
| lambda=0.10), where it is calculated at foreign lambda = 0.15 in the
lambda=0.1 trajectory. This I called "right-side" neighbor
distributions, because the foreign lambda is larger then the native
lambda. The same I called the "left-side" distributions.

> Either the neighboring lambda windows overlap or don't.
>

My problem is, that I am not sure, what "neighboring lambda windows"
means in the nomenclature of
N(Delta H(lambda=0.15) | lambda=0.10) .
As I already mentioned, if one takes a hypothetical step size equal to
1, one gets from the histogram only the two distributions
N(Delta H(lambda=1) | lambda=0) AND N(Delta H(lambda=0) | lambda=1) ,
which then should overlap, to get an adequate free energy estimation, is
that right? If they do not overlap, one has to simulate more alchemical
states inbetween. But that would result, that e.g.  N(Delta
H(lambda=0.15) | lambda=0.10) AND N(Delta H(lambda=0.10) | lambda=0.15)
have to overlap.

>> So, concluding this, the last two cases should be right, but refering
>> to the
>> "mailing-list-question" of Fabian Casteblanco
>> http://gromacs.5086.x6.nabble.com/Free-energy-sampling-using-G-bar-td4455419.html#a4455420
>>
>> Justin Lemkul replies, that "the histograms look fine [...]. Lots of
>> overlap.", which would result, that all the "left-side" and all the
>> "right-side" neighbor distributions have to overlap, I think
>>

According to the Post of Fabian Casteblanco, you (Justin Lemkul) said,
that the histogram looks o.k., so the overlap should be large enough.
But if I am looking for example at the first eight distributions of him
https://www.dropbox.com/s/dzyva125yrw8ap3/From_FabianCasteblanco.png ,
one can see the large gap between the two groups of distributions.
Concluding this, it is enough that the following distributions have to
overlap:
N(Delta H(lambda=0) | lambda=0.05) AND N(Delta H(lambda=0.05) |
lambda=0.10)
N(Delta H(lambda=0.05) | lambda=0.10) AND N(Delta H(lambda=0.10) |
lambda=0.15)
...
and the s

Re: [gmx-users] Squishing or Stretching Membranes

[Mirco Wahab]

On 09.07.2013 16:11, Neha wrote:

I had a question about trjconv. After one of my simulations has ended I want
to use the final structure file to run some other simulations. However, what
I want to do is run an NVT run using the average box size of the earlier
run. Since the final structure file will most likely not be at the exact
average I was wondering if I could use trjconv -pbc mol to put all the atoms
in a box either smaller or bigger than the original.


You could dump many structures from the last part of the trajectory, and:
 - take one structure that has all box vectors almost at, but *below*
   your target size,
 - edit the bottom line of the coordinate file to the desired size,
 - run some steps steepest descent minimization in order to correct
   for some overstretched bonds of molecules crossing the PBC,
 - run

The absolute last configuration of your run has no "specific meaning"
in a statistical sense. You can use any other configuration from
the equilibrium-part of the run.

my € 0.02

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[gmx-users] Multiple LINCS Warnings in NVT Equillibration

[ashish24294]

I am simulating one urea molecule in water and am struggling with it nvt.log
  



*The .mdp for energy minimization is*

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 100.0 ; 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
energygrps  = URE

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and 
long range forces
ns_type = grid  ; Method to determine neighbor list (simple, 
grid)
rlist   = 1.0   ; Cut-off for making neighbor list (short range 
forces)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)




/*And the nvt.mdp is:
*/
title   = UREA_in_WATER NVT equillibration

; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
energygrps  = URE
; Bond parameters
continuation= no; first dynamics run
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 cells
nstlist = 5 ; 10 fs
rlist   = 0.75   ; short-range neighborlist cutoff (in nm)
rcoulomb= 0.75   ; short-range electrostatic cutoff (in nm)
rvdw= 0.75   ; 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
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = URE_Water; two coupling groups - more accurate
tau_t   = 0.1 ; time constant, in ps
ref_t   = 300   ; reference temperature, one for
each group, in K
; Pressure coupling
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

*The resultant nvt.log has been attached*



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[gmx-users] Squishing or Stretching Membranes

[Neha]

Hello everybody,

I had a question about trjconv. After one of my simulations has ended I want
to use the final structure file to run some other simulations. However, what
I want to do is run an NVT run using the average box size of the earlier
run. Since the final structure file will most likely not be at the exact
average I was wondering if I could use trjconv -pbc mol to put all the atoms
in a box either smaller or bigger than the original. 

If that is not possible, what Gromacs tools can I use to do what I described
above?

Thanks!



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[gmx-users] Re: Re: Which/What is the adequate overlap using g_BAR

[Mike Nemec]

Dear Gromacs People,

I want to calculate free energy differences between two states A and B
using g_BAR.

For this I read many papers concerning the overlap between neighboring
sample windows (Delta H) but I am still wondering about the following 
issue:


I know, that there has to be an adequate overlap to get accurate free
energy differences, but I am not sure, which neighboring sample
distributions have to overlap in the gromacs nomenclature.

Do the neighboring distributions N(Delta H(lambda=0.05) | lambda=0) AND
N(Delta H(lambda=0) | lambda=0.05) have to overlap? Or shall there be an
overlap between neighboring distributions calculated from the left side

N(Delta H(lambda=0.05) | lambda=0) ; N(Delta H(lambda=0.10) |
lambda=0.05) ; N(Delta H(lambda=0.15) | lambda=0.10) ...

and then neighboring from the right side

N(Delta H(lambda=0) | lambda=0.05) ; N(Delta H(lambda=0.05) |
lambda=0.10) ; N(Delta H(lambda=0.10) | lambda=0.15) ... ?

I am puzzled, because if one takes a hypothetic stepsize of "1", then
one only gets two distributions

N(Delta H(lambda=1) | lambda=0) AND N(Delta H(lambda=0) | lambda=1)

which then should overlap to get a right free energy difference
estimation. Am I right?


Perhaps I'm a bit confused on how you're presenting the question. Are you
asking about "forward" and "reverse" transformations giving an equivalent
result?  Keep in mind that there is no such directionality in these 
types of
transformations, as long as you're not using a slow-growth method.  
Otherwise, I
don't see how one can have left-handed overlap but not right-handed 
overlap in
adjacent distributions. 

Sorry for the misunderstanding. What I was asking is the following:

From the histogram, one gets distributions, e.g. N(Delta H(lambda=0.15) 
| lambda=0.10), where it is calculated at foreign lambda = 0.15 in the 
lambda=0.1 trajectory. This I called "right-side" neighbor 
distributions, because the foreign lambda is larger then the native 
lambda. The same I called the "left-side" distributions.



Either the neighboring lambda windows overlap or don't.



My problem is, that I am not sure, what "neighboring lambda windows" 
means in the nomenclature of

N(Delta H(lambda=0.15) | lambda=0.10) .
As I already mentioned, if one takes a hypothetical step size equal to 
1, one gets from the histogram only the two distributions

N(Delta H(lambda=1) | lambda=0) AND N(Delta H(lambda=0) | lambda=1) ,
which then should overlap, to get an adequate free energy estimation, is 
that right? If they do not overlap, one has to simulate more alchemical 
states inbetween. But that would result, that e.g.  N(Delta 
H(lambda=0.15) | lambda=0.10) AND N(Delta H(lambda=0.10) | lambda=0.15) 
have to overlap.


So, concluding this, the last two cases should be right, but refering 
to the

"mailing-list-question" of Fabian Casteblanco
http://gromacs.5086.x6.nabble.com/Free-energy-sampling-using-G-bar-td4455419.html#a4455420 


Justin Lemkul replies, that "the histograms look fine [...]. Lots of
overlap.", which would result, that all the "left-side" and all the
"right-side" neighbor distributions have to overlap, I think



According to the Post of Fabian Casteblanco, you (Justin Lemkul) said, 
that the histogram looks o.k., so the overlap should be large enough. 
But if I am looking for example at the first eight distributions of him

https://www.dropbox.com/s/dzyva125yrw8ap3/From_FabianCasteblanco.png ,
one can see the large gap between the two groups of distributions. 
Concluding this, it is enough that the following distributions have to 
overlap:
N(Delta H(lambda=0) | lambda=0.05) AND N(Delta H(lambda=0.05) | 
lambda=0.10)
N(Delta H(lambda=0.05) | lambda=0.10) AND N(Delta H(lambda=0.10) | 
lambda=0.15)

...
and the same if the foreign lambda is smaller than the current one.
Why is this true? Which distributions in detail have to overlap? And why 
should not e.g.  N(Delta H(lambda=0.05) | lambda=0.10) AND N(Delta 
H(lambda=0.05) | lambda=0) overlap, as they are distributions at 
lambda=0.05 calculated from an arbitrary state A (lambda=0) and an 
arbitrary state B (lambda=0.10)? Maybe there is a simple point I just do 
not see or do not understand... I would be really glad, if someone could 
clarify this for me, because it is an important point for validating the 
method.



Depending on your answer, can you please explain, why thedistributions
of your answer have to overlap, and not the others?


For this case I calculated the free energy difference with g_BAR of one
tripeptide Valine-Leucine-Valine where thepartial charges of the Leucine
are turned to "0" from state A to B in steps of "0.02" (see attachement,


At the following URLs
https://www.dropbox.com/s/crwucp7uwutisly/Overlap.png
https://www.dropbox.com/s/17jouggywkwm1fi/Overlap_VLV_L2V_DTA1_OFF_Histo.xvg.pdf
you see at the distributions I get from decharging the partial charges 
of Leucine. For me, it looks very similar to the histogram generated by 
Fabian Casteblanco.

[gmx-users] the principle of pulling

[wanghua]

Dear,  i am doing some simulation about pulling alkane into my micelle in
umbrella sampling. i want to ask somethin about the output result in the
pullf.xvg file. In the file, there are two lines data, one is time and the
other is force.  I want to know how the force come? or is there any formula
about calculating the force? And, I do not understant the principle about
the pulling in GMX after I learing the manual. Is there any literature or
book about the pulling. Thanks in advance!



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[gmx-users] the principle of pulling

[????]

Dear,  i am doing some simulation about pulling alkane into my micelle in 
umbrella sampling. i want to ask somethin about the output result in the 
pullf.xvg file. In the file, there are two lines data, one is time and the 
other is force.  I want to know how the force come? or is there any formula 
about calculating the force? And, I do not understant the principle about the 
pulling in GMX after I learing the manual. Is there any literature or book 
about the pulling. Thanks in advance!-- 
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[gmx-users] Re: g_cluster

[maggin]

hi, Justin

I read the paper Daura(1999) 
and other papers:
"Ensemble-based convergence analysis of biomolecular trajectories"(2006)
"Helix propensities of short peptide: Molecular dynamics versus
bioinformatics" (2003)
"Assessing equilibration and convergence in biomolecular simulation" (2002)

but it seems no clearly concrete answer how to operation to do convergence
analysis based on cluster analysis.

So, I still confused  a quantitative justification for the simulations'
convergence from g_cluster.

Thank you very much!

maggin



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Re: [gmx-users] Get some specific frames of traj

[Justin Lemkul]

On 7/9/13 7:14 AM, Shima Arasteh wrote:

I tried the tpr file for -s, but doesn't make difference.


g_select -s npt_6.gro -f md_0_1.trr -select 'resname SOL and within 0.01
of (3.6, 3.6, 6.3)' -seltype res_com -selrpos res_com -os

Would you please give me suggestions? I found some resemble commands in mailing 
list but didn't find the problem with my command.



Use brackets instead of parenthesis.  I think there is a typo in the help 
information that was recently fixed.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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] Which/What is the adequate overlap using g_BAR

[Justin Lemkul]

On 7/8/13 4:27 PM, mike.ne...@stud.uni-due.de wrote:

Dear Gromacs People,

I want to calculate free energy differences between two states A and B
using g_BAR.

For this I read many papers concerning the overlap between neighboring
sample windows (Delta H) but I am still wondering about the following issue:

I know, that there has to be an adequate overlap to get accurate free
energy differences, but I am not sure, which neighboring sample
distributions have to overlap in the gromacs nomenclature.

Do the neighboring distributions N(Delta H(lambda=0.05) | lambda=0) AND
N(Delta H(lambda=0) | lambda=0.05) have to overlap? Or shall there be an
overlap between neighboring distributions calculated from the left side

N(Delta H(lambda=0.05) | lambda=0) ; N(Delta H(lambda=0.10) |
lambda=0.05) ; N(Delta H(lambda=0.15) | lambda=0.10) ...

and then neighboring from the right side

N(Delta H(lambda=0) | lambda=0.05) ; N(Delta H(lambda=0.05) |
lambda=0.10) ; N(Delta H(lambda=0.10) | lambda=0.15) ... ?

I am puzzled, because if one takes a hypothetic stepsize of "1", then
one only gets two distributions

N(Delta H(lambda=1) | lambda=0) AND N(Delta H(lambda=0) | lambda=1)

which then should overlap to get a right free energy difference
estimation. Am I right?


Perhaps I'm a bit confused on how you're presenting the question.  Are you 
asking about "forward" and "reverse" transformations giving an equivalent 
result?  Keep in mind that there is no such directionality in these types of 
transformations, as long as you're not using a slow-growth method.  Otherwise, I 
don't see how one can have left-handed overlap but not right-handed overlap in 
adjacent distributions.  Either the neighboring lambda windows overlap or don't.



So, concluding this, the last two cases should be right, but refering to the
"mailing-list-question" of Fabian Casteblanco
http://gromacs.5086.x6.nabble.com/Free-energy-sampling-using-G-bar-td4455419.html#a4455420
Justin Lemkul replies, that "the histograms look fine [...]. Lots of
overlap.", which would result, that all the "left-side" and all the
"right-side" neighbor distributions have to overlap, I think

Depending on your answer, can you please explain, why thedistributions
of your answer have to overlap, and not the others?


For this case I calculated the free energy difference with g_BAR of one
tripeptide Valine-Leucine-Valine where thepartial charges of the Leucine
are turned to "0" from state A to B in steps of "0.02" (see attachement,
representative 4 neighboring distributions). In the case, that all the
"left side calculated" and all the "right side calculated" neighbor
distributions have to overlap, the overlap in the attached file is great,
isn't it?
But is that really the correct overlap?



The list does not accept attachments.  Please provide a URL to share the file.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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] Get some specific frames of traj

[Shima Arasteh]

I tried the tpr file for -s, but doesn't make difference. 


g_select -s npt_6.gro -f md_0_1.trr -select 'resname SOL and within 0.01 
of (3.6, 3.6, 6.3)' -seltype res_com -selrpos res_com -os

Would you please give me suggestions? I found some resemble commands in mailing 
list but didn't find the problem with my command.

Thanks in advance.


Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Monday, July 8, 2013 9:14 PM
Subject: Re: [gmx-users] Get some specific frames of traj



On 7/8/13 7:50 AM, Shima Arasteh wrote:
> Thanks for your earlier suggestions.
> I used the command
> g_select -s npt_6.gro -f md_0_1.trr -select 'resname SOL and within 0.1 of 
> (36.0, 36.0, 63.0)' -seltype res_com -selrpos res_com -os
> to find water molecule around a specified coordinate. But I  get this error:
> Input error or input inconsistency:
> selection(s) could not be parsed
>
>
> Would you please help me with this command? I have not yet tried g_select 
> command.
>

g_select -select 'help all' provides a huge amount of information.  Have you 
tried passing a .tpr file to -s instead?  Are your units right?  It would seem 
your box is very big.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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] g_cluster

[Justin Lemkul]

On 7/9/13 6:10 AM, maggin wrote:

Hi,

I have a qustion how to use g_cluster to judge convergence of the simulation
of peptide ?



Clustering can give you some insight into how homogeneous your structural 
ensemble is.  That is one way to assess convergence.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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] cuda problem

[Szilárd Páll]

On Tue, Jul 9, 2013 at 11:20 AM, Albert  wrote:
> On 07/09/2013 11:15 AM, Szilárd Páll wrote:
>>
>> Tesla C1060 is not compatible - which should be shown in the log and
>> standard output.
>>
>> Cheers,
>> --
>> Szilárd
>
>
> THX for kind comments.
>
> do you mean C1060 is not compatible with cuda-5.0 toolkit? or it is not
> compatable with Gromacs-4.6.3?I only obtained the following information in
> the log file
>
>
> 2 GPUs detected on host c0107:
>   #0: NVIDIA Tesla C2075, compute cap.: 2.0, ECC: yes, stat: compatible
>   #1: NVIDIA Tesla C2075, compute cap.: 2.0, ECC: yes, stat: compatible
>
> 2 GPUs auto-selected for this run: #0, #1

Those are not C1060-s (which is compute capability 1.3, hence not
compatible with GROMACS), but C2075-s!

>
> NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0, known
> to
>   cause performance loss. Switching to the alternative polling GPU wait.
>   If you encounter issues, switch back to standard GPU waiting by
> setting
>   the GMX_CUDA_STREAMSYNC environment variable.

As I said before, this refer to the NVIDIA driver. You can ignore
this, but you'd be better off with newer drivers.

>
> Non-default thread affinity set probably by the OpenMP library,
> disabling internal thread affinity

This means that either you, or the job scheduler set GOMP_CPU_
AFFINITY or KMP_AFFINITY. This may affect performance negatively, but
you'll have to try yourself.

--
Szilárd

>
>
> best
>
> Albert
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[gmx-users] g_cluster

[maggin]

Hi,

I have a qustion how to use g_cluster to judge convergence of the simulation
of peptide ?

Thank you very much!

maggin







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Re: [gmx-users] Xe atom

[Dr. Vitaly Chaban]

Is this, http://en.wikipedia.org/wiki/Xenon, your "Xe" ? If so, it will
obviously not sit in the binding site


Dr. Vitaly V. Chaban


On Tue, Jul 9, 2013 at 10:39 AM, Divya Sunil wrote:

> thanks for the reply.. I am planning to place Xe in the protein binding
> site ( just like a metal atom). I made a topology file with xe charge and
> mass. I have two options to implement the simulation. 1. like
> protein-ligand simulation. 2. replacing a number of solvent (water)
> molecules with xe in the cubic system. for these purposes what is the
> correct procedure?... do I need to simply add the xe parameters to .gro
> file and topol file?  or may i need to make changes in forcefield?  pls help
>
> Thanking you
> Divya
>
>
> On 8 July 2013 19:16, Dr. Vitaly Chaban  wrote:
>
>> I am a too curious person not to ask WHY Xe is of interest in connection
>> with the protein..?
>>
>>
>> Dr. Vitaly V. Chaban
>>
>>
>> On Mon, Jul 8, 2013 at 6:45 PM, Justin Lemkul  wrote:
>>
>> >
>> >
>> > On 7/8/13 9:21 AM, divyasunil wrote:
>> >
>> >> Hello,
>> >>
>> >> Please help me to add Xe atom to GROMOS96 53a6 force field. I need to
>> >> carry
>> >> out a protein-Xe simulation . I tried myself but failed.
>> >>
>> >>
>> >
>> >
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>
>
>
> --
> "A man is great by deeds, not by birth."
>
> ##
> Dr. Divya G. Nair
> Post Doctoral Fellow
> Institute of Biophysics and Physical Biochemistry
> University of Regensburg
> Regensburg-93040
> Germany
> ##
>
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Re: [gmx-users] cuda problem

[Albert]

On 07/09/2013 11:15 AM, Szilárd Páll wrote:

Tesla C1060 is not compatible - which should be shown in the log and
standard output.

Cheers,
--
Szilárd


THX for kind comments.

do you mean C1060 is not compatible with cuda-5.0 toolkit? or it is not 
compatable with Gromacs-4.6.3?I only obtained the following information 
in the log file



2 GPUs detected on host c0107:
  #0: NVIDIA Tesla C2075, compute cap.: 2.0, ECC: yes, stat: compatible
  #1: NVIDIA Tesla C2075, compute cap.: 2.0, ECC: yes, stat: compatible

2 GPUs auto-selected for this run: #0, #1


NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0, 
known to
  cause performance loss. Switching to the alternative polling GPU 
wait.
  If you encounter issues, switch back to standard GPU waiting by 
setting

  the GMX_CUDA_STREAMSYNC environment variable.


Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity



best
Albert
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Re: [gmx-users] cuda problem

[Szilárd Páll]

Tesla C1060 is not compatible - which should be shown in the log and
standard output.

Cheers,
--
Szilárd


On Tue, Jul 9, 2013 at 10:54 AM, Albert  wrote:
> Dear:
>
>  I've installed a gromacs-4.6.3 in a GPU cluster, and I obtained the
> following information for testing:
>
> NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0, known
> to
>   cause performance loss. Switching to the alternative polling GPU wait.
>   If you encounter issues, switch back to standard GPU waiting by
> setting
>   the GMX_CUDA_STREAMSYNC environment variable.
>
> The cuda version in the GPU cluster is 4.2 and the GPU is: Tesla C1060
>
> I notice that the performanc is really slow. I am just wondering how can we
> solve this problem? which directory should I set up for GMX_CUDA_STREAMSYNC?
>
> THX
>
> Albert
> --
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Re: [gmx-users] cuda problem

[Szilárd Páll]

PS: the error message is referring the to *driver* version, not the
CUDA toolkit/runtime version.
--
Szilárd


On Tue, Jul 9, 2013 at 11:15 AM, Szilárd Páll  wrote:
> Tesla C1060 is not compatible - which should be shown in the log and
> standard output.
>
> Cheers,
> --
> Szilárd
>
>
> On Tue, Jul 9, 2013 at 10:54 AM, Albert  wrote:
>> Dear:
>>
>>  I've installed a gromacs-4.6.3 in a GPU cluster, and I obtained the
>> following information for testing:
>>
>> NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0, known
>> to
>>   cause performance loss. Switching to the alternative polling GPU wait.
>>   If you encounter issues, switch back to standard GPU waiting by
>> setting
>>   the GMX_CUDA_STREAMSYNC environment variable.
>>
>> The cuda version in the GPU cluster is 4.2 and the GPU is: Tesla C1060
>>
>> I notice that the performanc is really slow. I am just wondering how can we
>> solve this problem? which directory should I set up for GMX_CUDA_STREAMSYNC?
>>
>> THX
>>
>> Albert
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] cuda problem

[Albert]

Dear:

 I've installed a gromacs-4.6.3 in a GPU cluster, and I obtained the 
following information for testing:


NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0, 
known to
  cause performance loss. Switching to the alternative polling GPU 
wait.
  If you encounter issues, switch back to standard GPU waiting by 
setting

  the GMX_CUDA_STREAMSYNC environment variable.

The cuda version in the GPU cluster is 4.2 and the GPU is: Tesla C1060

I notice that the performanc is really slow. I am just wondering how can 
we solve this problem? which directory should I set up for 
GMX_CUDA_STREAMSYNC?


THX

Albert
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Re: [gmx-users] Xe atom

[Divya Sunil]

thanks for the reply.. I am planning to place Xe in the protein binding
site ( just like a metal atom). I made a topology file with xe charge and
mass. I have two options to implement the simulation. 1. like
protein-ligand simulation. 2. replacing a number of solvent (water)
molecules with xe in the cubic system. for these purposes what is the
correct procedure?... do I need to simply add the xe parameters to .gro
file and topol file?  or may i need to make changes in forcefield?  pls help

Thanking you
Divya


On 8 July 2013 19:16, Dr. Vitaly Chaban  wrote:

> I am a too curious person not to ask WHY Xe is of interest in connection
> with the protein..?
>
>
> Dr. Vitaly V. Chaban
>
>
> On Mon, Jul 8, 2013 at 6:45 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 7/8/13 9:21 AM, divyasunil wrote:
> >
> >> Hello,
> >>
> >> Please help me to add Xe atom to GROMOS96 53a6 force field. I need to
> >> carry
> >> out a protein-Xe simulation . I tried myself but failed.
> >>
> >>
> >
> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> 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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##
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RE: [gmx-users] Stimulation stopped at 2ns

[Florian Dommert]

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Nuno Azoia
> Sent: Monday, July 08, 2013 11:21 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Stimulation stopped at 2ns
> 
> On 8 July 2013 22:12, Justin Lemkul  wrote:
> 
> >
> >
> > On 7/8/13 5:08 PM, Rama Krishna Koppisetti wrote:
> >
> >> Thanks Justin for your reply,
> >>
> >> I found something like this, in .log file,nsteps=100 but in .mdp
file
> >>
> >
> > Then you're not using the .mdp file you think you are and the run is
only
> > scheduled for 2 ns.
> 
> 
> After changing the .mdp file, did you run grompp again? And did you get a
> new .tpr file? I already had a similar problem. Sometimes; and I not sure
> about the gromacs version on that time, I just run grompp with new
> parameters in the .mdp file but grompp did not change the .tpr file, if
> already present.
> 

Did you already ran gmxdump on the tpr file you used? Then you will
immediately see, how many steps are set in the tpr file.

/Flo


> 
> Cheers
> Nuno Azoia
> 
> >
> >
> >  it is nsteps=500. I don't see any stdout and stderr files.
> >>
> >>
> > These are standard streams, not files.  Some queuing systems and other
> > software save their output, others don't.
> >
> > -Justin
> >
> >
> >  __**_
> >> On Mon, Jul 8, 2013 at 3:50 PM, Justin Lemkul  wrote:
> >>
> >>
> >>>
> >>> On 7/8/13 4:33 PM, Rama wrote:
> >>>
> >>>  Dear All,
> 
>  I'm trying to do long stimulation run but every time it stops at 2ns,
>  below
>  pasted .mdp file parameters. How to run 10ns or more ns stimulation
run?
>  Do
>  I need to change any parameters in .mdp file or else where.
> 
> 
>   There is nothing in the .mdp file that would cause the run to stop.
> >>>   Either the simulation is crashing or you have some queuing system
that
> >>> is
> >>> terminating the job.  Check stdout, stderr, and .log file(s) for
> >>> information.
> >>>
> >>> -Justin
> >>>
> >>>
> >>>   Thanks in Advance.
> >>>
>  -
> 
>  title   = Protein-DMPC bilayer Production MD
>  ; Run parameters
>  integrator  = md; leap-frog integrator
>  nsteps  = 500   ; 2 * 500 = 1 ps (10 ns)
>  dt  = 0.002 ; 2 fs
>  ; Output control
>  nstxout = 10; save coordinates every 200
ps
>  nstvout = 10; save velocities every 200
ps
>  nstxtcout   = 5 ; xtc compressed trajectory output
every
>  100 ps
>  nstenergy   = 5 ; save energies every 100 ps
>  nstlog  = 10; update log file every 200
ps
>  ; Bond parameters
>  continuation= yes   ; Restarting after NPT
>  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   = 1.2   ; short-range neighborlist cutoff (in
>  nm)
>  rcoulomb= 1.2   ; short-range electrostatic cutoff
(in
>  nm)
>  rvdw= 1.2   ; 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  = Nose-Hoover   ; More accurate
thermostat
>  tc-grps = CA_ZN_DMPC_ProteinSOL_CL  ; three coupling
groups
>  -
>  more accurate
>  tau_t   =   0.5   0.5
> ; time
>  constant, in ps
>  ref_t   =   310   310
> ; 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   = 2.0   ; time constant, in
ps
>  ref_p   = 1.0   1.0 ; reference pressure,
>  x-y, z (in bar)
>  compressibility = 4.5e-54.5e-5  ; isothermal compressibility,
>  bar^-1
>  ; Periodic boundary conditions
>  pbc = xyz   

RE: [gmx-users] Calculating shear viscosity using none-equilibrium MD: Viscosity dependent on acceleration magnitude

[Florian Dommert]

Hi,

 I am not an expert in non-EQ MD, but a simulation time of 1ns for a
collective property in a honey-like substance like an IL sounds very short.
However, from my colleagues in the group of Prof. Müller-Plathe, who applied
non-EQ MD to derive viscosities, I heard that this method is quite reliable.
Take a look at their papers. As far as I can remember, the first authors of
the papers were Whei Zhao or Simon Butler.

/Flo

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Boning Wu
> Sent: Tuesday, July 09, 2013 3:00 AM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Calculating shear viscosity using none-equilibrium
MD:
> Viscosity dependent on acceleration magnitude
> 
> Hi GMX Users,
>I want to calculate the shear viscosity of an ionic liquid. Thus I
> applied the cos-acceleration in my box. However, I found that my
calculated
> viscosity got by "g_energy" is significantly dependent on magnitude of the
> acceleration. I don't know why. Even if this is a none-Newton liquid,why
> viscosity cannot converge at such a slow acceleration  My system consists
> of 216 ion pairs, and it has been equibrated under NPT for 5 ns. The box
> length is about 5 nm.
> 
> ***
> Magnitude of the acceleration(nm/ps2)   Viscosity(cP)
> 0.01 6102
> 0.03 4452
> 0.06 3580
> 0.1   872
> 0.5   48.5
> Experimental Value85
> ***
> Here is my mdp file
> 
> **
> title=  
> cpp  = /lib/cpp
> define   =
> integrator   = md
> dt   = 0.001
> nsteps   = 100
> nstxout  = 5
> nstvout  = 5
> nstlog   = 5
> nstenergy= 100
> nstxtcout= 5000
> xtc-grps =  
> nstlist  = 10
> ns-type  = grid
> rlist= 1.5
> coulombtype  = PME
> rcoulomb = 1.5
> rvdw = 1.5
> tcoupl   = Berendsen
> tc-grps  =  
> tau-t= 0.1 0.1
> ref-t= 298 298
> Pcoupl   = NO
> ref-p= 1.0
> gen-vel  = yes
> gen-temp = 298
> gen-seed = 173529
> constraints  = none
> cos-acceleration = 0.5
> ***
> Thank you advance for your help!
> Boning
> 
> --
> Boning Wu
> Graduate student
> Department of Chemistry and Chemical Biology
> Rutgers, the State University of New Jersey
> Piscataway, NJ, 08854
> boning...@rutgers.edu
> --
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RE: [gmx-users] g_current

[Florian Dommert]

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Nilesh Dhumal
> Sent: Tuesday, July 09, 2013 5:06 AM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] g_current
> 
> Thanks for reply.
> 
> Still I have a question why it is -inf  (infinity)  at the end.

This is a good question. At the moment, the only thing I can imagine is a
faulty normalization, because the value of the integral at t=0 equals always
zero. However, if you integrate the first row with another tool, such as
g_analyze for example, the same values as in the second row show appear.

As soon as I have some time left, I will take a look at the code and report
back. 

/Flo

> 
> Nilesh
> 
> > Hi,
> >
> >  I would say the problem is too less statistics. In the paper where the
> > tool
> > was introduced, a simulation of 100ns has been performed in order to
> > achieved sufficient sampling.
> >
> > The order of magnitude is given due to the units.
> >
> > Simulate for a longer time to get rid of the noise. Calculating these
kind
> > of correlations functions is really not a simple task.
> >
> > Schroeder et al. have published an article about fitting of dielectric
> > spectra for ionic liquids, where this problem is discussed in detail.
> >
> > Cheers,
> > Flo
> >
> >> -Original Message-
> >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> >> boun...@gromacs.org] On Behalf Of Nilesh Dhumal
> >> Sent: Monday, July 08, 2013 10:32 PM
> >> To: gmx-users@gromacs.org
> >> Subject: [gmx-users] g_current
> >>
> >> Hello,
> >> I am calculating the correlation of rotational and translation dipole
> >> moment of ionic liquids. I run the 1 ns simulation and saved the
> >> trajectory at 1 fs.
> >>
> >> g_current -f md.trr -s md.tpr -n index.ndx -mc
> >>
> >> I selected "system" group.
> >>
> >> Here I pasted the initial j(t) vales and the final value is infinity.
> >>
> >> # This file was created Sun Jul  7 20:51:59 2013
> >> # by the following command:
> >> # g_current -f md.trr -s md.tpr -e 10.0 -mc
> >> #
> >> # g_current is part of G R O M A C S:
> >> #
> >> # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
> >> #
> >> @title "M\sD\N - current  autocorrelation function"
> >> @xaxis  label "Time (ps)"
> >> @yaxis  label "< M\sD\N (0)\c7\CJ(t) >  (e nm/ps)\S2"
> >> @TYPE xy
> >> # time   M_D(0) J(t) acf Integral acf
> >> 0.000   -5.20584e-15 0
> >> 0.001   -6.97466e-15-1.42702e-17
> >> 0.002   -6.97511e-15-5.25081e-17
> >> 0.003   -6.97474e-15-9.07484e-17
> >> 0.004   -6.97391e-15-1.28987e-16
> >>
> >>
> >>
> >> Why final value is infinity? If I do autocorrelation function of these
> >> values, I get all values 0.
> >>
> >> Why J(t)values are in range of e-15?
> >>
> >> Nilesh
> >>
> >>
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
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> >
> 
> 
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