[gmx-users] umbrella sampling

[spss4]

Hi all
I am trying to do umbrella sampling of protein with radius of gyration as
reaction coordinate using gromacs-2016.3 patched with plumed-2.3.2. I have
chosen 13 configurations of protein for sampling. Now I want to analyse the
data. So how to plot histogram and PMF w.r.t radius of gyartion? Can anyone
help me? I am new in this field.

Thanks
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[gmx-users] average pressure

[Mahboobeh Eslami]

Hi all GMX usereI have a large system composed of three protein chains. I 
simulated it in a triclinic box. I used Parrinello-Rahman with tau-p=2  in NPT 
equilibration step for 1000 ps. When I checked average pressure in this step, I 
find an average pressure of ~ 22 bar, rather than 1 bar. I extended this step 
for 3000 ps but I get similar value for average pressure. Which parameter must 
I change to get better average pressure?Please guide meThank you so much
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[gmx-users] average pressure

[Mahboobeh Eslami]

Hi all GMX usereI have a large system composed of three protein chains. I 
simulated it in a triclinic box. I used Parrinello-Rahman with tau-p=2  in NPT 
equilibration step. When I checked average pressure in this step, I find an 
average pressure of ~ 22 bar, rather than 1 bar. Which parameter must I change 
to get better average pressure?Please guide meThank you so mich 
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[gmx-users] 2016.3 build issues Cray/KNL/HPC system, hwloc

[Sedova, Ada A.]

Hi,


I'm trying to build 2016.3 on the new ornl KNL which is, also, a cray. I 
succeeded multiple times using Intel PrgEnv to get the cmake to finish without 
error, using:


make .. -DCMAKE_INSTALL_PREFIX=/ccs/home/adaa/gromacs-2016.3/Install 
-DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_BUILD_HELP=OFF -DGMX_HWLOC=OFF 
-DGMX_SIMD=AVX_512_KNL -DGMX_FFT_LIBRARY=mkl -DGMX_OPENMP_MAX_THREADS=256 > 
1.out 2> 2.out

and also, with the -DBUILD_SHARED_LIBS=OFF option as well. Some of these flags 
I got from this website from Intel:

https://software.intel.com/en-us/articles/recipe-building-and-running-gromacs-on-intel-processors

After having some trouble getting cmake to complete without error. This was 
while trying both GCC programming environment, and with/without fftw module 
loaded. No matter what library paths and include paths I gave, cmake was unable 
to find required libraries until I used mkl and Intel compiler/PrgEnv.

Now, when I try to make, it crashed while attempting several compile lines in 
share/template/CMakeFiles/template.dir/link.txt and 
src/programs/CMakeFiles/gmx.dir/link.txt. I manually removed the -lhwloc flag 
and was able to make it past 98% to 100%. Then I get bunch more errors 
regarding hwloc, which can't be fixed as easily.

I saw some threads regarding this:

https://redmine.gromacs.org/issues/1919#change-14889

and I was wondering if there is any way to disable hwloc in the build, or some 
other work around. The
-DGMX_HWLOC=OFF flag apparently does not do it. I was having some trouble with 
using dynamic libraries, and I think cray does not really like the use of 
static libraries, at least on this system.

Calling hwloc from the machine's home node returns an unknown command error.

Thanks,

Ada





Ada Sedova

Postdoctoral Research Associate

Scientific Computing Group, NCCS

Oak Ridge National Laboratory, Oak Ridge, TN
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[gmx-users] COM-Pulling-Non linearity of pulled group

[Haidy Metwally]

Hello,


I tried to do COM-pulling simulation (using Gromacs 5 .0.4) to pull a molecule  
away from sodium ion that is bound to acidic site of protein. My reference 
group is protein backbone. I do that in presence of solvent. The main problem 
is that my pulled group is not pulled in linear fashion, it rotates around the 
solvent droplet so  when it is being pulled it shuffle around in different 
directions.  This happens even if I changed the pull-geometry to direction 
using a vector. Also, I tried to change the pull -dimension from YYY to NNY and 
the movement was not in z- direction.The only way I can get rid of that 
rotation or shuffling around is do my pulling without solvent and I need to see 
the pulling effect in the presence of solvent. I wonder if there is a 
possibility that my reference group is moving in the solvent and so the spring 
moves with it,although the reference is supposed to be fixed.


Can anyone help me in that?


Any suggestions will be appreciated


Here is a copy of my .mdp file
title   = Umbrella pulling simulation
define  = -DPOSRES_Protein

; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 25; 500 ps
nstcomm = 10
; Output parameters
nstxout = 5000  ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout   = 500   ; every 1 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes   ; continuing from md run
; Single-range cutoff scheme
nstlist = 50
ns_type = simple
cutoff-scheme   =  verlet
comm_mode =  linear
coulombtype =  cut-off
vdwtype =  cut-off
rlist  = 333.3
rcoulomb= 333.3
rvdw= 333.3
Tcoupl= nose-hoover
ref_t= 370
tau_t   = 0.5
tc-grps= system
nsttcouple  = 1
;Pressure coupling
Pcoupl  = NO
;Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Pull code
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim   = Y Y Y
pull_start   = yes   ; define initial COM distance > 0
pull_ngroups = 2
pull_ncoords  = 1
pull_group1_name= X ;its is called like that in 
index file
pull_group2_name= Backbone
pull_coord1_groups  = 1 2
pull_coord1_rate= 0.02  ;
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2


Thanks alot

Best Regards,

Haidy Metwally

PhD. Candidate




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Re: [gmx-users] gmx mindist

[Justin Lemkul]

On 8/31/17 4:06 AM, ‪Mohammad Roostaie‬ ‪ wrote:

Hi,
Which distance does the gmx mindist command compute? Is it the minimum distance 
between the center of mass of the first group due to the other group?


It's explained in the second sentence of the help text.

-Justin

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Re: [gmx-users] Energy drift combining tabulated potentials and group cut-off.

[Mark Abraham]

Hi,

There's not easy answers to such questions. A practical implementation of
MD that can actually do most relevant kinds of science in relevant time
frames can't have bitwise conservation. Drift accumulates from multiple
aspects of the implementation, too, including the system size, and
constraint algorithm, which can dominate over the effects of missing
interactions over the lifetime of pair lists. See the discussion in the
GROMACS reference manual, e.g. figure 3.5.

One proper question to ask is at what point your protocol correctly models
whatever relevant physical data exists that is relevant to what you want to
observe. Drift that is too large is likely to affect observables, but will
affect different ones differently.

Mark

On Fri, Sep 1, 2017 at 12:12 PM  wrote:

> Dear GROMACS Community,
>
> I am trying to do a simulation using a tabulated potential which forces
> me to use the group cut-off. I get a drift in the conserved quantity of
> -600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules
> and a Na+ ion. I imagine that eventhough it will soon be deprecated the
> group cutoff scheme still works correctly. I have tryed to change the
> parameters without success and in any case the ones I use seem
> reasonable (in my experience using other programs). The rdfs of the
> system look normal so I ruled out topology problems.
>
> It seems that the problem is in the group cut-off since
> when I change the tabulated potential for a regular vdw the problem
> persists. I have followed the instructions of:
>
> http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf
>
> to implement the tabulated potentials.
>
> Is this the kind of energy drift acceptable? I have pasted a copy .mdp
>
> Thanks for your help,
>
> Sergio Perez-Conesa
>
> integrator = md
> dt = 0.001
> nsteps = 10
> init-step = 0
> cutoff-scheme = group
> nst-list = 1
> verlet-buffer-tolerance = 0.0005
> ns-type = grid
> rlist = 1.3
> pbc = xyz
> coulombtype = PME-switch
> rcoulomb = 1.
> rcoulomb-switch = 0.95
> pme-order = 4
> fourierspacing = 0.1
> ewald-rtol = 1.e-5
> vdwtype = user
> rvdw = 1.0
> DispCorr = No
> tcoupl = v-rescale
> tc-grps = System
> ;nsttcouple = 1
> tau-t = ref-t = 300.0
> constraints = all-angles
> constraint-algorithm = LINCS
> lincs_iter = 1
> lincs_order = 4
> energygrps = NA OW
> energygrp_table = NA OW
> comm-mode = linear
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[gmx-users] Energy drift combining tabulated potentials and group cut-off.

[serpercon]

Dear GROMACS Community, 

I am trying to do a simulation using a tabulated potential which forces
me to use the group cut-off. I get a drift in the conserved quantity of
-600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules
and a Na+ ion. I imagine that eventhough it will soon be deprecated the
group cutoff scheme still works correctly. I have tryed to change the
parameters without success and in any case the ones I use seem
reasonable (in my experience using other programs). The rdfs of the
system look normal so I ruled out topology problems.  

It seems that the problem is in the group cut-off since
when I change the tabulated potential for a regular vdw the problem
persists. I have followed the instructions of: 

http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf 

to implement the tabulated potentials. 

Is this the kind of energy drift acceptable? I have pasted a copy .mdp  

Thanks for your help, 

Sergio Perez-Conesa 

integrator = md 
dt = 0.001 
nsteps = 10 
init-step = 0 
cutoff-scheme = group 
nst-list = 1 
verlet-buffer-tolerance = 0.0005 
ns-type = grid 
rlist = 1.3 
pbc = xyz 
coulombtype = PME-switch 
rcoulomb = 1. 
rcoulomb-switch = 0.95 
pme-order = 4 
fourierspacing = 0.1 
ewald-rtol = 1.e-5 
vdwtype = user 
rvdw = 1.0 
DispCorr = No 
tcoupl = v-rescale 
tc-grps = System 
;nsttcouple = 1 
tau-t = ref-t = 300.0 
constraints = all-angles 
constraint-algorithm = LINCS 
lincs_iter = 1 
lincs_order = 4 
energygrps = NA OW 
energygrp_table = NA OW 
comm-mode = linear
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Re: [gmx-users] g_mmpbsa compilation error

[Mark Abraham]

Hi,

This does not look like an issue with building GROMACS - g_mmpbsa is not an
official GROMACS tool, so you should perhaps inquire elsewhere also.

Mark

On Fri, Sep 1, 2017 at 11:55 AM neha chaudhary 
wrote:

> Hi,
>
> I am trying to compile g_mmpbsa with APBS for gromacs-5.1.2. APBS and
> gromacs installed properly but during cmake for g_mmpbsa I am facing the
> following error:
>
> -- Found z library: /usr/lib/x86_64-linux-gnu/libz.so
> CMake Error at cmake/FindGROMACS.cmake:203 (list):
>   list index: 2 out of range (-2, 1)
> Call Stack (most recent call first):
>   src/CMakeLists.txt:62 (find_package)
>
>
> -- Found Gromacs include directory: /usr/local/gromacs/include
> -- Configuring incomplete, errors occurred!
>
> Can anyone help me with this?
>
>
> Best Regards,
>
> Neha
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Re: [gmx-users] g_mmpbsa compilation error

[Vytautas Rakeviius]

Likely you cmake is far newer than Gromacs (cmake --version to figure that 
out). You should try Gromacs 2016.3
 

On Friday, September 1, 2017, 12:55:14 PM GMT+3, neha chaudhary 
 wrote:  
 
 Hi,

I am trying to compile g_mmpbsa with APBS for gromacs-5.1.2. APBS and
gromacs installed properly but during cmake for g_mmpbsa I am facing the
following error:

-- Found z library: /usr/lib/x86_64-linux-gnu/libz.so
CMake Error at cmake/FindGROMACS.cmake:203 (list):
  list index: 2 out of range (-2, 1)
Call Stack (most recent call first):
  src/CMakeLists.txt:62 (find_package)


-- Found Gromacs include directory: /usr/local/gromacs/include
-- Configuring incomplete, errors occurred!

Can anyone help me with this?


Best Regards,

Neha
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[gmx-users] g_mmpbsa compilation error

[neha chaudhary]

Hi,

I am trying to compile g_mmpbsa with APBS for gromacs-5.1.2. APBS and
gromacs installed properly but during cmake for g_mmpbsa I am facing the
following error:

-- Found z library: /usr/lib/x86_64-linux-gnu/libz.so
CMake Error at cmake/FindGROMACS.cmake:203 (list):
  list index: 2 out of range (-2, 1)
Call Stack (most recent call first):
  src/CMakeLists.txt:62 (find_package)


-- Found Gromacs include directory: /usr/local/gromacs/include
-- Configuring incomplete, errors occurred!

Can anyone help me with this?


Best Regards,

Neha
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Re: [gmx-users] Regarding NPT simulation and box length variation

[Mark Abraham]

Hi,

Note that I said solute, not solvent.

There are no relevant gaps after an effective NPT equilibration. The usual
force fields do not permit it.

"Gap" is a quite non-specific description, but the appearance of such is
usually because the contents of the simulation cell look like a jigsaw
piece (that obviously tessellates with itself). If you still think you have
an issue, please upload some images to a file-sharing service and share us
a link.

Mark

On Fri, Sep 1, 2017 at 10:12 AM Dilip H N  wrote:

> Sir,
> There is no any solvent that is protruding outside the box...all the
> molecules are within the box itself, and still i am able to view the
> gaps/empty area at some regions in the box...(which is indicating that the
> box length is slightly bigger)
> So how can i make sure that there are no any gaps in my box system and
> hence proceed or further compress the box ..
>
> These gaps can affect the analysis part like during calculating rdf, cn,
> hydrogen bond dynamics, etc...i hope so... Or doen't it affect... any
> ideas..??
>
> Thank you...
>
>
>
>  Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22
> >
>
> On Fri, Sep 1, 2017 at 12:21 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > These "gaps" are probably just what you expect with
> > http://www.gromacs.org/Documentation/Terminology/
> > Periodic_Boundary_Conditions
> > for
> > the configuration you are viewing. For example, if the solute protrudes
> out
> > one side of the box, then there will be a matching gap on the other side
> of
> > the box, because that's what PBC means. If you want to view a
> space-filled
> > box, then you need to e.g. use trjconv to make it so.
> >
> > NPT isn't going to tolerate a region of vacuum ;-)
> >
> > Mark
> >
> > On Fri, Sep 1, 2017 at 8:32 AM Dilip H N 
> > wrote:
> >
> > > Hello,
> > > I am having a peptide and  water mixture in a cubic box of say 2.5 2.5
> > 2.5
> > > nm. and if i view in vmd i am able to see there are empty spaces/gaps
> at
> > > some areas/regions (or in other words the box length is slightly
> bigger),
> > > so i ran the energy minimization(with em.mdp) and followed by npt
> > > simulation (with npt.mdp), to know the box length by allowing it to
> > > fluctuate...
> > > But after npt simulation if i view the final structure/full trajectory
> in
> > > vmd, the box length has decreased slightly, but still i am able to see
> > > there are empty spaces/gaps within the box. Is it ok with the gaps at
> > some
> > > areas or the molecules should be compactly arranged within the box..??
> > >
> > > I am trying with the following commands:-
> > > gmx insert-molecules -f abc.gro -ci def.gro -nmol xxx -o ghi.gro #
> > > inserting molecules
> > > gmx solvate -cp ghi.gro -cs spc216.gro -o jkl.gro -maxsol xxx#
> > > solvating with water
> > > gmx grompp -f em.mdp -c jkl.gro -p topol.top -o em.tpr
>   #
> > > energy minimization
> > > gmx mdrun -v -s em.tpr -deffnm em
> > > gmx grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr
> #
> > > npt simulation
> > > gmx mdrun -v -s npt.tpr -deffnm npt
> > >
> > > The gmx solvate command solvates with the empty spaces... and still
> after
> > > energy minimization and npt simulation i am able to see some gaps in
> the
> > > box through vmd.
> > > How to get rid of these spaces inside the box.. or get the box
> compressed
> > > still further with whole mixture of molecules are within the box.
> > > So how can i solve this issue..?? Do i need to modify anything in the
> > .mdp
> > > files..or any where else..??
> > > Here are the em.mdp and npt.mdp files attached...
> > >
> > > Any suggestions are highly appreciated 
> > >
> > > Thank you...
> > >
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Ph.D Student
> > >
> > >
> > >
> > >  Sent with Mailtrack
> > > <
> > > https://mailtrack.io/install?source=signature&lang=en&;
> > referral=cy16f01.di...@nitk.edu.in&idSignature=22
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > >
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> > --
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> >
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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> * Please search the a

Re: [gmx-users] Regarding NPT simulation and box length variation

[Dilip H N]

Sir,
There is no any solvent that is protruding outside the box...all the
molecules are within the box itself, and still i am able to view the
gaps/empty area at some regions in the box...(which is indicating that the
box length is slightly bigger)
So how can i make sure that there are no any gaps in my box system and
hence proceed or further compress the box ..

These gaps can affect the analysis part like during calculating rdf, cn,
hydrogen bond dynamics, etc...i hope so... Or doen't it affect... any
ideas..??

Thank you...



 Sent with Mailtrack


On Fri, Sep 1, 2017 at 12:21 PM, Mark Abraham 
wrote:

> Hi,
>
> These "gaps" are probably just what you expect with
> http://www.gromacs.org/Documentation/Terminology/
> Periodic_Boundary_Conditions
> for
> the configuration you are viewing. For example, if the solute protrudes out
> one side of the box, then there will be a matching gap on the other side of
> the box, because that's what PBC means. If you want to view a space-filled
> box, then you need to e.g. use trjconv to make it so.
>
> NPT isn't going to tolerate a region of vacuum ;-)
>
> Mark
>
> On Fri, Sep 1, 2017 at 8:32 AM Dilip H N 
> wrote:
>
> > Hello,
> > I am having a peptide and  water mixture in a cubic box of say 2.5 2.5
> 2.5
> > nm. and if i view in vmd i am able to see there are empty spaces/gaps at
> > some areas/regions (or in other words the box length is slightly bigger),
> > so i ran the energy minimization(with em.mdp) and followed by npt
> > simulation (with npt.mdp), to know the box length by allowing it to
> > fluctuate...
> > But after npt simulation if i view the final structure/full trajectory in
> > vmd, the box length has decreased slightly, but still i am able to see
> > there are empty spaces/gaps within the box. Is it ok with the gaps at
> some
> > areas or the molecules should be compactly arranged within the box..??
> >
> > I am trying with the following commands:-
> > gmx insert-molecules -f abc.gro -ci def.gro -nmol xxx -o ghi.gro #
> > inserting molecules
> > gmx solvate -cp ghi.gro -cs spc216.gro -o jkl.gro -maxsol xxx#
> > solvating with water
> > gmx grompp -f em.mdp -c jkl.gro -p topol.top -o em.tpr  #
> > energy minimization
> > gmx mdrun -v -s em.tpr -deffnm em
> > gmx grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr#
> > npt simulation
> > gmx mdrun -v -s npt.tpr -deffnm npt
> >
> > The gmx solvate command solvates with the empty spaces... and still after
> > energy minimization and npt simulation i am able to see some gaps in the
> > box through vmd.
> > How to get rid of these spaces inside the box.. or get the box compressed
> > still further with whole mixture of molecules are within the box.
> > So how can i solve this issue..?? Do i need to modify anything in the
> .mdp
> > files..or any where else..??
> > Here are the em.mdp and npt.mdp files attached...
> >
> > Any suggestions are highly appreciated 
> >
> > Thank you...
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
> >  Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature&lang=en&;
> referral=cy16f01.di...@nitk.edu.in&idSignature=22
> > >
> > --
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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