[gmx-users] Problem with the autocorrelation of Rg

[faride badalkhani]

Dear GROMACS users,

I am performing umbrella sampling on a polymer-ligand system and I generate
configurations successfully but the problem is that when I plot the
autocorrelation function of Rg for each window it is zero for the whole
time of simulation. I changed the run time for each window but nothing
changed. Moreover, the initial polymer-ligand structure is equilibrated
well.
Any comment or suggestion will be greatly appreciated.

Best,
Farideh
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[gmx-users] NOTE: Cannot set thread affinities on the current platform.

[liming_52]

Dear gmx users,
I ran a md in Cygwin. Howerver, when I ran "gmx mdrun -deffnm nvt". There were 
errors as follows:

$ gmx mdrun -deffnm nvt

:-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:

GROMACS is written by:

Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar

Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch

Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen

Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner

Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff

Erik Marklund Teemu Murtola Szilard Pall Sander Pronk

Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers

Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf

and the project leaders:

Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.

Copyright (c) 2001-2015, The GROMACS development team at

Uppsala University, Stockholm University and

the Royal Institute of Technology, Sweden.

check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it

under the terms of the GNU Lesser General Public License

as published by the Free Software Foundation; either version 2.1

of the License, or (at your option) any later version.

GROMACS: gmx mdrun, VERSION 5.1.4

Executable: /usr/local/gromacs/bin/gmx.exe

Data prefix: /usr/local/gromacs

Command line:

gmx mdrun -deffnm nvt

　

Running on 1 node with total 24 logical cores

Hardware detected:

CPU info:

Vendor: GenuineIntel

Brand: Intel(R) Xeon(R) CPU E5-2620 v2 @ 2.10GHz

SIMD instructions most likely to fit this hardware: AVX_256

SIMD instructions selected at GROMACS compile time: AVX_256

Reading file nvt.tpr, VERSION 5.1.4 (single precision)

Changing nstlist from 10 to 20, rlist from 1 to 1.03

　

Will use 18 particle-particle and 6 PME only ranks

This is a guess, check the performance at the end of the log file

Using 24 MPI threads

Using 1 OpenMP thread per tMPI thread

　

　

　

　

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.NOTE: Cannot set 
thre ad affinities on the current platform.NOTE: Cannot set thread affinities 
on the current platform.

NOTE: Cannot set thread affinities on the current platform.NOTE: Cannot set 
thre ad affinities on the current platform.

　

　

　

　

　

NOTE: Cannot set thread affinities on the current platform.NOTE: Cannot set 
thre ad affinities on the current platform.

　

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

　

　

NOTE: Cannot set thread affinities on the current platform.NOTE: Cannot set 
thre ad affinities on the current platform.NOTE: Cannot set thread affinities 
on the current platform.

　

　

NOTE: Cannot set thread affinities on the current platform.

And the cpus were not used for calculation, the md will be continued without 
stopping. How should I solve this problem?
Any reply will be appreciated.





--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China
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[gmx-users] Using backward.py with Gromacs 5.x?

[SRINIVAS MUSHNOORI]

Dear GROMACS users,

I'm attempting to backmap from a MARTINI CG representation to a CHARMM AA
representation for my biomolecular system.

The command I am using is:
**./initram.sh -f FNF150-40out.gro -o charmm_FNF150-40.gro -to charmm36 -p
FNF150-40.top**


And the output I get is:
**Checking dependencies:backward.py ...
/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.pygrompp ...
Missing dependency: grompp**


Now doing a bit of googling seemed to shed some light on the issue: GROMACS
5.x domes not seem to use a separate executable called "grompp" or even
"mdrun" for that matter. Instead it simply uses one executable called gmx.
Changing the dependency to the path of my gmx executable inside initram.sh
and then attempting to run it gives me the following error:
**Checking dependencies:backward.py ...
/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.py/usr/local/gromacs/bin/gmx

... /usr/local/gromacs/bin/gmxTraceback (most recent call last):  File
"/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.py", line
644, in struc =
Structure(options["-f"].value,strict=options["-strict"].value)  File
"/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.py", line
411, in __init__crsp.append(crsp[-1])IndexError: list index out of
range*
*
I am unsure how to go about running the script. Any assistance on the
matter will be immensely helpful.

Thank you!

Sincerely yours,

Srinivas Mushnoori
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[gmx-users] simulations with wall potential

[Beibei Wang]

Hi everyone,

I am trying to simulate a polymer in a water box with Martini force field, and 
with a constant thickness. To realize this, I am testing simulations with wall 
potential. My mdp file is as following:

integrator   = md
dt   = 0.002
nsteps   = 50
nstcomm  = 10

nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 1000
nstenergy= 5000

nstxtcout= 5000
xtc_precision= 100
xtc-grps =
energygrps   = Sol W

cutoff-scheme= group
nstlist  = 10
ns_type  = grid
pbc  = xy
periodic-molecules   = no
rlist= 1.4

coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch  = 0.9
rvdw = 1.2

;walls
nwall = 2
wall-atomtype = P5 P5 ;P5 is a Martini particle type
wall-type = 10-4
wall-r-linpot = 1 1
wall-density = 1.2 1.2
wall-ewald-zfac   = 3

tcoupl   = berendsen
tc-grps  = Sytem ;W
tau_t= 1.0 ;1.0
ref_t= 310 ;310
pcoupl   = no ; no pressure coupling in NVT

gen_vel  = yes
gen_temp = 310
gen_seed = -1


constraints  = none
constraint_algorithm = Lincs
unconstrained_start  = no
lincs_order  = 4
lincs_warnangle  = 30

The system box was 7.0 by 7.0 by 7.0 nm, was placed at zero point by editconf 
initially. Here is the head of my system:

1GLF B41   4.487   3.844   3.538
1GLF B52   4.360   4.133   3.770
1GLF B63   4.286   3.687   3.477
2GLF B14   4.409   4.396   3.647
2GLF B25   4.119   4.561   3.704
2GLF B36   4.533   4.499   3.435
2GLF B47   4.022   4.860   3.578
2GLF B58   3.961   4.977   3.209

But soon as the simulations started, some water molecules moved across the 
walls, and far away in Z direction. The main box was moved in Z direction as 
well:

1GLF B41   3.175   4.176-309.166  0.0008  0.0012 -0.3582
1GLF B52   3.082   4.558-309.239  0.0010 -0.0008 -0.3564
1GLF B63   3.188   3.981-309.342 -0.0042  0.0017 -0.3578
2GLF B14   2.936   4.683-309.448  0.0004 -0.0040 -0.3567
2GLF B25   2.602   4.708-309.427  0.0010  0.0007 -0.3586
2GLF B36   2.990   4.709-309.710  0.0004  0.0001 -0.3614
2GLF B47   2.375   4.788-309.664  0.0026 -0.0004 -0.3591
2GLF B58   2.150   4.640-309.969 -0.0006 -0.0007 -0.3620

As I used NVT ensemble, the box size shown in the gro file was still 7.0 by 7.0 
by 7.0 nm. But I am sure in this case how the wall potential was applied. Where 
is the two walls? Are they still at z=0 and box_z?

Could anyone help to check if there are anything wrong in my input files? I 
have tried to change wall-atomtype, wall-type, wall-r-linpot, and wall-density, 
with higher wall-density (such as 12), the box was separated into parts with a 
huge z range (see the following figure). The figure is hard to see, the light 
blue "particles" you could see are my system.

[cid:image001.jpg@01D27491.8FEB2D00]

Thanks very much.
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Re: [gmx-users] gmx make_ndx: select last created group without knowing its number

[Mark Abraham]

Hi,

Sure, you can give and refer to groups either by name or number, so there
are many possible solutions for you. Easiest is to give it a name at the
time you make it, and then use that name later. Otherwise, you could delete
all the other groups so that the group you want is always group 1.

Mark

On Sun, Jan 22, 2017 at 1:51 PM CLARK NICOLAS Joan 
wrote:

> Dear gmx users,
>
>
> I want to check how big are the biasing forces of a collective variable
> compared to the normal MD forces. As my collective variable only takes into
> account certain atoms of the system, I'd like to use make_ndx to create a
> group containing these atoms and give a name to that group so that I can
> use it later in a script
>
>
> The problem is that I am running this calculation for a lot of systems,
> some of them with ligands, some of them without, so I would like to use a
> script to create these groups for all my systems.
>
>
> As the number of the last created group will not always be the same, I was
> wondering if there is any option in make_ndx that allows to select the last
> group on the list so i can give it a suitable name without knowing its
> group number.
>
>
> Thanks,
>
> Joan
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> --
> Gromacs Users mailing list
>
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> posting!
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[gmx-users] gmx make_ndx: select last created group without knowing its number

[CLARK NICOLAS Joan]

Dear gmx users,


I want to check how big are the biasing forces of a collective variable 
compared to the normal MD forces. As my collective variable only takes into 
account certain atoms of the system, I'd like to use make_ndx to create a group 
containing these atoms and give a name to that group so that I can use it later 
in a script


The problem is that I am running this calculation for a lot of systems, some of 
them with ligands, some of them without, so I would like to use a script to 
create these groups for all my systems.


As the number of the last created group will not always be the same, I was 
wondering if there is any option in make_ndx that allows to select the last 
group on the list so i can give it a suitable name without knowing its group 
number.


Thanks,

Joan
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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Re: [gmx-users] Simulation in vacuum

[Mark Abraham]

Hi,

Like the messages say, you can only use the Verlet scheme with periodic
systems. Use the group scheme.

Mark

On Sun, 22 Jan 2017 06:54 Мижээ Батсайхан  wrote:

> Dear Erik,
>
> Thank you very much for helping me.
> I have got 2 errors from grompp using gromacs v5.1.
>
> ERROR 1 [file nve.mdp]:
>   With Verlet lists only full pbc or pbc=xy with walls is supported
>
> ERROR 2 [file nve.mdp]:
>   With Verlet lists nstlist should be larger than 0
>
> How can I fix these? I copied my mdp file.
>
> #
> title   = NVE equilibration
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 1  ; 1 * 1 fs= 10 ps = 100 ns
> dt  = 0.001 ; 1 fs
> ; mode for center of mass motion removal
> comm-mode= Angular
>
> ; Output control
> nstxout = 5000
> nstvout = 5000
> nstenergy   = 5000
> nstlog  = 500
> ;energygrps  =
>
> ; Bond parameters
> continuation= no
> constraint_algorithm = lincs
> constraints = hbonds
> lincs_iter  = 2
> lincs_order = 4
>
> ; Neighborsearching PARAMETERS
> vdw-type= cut-off
> verlet-buffer-tolerance = -1
> rlist = 1
> nstlist = 0
> ns_type = grid
> pbc = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype  = cut-off
> rcoulomb-switch  = 0
> rcoulomb = 0.0
> rvdw = 0.0
> rvdw-switch  = 0.0
> fourierspacing   = 0.16
> epsilon_r= 1
> epsilon_rf   = 78
> ; EWALD/PME/PPPM parameters
> pme_order= 4  ; cubic interpolation
>
> ; Temperature coupling
> tcoupl  = no
> ;tc-grps =
> ;tau_t   = 0.1
> ;ref_t   = 300
> ; Pressure coupling
> pcoupl  = no; no pressure coupling in NVT
> ; Dispersion correction
> ; Velocity generation
> gen_vel = yes   ; assign velocities from Maxwell distribution
> gen_temp= 300   ; temperature for Maxwell distribution
> gen_seed= -1   ; generate a random seed
> 
>
>
>
>
> Best regards,
> Mijiddorj
>
> > --
> > >
> > > Message: 4
> > > Date: Fri, 20 Jan 2017 10:30:59 +
> > > From: Erik Marklund 
> > > To: "gmx-us...@gromacs.org" 
> > > Subject: Re: [gmx-users] Simulation in vacuum
> > > Message-ID: <7745284c-ea36-4189-80a6-0a6ab4986...@kemi.uu.se>
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > Dear Mijiddorj,
> > >
> > > We have had good energy conservation with bond constraints and a 1 fs
> > time
> > > step under double precision, using a setup similar to yours. We did not
> > > remove rotation however, because we wanted to honour the rotational
> > > temperature of the system. Whether that is an important choice or not
> is
> > > for you to decide, but do note that the spinning ice cube effect is an
> > > artefact arising from the thermostat, which is turned off in your
> setup.
> > >
> > > Whether bonds should be constrained or not is related to what your
> > > scientific questions are, and the time step depends on what bonds are
> > > constrained, if any. I can?t remember what LINCS parameters we used,
> but
> > be
> > > prepared to increase the order and/or iter. Consult the manual for
> > details.
> > >
> > > Kind regards,
> > > Erik
> > >
> > > __
> > > Erik Marklund, PhD
> > > Marie Sk?odowska Curie INCA Fellow
> > > Department of Chemistry ? BMC
> > > Uppsala Universtity
> > > erik.markl...@kemi.uu.se
> > >
> > > On 20 Jan 2017, at 11:01, ? ?   > > b.mijidd...@gmail.com>> wrote:
> > >
> > > Dear gmx users,
> > >
> > > I would like to get experience of simulation in vacuum. Please suggest
> me
> > > tutorials, and advice me.
> > >
> > > I read about following comments which written on Shourjiya Sanyal
> > tutorial.
> > > Can you discuss about it?
> > >
> > > In vacuum simulation, integration should be reduced compared to solvent
> > > phase simulation. Periodic boundary conditions, non-bonded interaction
> > > cutoffs, temperature coupling and pressure coupling were all turned
> off.
> > > Center of mass translation and rotation around the center of mass are
> to
> > be
> > > removed to avoid the fast spin of the protein. One should also
> constrain
> > > the hydrogen bond using algorithms like SHAKE/LINCS.
> > >
> > > http://www.shourjya.thinkbiosolution.com/md-
> > simulation-in-gas-phasevacuum-
> > > with-gromacs/
> > >
> > >
> > > Best regards,
> > > Mijiddorj
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For