[gmx-users] regarding hydrogen bond correlation function for Cdd for TIP4P/2005 water model

[Abhinav Srivastava (P14CHM002)]

Dear Gromacs Users,

Kindly consider this as my query mail as in the last mail, subject line was
not complete. I apologize for the same .
I am trying to calculate hydrogen bond correlation function Cdd(t) for bulk
water (TIP4P/2005 water) using reversible geminate recombination as
mentioned in
Markovitch et al., J. Chem. Phys.,129,084505(2008).

Following is the command which I have used :

g_hbond -f NVT.xtc -s NVT.tpr -n bulk-water.ndx -b 0 -e 100 -P 1 -temp 308
-geminate dd -ac Cdd-bulk-water.xvg

I have simulated two systems viz. smaller system consisting of 851 water
molecules and a bigger system consisting of 1944 water molecules. I am not
able to get t^-3/2 scaling in hydrogen bond correlation function for Cdd
case in both these systems. It would be nice if you can please help me.
Thanks in advance.

-- 
*Abhinav Srivastava*
*Research Scholar*
Indian Institute of Technology, Jodhpur
Rajasthan
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[gmx-users] regarding

[Abhinav Srivastava (P14CHM002)]

Dear Gromacs Users,

I am trying to calculate hydrogen bond correlation function Cdd(t) for bulk
water (TIP4P/2005 water) using reversible geminate recombination as
mentioned in
Markovitch et al., J. Chem. Phys.,129,084505(2008).

Following is the command which I have used :

g_hbond -f NVT.xtc -s NVT.tpr -n bulk-water.ndx -b 0 -e 100 -P 1 -temp 308
-geminate dd -ac Cdd-bulk-water.xvg

I have simulated two systems viz. smaller system consisting of 851 water
molecules and a bigger system consisting of 1944 water molecules. I am not
able to get t^-3/2 scaling in hydrogen bond correlation function for Cdd
case in both these systems. It would be nice if you can please help me.
Thanks in advance.

-- 
*Abhinav Srivastava*
*Research Scholar*
Indian Institute of Technology, Jodhpur
Rajasthan
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Re: [gmx-users] Equilibration

[Dallas Warren]

That ultimately depends on what physical property you are hoping to
show is at "equilibrium".  For example, see
https://twitter.com/dr_dbw/status/907735156382777344 for how
temperature, total energy, volume, density and pressure change with
time for an example system.  Pressure and temperature you don't see
any trends, since those happen in rapid time frames so they have
reached equilibrium very rapidly, <<1ns.  You can see that
density/volume have a change during first 10ns, then things settle
down, so they have reached equilibrium within 10ns.  Total energy has
a slight downward trend, but it is difficult to see for sure. Then if
you look at a different property, say solvent accessible surface area,
see https://twitter.com/dr_dbw/status/907736554939891712, then you can
see that by the end of the 50ns it may have reach equilibrium, but
there is insufficient data to say for sure.

Catch ya,

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


On 13 September 2017 at 05:15, ÁLVARO RODRIGO RUIZ FERNÁNDEZ
 wrote:
> Dear users,
>
> I need to demonstrate that my box is in equilibrium. What is the maximum
> slope of the energy or the volume in function of time to demosntrate it? .
> Or exist anothe parameter to follow. Thank you very much.
>
> --
>
> *Dr. Álvaro  Ruiz  *
>
>
>
> *Physicochemical Molecular LaboratoryDepartamento de QuímicaFacultad de
> CienciasUniversidad de Chile*Mobile: +56-9-51178101
> Office: +56-2-9787443
> arr...@ug.uchile.cl
> --
> 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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> mail to gmx-users-requ...@gromacs.org.
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[gmx-users] COM-pulling

[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


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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[gmx-users] Equilibration

[ÁLVARO RODRIGO RUIZ FERNÁNDEZ]

Dear users,

I need to demonstrate that my box is in equilibrium. What is the maximum
slope of the energy or the volume in function of time to demosntrate it? .
Or exist anothe parameter to follow. Thank you very much.

-- 

*Dr. Álvaro  Ruiz  *



*Physicochemical Molecular LaboratoryDepartamento de QuímicaFacultad de
CienciasUniversidad de Chile*Mobile: +56-9-51178101
Office: +56-2-9787443
arr...@ug.uchile.cl
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[gmx-users] COM-RDF calculation

[Maghesree Chakraborty]

Hello,
I am trying to calculate the center of mass (COM) rdfs for methanol
molecules.

I have noticed that in gromacs 2016 there is neither -com nor -rdf option
for gmx rdf. I have used the following instead:

gmx rdf -f traj.trr -n index.ndx -s topol.tpr -pbc -seltype whole_mol_com
-selrpos whole_mol_com

I am wondering if I am calculating the COM-COM rdf correctly with the
specified options. It will be great if someone can confirm if this is
correct or let me know where I am wrong. Thank you.

Regards,
M. Chakraborty
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Re: [gmx-users] gromacs error

[Mark Abraham]

Hi,

It's hard to say, but you should look at the log file and terminal output,
and install the latest in the series of bug fixes... 5.0.7 rather than
choose a version known to have dozens more bugs...

Mark

On Tue, Sep 12, 2017 at 3:55 PM Vidya R  wrote:

> Hi,
>
> I fixed that error.
>
> However,I now encounter a new one...
>
> GROMACS:gmx grompp, VERSION 5.0.2
>
> GROMACS is written by:
> Emile Apol Rossen Apostolov   Herman J.C. Berendsen Par
> Bjelkmar
> Aldert van Buuren  Rudi van DrunenAnton Feenstra Sebastian Fritsch
> Gerrit GroenhofChristoph Junghans Peter Kasson   Carsten Kutzner
> Per LarssonJustin A. Lemkul   Magnus LundborgPieter Meulenhoff
> Erik Marklund  Teemu Murtola  Szilard Pall   Sander Pronk
> Roland Schulz  Alexey ShvetsovMichael Shirts Alfons Sijbers
> Peter Tieleman 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) 2001-2014, 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 grompp, VERSION 5.0.2
> Executable:   /usr/local/gromacs/bin/gmx
> Library dir:  /usr/local/gromacs/share/gromacs/top
> Command line:
>   gmx grompp -f mdp/min.mdp -o min -pp min -po min
>
> Setting the LD random seed to 1842076191
> Generated 349030 of the 349030 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 349030 of the 349030 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'LIG'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Removing all charge groups because cutoff-scheme=Verlet
> Number of degrees of freedom in T-Coupling group rest is 11837.00
> Estimate for the relative computational load of the PME mesh part: 0.17
>
> gcq#309: "Nobody Never Learnt No-Nothing from No History" (Gogol Bordello)
>
> GROMACS:gmx mdrun, VERSION 5.0.2
>
> GROMACS is written by:
> Emile Apol Rossen Apostolov   Herman J.C. Berendsen Par
> Bjelkmar
> Aldert van Buuren  Rudi van DrunenAnton Feenstra Sebastian Fritsch
> Gerrit GroenhofChristoph Junghans Peter Kasson   Carsten Kutzner
> Per LarssonJustin A. Lemkul   Magnus LundborgPieter Meulenhoff
> Erik Marklund  Teemu Murtola  Szilard Pall   Sander Pronk
> Roland Schulz  Alexey ShvetsovMichael Shirts Alfons Sijbers
> Peter Tieleman 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) 2001-2014, 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 5.0.2
> Executable:   /usr/local/gromacs/bin/gmx
> Library dir:  /usr/local/gromacs/share/gromacs/top
> Command line:
>   gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm min
>
> Reading file min.tpr, VERSION 5.0.2 (single precision)
> Using 1 MPI thread
> Using 8 OpenMP threads
> mpirun noticed that job rank 0 with PID 18038 on node compute-0-20.local
> exited on signal 11 (Segmentation fault).
>
>
> What is segmentation fault?
>
> What am I supposed to do?
>
> Please tell me.
>
> Thanks,
> Vidya.R
>
>
> On Mon, Sep 11, 2017 at 7:27 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Yeah I've never seen that, so I assume it's something weird related to
> how
> > GROMACS was originally compiled vs how the system has been updated since.
> > Since a rebuild is the way to investigate that, definitely update to at
> > least the latest 5.0.x while you do it.
> >
> > Mark
> >
> > On Mon, Sep 11, 2017 at 3:36 PM Wes Barnett 
> > wrote:
> >
> > > On Mon, Sep 11, 2017 at 8:44 AM, Vidya R 
> > wrote:
> > >
> > > > Hi,
> > > >
> > > >
> > > > When I give these two commands
> > > >
> > > > gmx grompp -f mdp/min.mdp -o min -pp min -po min
> > > > gmx mdrun -deffnm min
> > > >
> > > > I get this error.
> > > >
> > > > What to do?
> > > >
> > > >
> > > >
> > > > Reading file min.tpr, VERSION 5.0.2 (single precision)
> > > > tMPI error: 

Re: [gmx-users] gromacs error

[Vidya R]

Hi,

I fixed that error.

However,I now encounter a new one...

GROMACS:gmx grompp, VERSION 5.0.2

GROMACS is written by:
Emile Apol Rossen Apostolov   Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren  Rudi van DrunenAnton Feenstra Sebastian Fritsch
Gerrit GroenhofChristoph Junghans Peter Kasson   Carsten Kutzner
Per LarssonJustin A. Lemkul   Magnus LundborgPieter Meulenhoff
Erik Marklund  Teemu Murtola  Szilard Pall   Sander Pronk
Roland Schulz  Alexey ShvetsovMichael Shirts Alfons Sijbers
Peter Tieleman 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) 2001-2014, 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 grompp, VERSION 5.0.2
Executable:   /usr/local/gromacs/bin/gmx
Library dir:  /usr/local/gromacs/share/gromacs/top
Command line:
  gmx grompp -f mdp/min.mdp -o min -pp min -po min

Setting the LD random seed to 1842076191
Generated 349030 of the 349030 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 349030 of the 349030 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'LIG'
Excluding 2 bonded neighbours molecule type 'SOL'
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group rest is 11837.00
Estimate for the relative computational load of the PME mesh part: 0.17

gcq#309: "Nobody Never Learnt No-Nothing from No History" (Gogol Bordello)

GROMACS:gmx mdrun, VERSION 5.0.2

GROMACS is written by:
Emile Apol Rossen Apostolov   Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren  Rudi van DrunenAnton Feenstra Sebastian Fritsch
Gerrit GroenhofChristoph Junghans Peter Kasson   Carsten Kutzner
Per LarssonJustin A. Lemkul   Magnus LundborgPieter Meulenhoff
Erik Marklund  Teemu Murtola  Szilard Pall   Sander Pronk
Roland Schulz  Alexey ShvetsovMichael Shirts Alfons Sijbers
Peter Tieleman 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) 2001-2014, 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 5.0.2
Executable:   /usr/local/gromacs/bin/gmx
Library dir:  /usr/local/gromacs/share/gromacs/top
Command line:
  gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm min

Reading file min.tpr, VERSION 5.0.2 (single precision)
Using 1 MPI thread
Using 8 OpenMP threads
mpirun noticed that job rank 0 with PID 18038 on node compute-0-20.local
exited on signal 11 (Segmentation fault).


What is segmentation fault?

What am I supposed to do?

Please tell me.

Thanks,
Vidya.R


On Mon, Sep 11, 2017 at 7:27 PM, Mark Abraham 
wrote:

> Hi,
>
> Yeah I've never seen that, so I assume it's something weird related to how
> GROMACS was originally compiled vs how the system has been updated since.
> Since a rebuild is the way to investigate that, definitely update to at
> least the latest 5.0.x while you do it.
>
> Mark
>
> On Mon, Sep 11, 2017 at 3:36 PM Wes Barnett 
> wrote:
>
> > On Mon, Sep 11, 2017 at 8:44 AM, Vidya R 
> wrote:
> >
> > > Hi,
> > >
> > >
> > > When I give these two commands
> > >
> > > gmx grompp -f mdp/min.mdp -o min -pp min -po min
> > > gmx mdrun -deffnm min
> > >
> > > I get this error.
> > >
> > > What to do?
> > >
> > >
> > >
> > > Reading file min.tpr, VERSION 5.0.2 (single precision)
> > > tMPI error: tMPI Initialization error (in valid comm)
> > >
> > > Thanks,
> > > Vidya.R
> > >
> >
> > I can't speak to that exact error, but there have been several bug fix
> > releases to the 5.0.x series since 5.0.2, so an upgrade may be in order.
> I
> > would even suggest upgrading to the latest release (2016.x series).
> >
> >
> > --
> > James "Wes" Barnett
> > Postdoctoral Research Scientist
> > Department of Chemical Engineering
> > Kumar Research Group 
> > Columbia University
> > 

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

[Abhishek Acharya]

Hello Wes,

I ran some more test simulations. I think the error is because I added
counterions to neutralize my system (it has a +2 charge) prior to the free
energy. Without the counterions, the simulations are running fine. Though,
I don't know whether such a behavior is expected. Such a setup (with
counterions) is not something unheard of.

Nevertheless, I read elsewhere that for solvation free energy calculation
of charged system, the uniform background charge as implemented in PME for
non-neutral systems may be desirable. Hence, I plan to run the simulations
without counterions.

Sincerely,
Abhishek




Abhishek Acharya
Research Associate,
Department of Molecular Nutrition
CSIR-Central Food Technological Research Institute,
Mysuru-570020

On Tue, Sep 12, 2017 at 5:22 PM, Wes Barnett  wrote:

> On Tue, Sep 12, 2017 at 12:17 AM, Abhishek Acharya <
> abhi117acha...@gmail.com
> > wrote:
>
> > Just to add to the above post, running a none to vdw-q tranformation
> using
> > the following parameters also results in the same error for simulation at
> > first lambda.
> >
>
>
> Do you get this error on a normal simulation as well? That is, if you run
> state 0 (with vdw and electrostatics on) without doing an free energy
> calculations, do you still get the error? Perhaps you are using too big a
> of a time step or your system is not equilibrated enough before using this
> time step. Or you may just have a bad starting configuration.
>
>
> >
> > 
> > 
> > 
> > vdw_lambdas  = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
> > 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00
> 1.00
> > 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00
> > 1.00 1.00
> > coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10
> 0.15
> > 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85
> 0.90
> > 0.95 1.00
> > ; We are not transforming any bonded or restrained interactions
> > bonded_lambdas   = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00
> > restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00
> > ; Masses are not changing (particle identities are the same at lambda = 0
> > and lambda = 1)
> > mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00
> > ; Not doing simulated temperting here
> > temperature_lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00
> > ; Options for the decoupling
> > sc-alpha = 0.5
> > sc-coul  = no   ; linear interpolation of Coulomb
> (none
> > in this case)
> > sc-power = 1
> > sc-sigma = 0.3
> > couple-moltype   = Protein  ; name of moleculetype to decouple
> > couple-lambda0   = none
> > couple-lambda1   = vdw-q
> > couple-intramol  = no
> > nstdhdl  = 10
> > 
> > 
> > 
> >
> > Thanks in advance.
> >
> > Abhishek Acharya
> > Research Associate,
> > Department of Molecular Nutrition
> > CSIR-Central Food Technological Research Institute,
> > Mysuru-570020
> >
> > On Tue, Sep 12, 2017 at 9:42 AM, Abhishek Acharya <
> > abhi117acha...@gmail.com>
> > wrote:
> >
> > > Hello GROMACS users,
> > >
> > > As Wes had advised previously in this thread, the issue with the vdw
> > > tranformations was rectified by removing the charges from the topology
> > > file. Thereafter, I also tried running free energy calculations using
> the
> > > following free-energy parameters:
> > >
> > > 
> > > 
> > > 
> > > free_energy  = yes
> > > init_lambda_state= 0
> > > delta_lambda = 0
> > > calc_lambda_neighbors= 1; only 

Re: [gmx-users] error sharing libraries...gromacs error

[Mark Abraham]

Hi,

That command doesn't compile with the gcc compiler, does it? I already
suggested what to do ;-)

Mark

On Tue, Sep 12, 2017 at 2:28 PM Vidya R  wrote:

> Hi,
>
> I now use
>
> export MPIRUN="/usr/mpi/gcc/openmpi-1.2.8/bin"
>
> But, how to fix that error?
>
> Thanks,
> Vidya.R
>
> On Tue, Sep 12, 2017 at 5:42 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > If you're trying to use the PGI compilers, then please don't because the
> > C++ performance is very poor. We recommend latest gcc or intel.
> >
> > Otherwise, configure GROMACS so that it uses the wrapper compilers when
> > buildling, e.g. cmake -DCMAKE_C_COMPILER=mpicc
> -DCMAKE_CXX_COMPILER=mpic++
> > etc. Organizing this stuff is their job.
> >
> > Mark
> >
> > On Tue, Sep 12, 2017 at 1:46 PM Vidya R  wrote:
> >
> > > Hi,
> > >
> > > I give these commands
> > >
> > > PATH=$PATH:"/usr/local/gromacs/bin/"
> > > export GMXLIB=/usr/local/gromacs/share/gromacs/top
> > > export LD_LIBRARY_PATH=/usr/lib
> > > export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun"
> > > export
> > >
> > > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/ansys_inc/v140/CFX/
> > tools/icemcfd-12.0-post-3/lib/linux-amd64
> > >
> > >
> > > before these
> > >
> > > gmx grompp -f mdp/min.mdp -o min -pp min -po min
> > > g_tune_pme -np 4 -s min.tpr -launch
> > >
> > >
> > >
> > > But, I am getting this error
> > >
> > > /usr/mpi/pgi/openmpi-1.2.8/bin/mpirun: error while loading shared
> > > libraries: libpgc.so: cannot open shared object file: No such file or
> > > directory
> > >
> > >
> > > But libpgc.so is in
> > > /usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64
> > >
> > > What to do?
> > >
> > > Can someone help me with the commands?
> > >
> > > Thanks,
> > > Vidya.R
> > > --
> > > 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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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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Re: [gmx-users] error sharing libraries...gromacs error

[Vidya R]

Hi,

I now use

export MPIRUN="/usr/mpi/gcc/openmpi-1.2.8/bin"

But, how to fix that error?

Thanks,
Vidya.R

On Tue, Sep 12, 2017 at 5:42 PM, Mark Abraham 
wrote:

> Hi,
>
> If you're trying to use the PGI compilers, then please don't because the
> C++ performance is very poor. We recommend latest gcc or intel.
>
> Otherwise, configure GROMACS so that it uses the wrapper compilers when
> buildling, e.g. cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++
> etc. Organizing this stuff is their job.
>
> Mark
>
> On Tue, Sep 12, 2017 at 1:46 PM Vidya R  wrote:
>
> > Hi,
> >
> > I give these commands
> >
> > PATH=$PATH:"/usr/local/gromacs/bin/"
> > export GMXLIB=/usr/local/gromacs/share/gromacs/top
> > export LD_LIBRARY_PATH=/usr/lib
> > export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun"
> > export
> >
> > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/ansys_inc/v140/CFX/
> tools/icemcfd-12.0-post-3/lib/linux-amd64
> >
> >
> > before these
> >
> > gmx grompp -f mdp/min.mdp -o min -pp min -po min
> > g_tune_pme -np 4 -s min.tpr -launch
> >
> >
> >
> > But, I am getting this error
> >
> > /usr/mpi/pgi/openmpi-1.2.8/bin/mpirun: error while loading shared
> > libraries: libpgc.so: cannot open shared object file: No such file or
> > directory
> >
> >
> > But libpgc.so is in
> > /usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64
> >
> > What to do?
> >
> > Can someone help me with the commands?
> >
> > Thanks,
> > Vidya.R
> > --
> > 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 (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>
> * 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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Re: [gmx-users] error sharing libraries...gromacs error

[Mark Abraham]

Hi,

If you're trying to use the PGI compilers, then please don't because the
C++ performance is very poor. We recommend latest gcc or intel.

Otherwise, configure GROMACS so that it uses the wrapper compilers when
buildling, e.g. cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++
etc. Organizing this stuff is their job.

Mark

On Tue, Sep 12, 2017 at 1:46 PM Vidya R  wrote:

> Hi,
>
> I give these commands
>
> PATH=$PATH:"/usr/local/gromacs/bin/"
> export GMXLIB=/usr/local/gromacs/share/gromacs/top
> export LD_LIBRARY_PATH=/usr/lib
> export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun"
> export
>
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64
>
>
> before these
>
> gmx grompp -f mdp/min.mdp -o min -pp min -po min
> g_tune_pme -np 4 -s min.tpr -launch
>
>
>
> But, I am getting this error
>
> /usr/mpi/pgi/openmpi-1.2.8/bin/mpirun: error while loading shared
> libraries: libpgc.so: cannot open shared object file: No such file or
> directory
>
>
> But libpgc.so is in
> /usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64
>
> What to do?
>
> Can someone help me with the commands?
>
> Thanks,
> Vidya.R
> --
> 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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Re: [gmx-users] Free Energy Calculations: Error during minimization step.

[Wes Barnett]

On Tue, Sep 12, 2017 at 12:17 AM, Abhishek Acharya  wrote:

> Just to add to the above post, running a none to vdw-q tranformation using
> the following parameters also results in the same error for simulation at
> first lambda.
>


Do you get this error on a normal simulation as well? That is, if you run
state 0 (with vdw and electrostatics on) without doing an free energy
calculations, do you still get the error? Perhaps you are using too big a
of a time step or your system is not equilibrated enough before using this
time step. Or you may just have a bad starting configuration.


>
> 
> 
> 
> vdw_lambdas  = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
> 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00
> 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00 1.00
> coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.15
> 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90
> 0.95 1.00
> ; We are not transforming any bonded or restrained interactions
> bonded_lambdas   = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00
> restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00
> ; Masses are not changing (particle identities are the same at lambda = 0
> and lambda = 1)
> mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00
> ; Not doing simulated temperting here
> temperature_lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00
> ; Options for the decoupling
> sc-alpha = 0.5
> sc-coul  = no   ; linear interpolation of Coulomb (none
> in this case)
> sc-power = 1
> sc-sigma = 0.3
> couple-moltype   = Protein  ; name of moleculetype to decouple
> couple-lambda0   = none
> couple-lambda1   = vdw-q
> couple-intramol  = no
> nstdhdl  = 10
> 
> 
> 
>
> Thanks in advance.
>
> Abhishek Acharya
> Research Associate,
> Department of Molecular Nutrition
> CSIR-Central Food Technological Research Institute,
> Mysuru-570020
>
> On Tue, Sep 12, 2017 at 9:42 AM, Abhishek Acharya <
> abhi117acha...@gmail.com>
> wrote:
>
> > Hello GROMACS users,
> >
> > As Wes had advised previously in this thread, the issue with the vdw
> > tranformations was rectified by removing the charges from the topology
> > file. Thereafter, I also tried running free energy calculations using the
> > following free-energy parameters:
> >
> > 
> > 
> > 
> > free_energy  = yes
> > init_lambda_state= 0
> > delta_lambda = 0
> > calc_lambda_neighbors= 1; only immediate neighboring windows
> > ; Vectors of lambda specified here
> > ; Each combination is an index that is retrieved from for each simulation
> > coul_lambdas  = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
> > 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00
> 1.00
> > 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00
> > 1.00 1.00
> > vdw_lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10
> 0.15
> > 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85
> 0.90
> > 0.95 1.00
> > bonded_lambdas   = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00
> > restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 

[gmx-users] error sharing libraries...gromacs error

[Vidya R]

Hi,

I give these commands

PATH=$PATH:"/usr/local/gromacs/bin/"
export GMXLIB=/usr/local/gromacs/share/gromacs/top
export LD_LIBRARY_PATH=/usr/lib
export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun"
export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64


before these

gmx grompp -f mdp/min.mdp -o min -pp min -po min
g_tune_pme -np 4 -s min.tpr -launch



But, I am getting this error

/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun: error while loading shared
libraries: libpgc.so: cannot open shared object file: No such file or
directory


But libpgc.so is in
/usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64

What to do?

Can someone help me with the commands?

Thanks,
Vidya.R
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Re: [gmx-users] dielectric constant -reg

[Mark Abraham]

Hi,

You haven't described what you're doing in enough detail for anybody to be
able to suggest where you or the code might be doing something wrong.

Mark

On Tue, Sep 12, 2017 at 12:36 PM Meagha ramana kumar 
wrote:

> hi mark,
>
> Same doubt in the following thread.
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-May/106078.html
>
> with epsilon_-surface =0, simulation runs fine. The problem starts when I
> give it a value. My model has only protein and doesn't have anything other
> than that.
> Moreover, i have read the .mdp file, as you have mentioned in the previous
> threads.
>
>
> thank u
> Meagha
>
> On Mon, Sep 11, 2017 at 9:53 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Clearly the .mdp file changes you say you are making aren't showing up
> > later in wherever you are observing a 1.12, but we'll need to see a lot
> > more detail of your process - e.g. command lines with the file names - to
> > suggest what might be wrong. That means you need to be able to copy and
> > paste them from a terminal or script, or you won't generally be able to
> > reconcile what you think you did with what you actually did.
> >
> > Mark
> >
> > On Mon, Sep 11, 2017 at 9:51 AM Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Change the mdp file and use that file to make a new tpr file and that
> the
> > > file to run a simulation.
> > >
> > > Mark
> > >
> > > On Mon, 11 Sep 2017 08:21 Meagha ramana kumar 
> wrote:
> > >
> > >> Hi gmx-users,
> > >>
> > >> My problem may sound silly, but please help me with it. I know how to
> > >> change dielectric constant for simulation. Yes I have read all the
> > previous
> > >> thread reading this and no one provided straight answer to this. I am
> > using
> > >> PME. I tried changing all the epsilon values but nothing helped and I
> > get
> > >> 1.12. will be thankful , if you guys help me out.
> > >>
> > >> Thank you
> > >> Meagha
> > >>
> > >>
> > >> Sent from Mail for Windows 10
> > >>
> > >> --
> > >> 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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> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > >> send a mail to gmx-users-requ...@gromacs.org.
> > >>
> > >
> > --
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Re: [gmx-users] dielectric constant -reg

[Meagha ramana kumar]

hi mark,

Same doubt in the following thread.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-May/106078.html

with epsilon_-surface =0, simulation runs fine. The problem starts when I
give it a value. My model has only protein and doesn't have anything other
than that.
Moreover, i have read the .mdp file, as you have mentioned in the previous
threads.


thank u
Meagha

On Mon, Sep 11, 2017 at 9:53 PM, Mark Abraham 
wrote:

> Hi,
>
> Clearly the .mdp file changes you say you are making aren't showing up
> later in wherever you are observing a 1.12, but we'll need to see a lot
> more detail of your process - e.g. command lines with the file names - to
> suggest what might be wrong. That means you need to be able to copy and
> paste them from a terminal or script, or you won't generally be able to
> reconcile what you think you did with what you actually did.
>
> Mark
>
> On Mon, Sep 11, 2017 at 9:51 AM Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Change the mdp file and use that file to make a new tpr file and that the
> > file to run a simulation.
> >
> > Mark
> >
> > On Mon, 11 Sep 2017 08:21 Meagha ramana kumar  wrote:
> >
> >> Hi gmx-users,
> >>
> >> My problem may sound silly, but please help me with it. I know how to
> >> change dielectric constant for simulation. Yes I have read all the
> previous
> >> thread reading this and no one provided straight answer to this. I am
> using
> >> PME. I tried changing all the epsilon values but nothing helped and I
> get
> >> 1.12. will be thankful , if you guys help me out.
> >>
> >> Thank you
> >> Meagha
> >>
> >>
> >> Sent from Mail for Windows 10
> >>
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Re: [gmx-users] libgomp: Thread creation failed: Cannot allocate memory

[Mark Abraham]

Hi,

Don't know, but likely something about your machine has changed since
GROMACS was built, e.g. OS upgrade. I suggest you recompile.

Mark

On Tue, Sep 12, 2017 at 12:08 PM Neha Gupta  wrote:

> Hi,
>
> When I give this command
>
> gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm min
>
>
> I get this error
> libgomp: Thread creation failed: Cannot allocate memory
>
>
> What is the reason?
>
> Thanks,
> Neha
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[gmx-users] libgomp: Thread creation failed: Cannot allocate memory

[Neha Gupta]

Hi,

When I give this command

gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm min


I get this error
libgomp: Thread creation failed: Cannot allocate memory


What is the reason?

Thanks,
Neha
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