Re: [gmx-users] Thought you'd find this interesting

[Oliver Schillinger]

Hi,
I doubt that a technical mailing list is the right place to advertise 
charity stuff. Especially if that means subscribing the mailing list to 
a newsletter.

I try to keep up reading this mailing list, scanning for
topics of interest to me, which becomes increasingly more difficult if I 
have to filter for spam.


Of course that's only my opinion.

Cheers,
Oliver


On 06/24/2013 06:55 AM, Anil Mhashal wrote:


Hi Discussion,


I’ve just learned about the water crisis and thought you would be interested to 
check out this story:

https://waterforward.charitywater.org/et/3ZYWubNN



Thanks,
Anil



--
Sent via WaterForward, an initiative of charity: water
WaterForward, 387 Tehama Street, San Francisco, CA 94103, USA.
Click here to unsubscribe: 
https://waterforward.charitywater.org/opt_out?et=3ZYWubNN



--
Oliver Schillinger
Master's student

Forschungszentrum Juelich GmbH
52425 Juelich | Germany

Building 5.8v, Room 3010
Phone: 02461-61-9532

Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
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Re: [gmx-users] Thought you'd find this interesting

[Anil Mhashal]

Dear all gmxuser,

I am extremely sorry for the post shared in the gmxuser mailing list.
This was done by mistake.

Please ignore the previous mail. I strongly apologize for the mail and the
inconvenience caused.
Anil


On 24 June 2013 12:50, Oliver Schillinger  wrote:

> Hi,
> I doubt that a technical mailing list is the right place to advertise
> charity stuff. Especially if that means subscribing the mailing list to a
> newsletter.
> I try to keep up reading this mailing list, scanning for
> topics of interest to me, which becomes increasingly more difficult if I
> have to filter for spam.
>
> Of course that's only my opinion.
>
> Cheers,
> Oliver
>
>
>
> On 06/24/2013 06:55 AM, Anil Mhashal wrote:
>
>>
>> Hi Discussion,
>>
>>
>> I’ve just learned about the water crisis and thought you would be
>> interested to check out this story:
>>
>> https://waterforward.**charitywater.org/et/3ZYWubNN
>>
>>
>>
>> Thanks,
>> Anil
>>
>>
>>
>> --
>> Sent via WaterForward, an initiative of charity: water
>> WaterForward, 387 Tehama Street, San Francisco, CA 94103, USA.
>> Click here to unsubscribe: https://waterforward.**
>> charitywater.org/opt_out?et=**3ZYWubNN
>>
>>
> --
> Oliver Schillinger
> Master's student
>
> Forschungszentrum Juelich GmbH
> 52425 Juelich | Germany
>
> Building 5.8v, Room 3010
> Phone: 02461-61-9532
>
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
>
> --
> 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/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Anil R.Mhashal
Research fellow
Soft Matter Theory Group,
Physical Chemistry Division,
National Chemical Laboratory,
Pune
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[gmx-users] TPI Results differ in v4.5.7 and v4.6.1

[Niels Müller]

Hi GMX Users,

We are computing the chemical potential of different gas molecules in a polymer 
melt with the tpi integrator.
The computations are done for CO2 and CH4.
The previous computations were done with v4.5.5 or 4.5.7 and gave equal results.

I recently switched to gromacs version 4.6.1, and the chemical potential 
computed by this version is shifted by a nearly constant factor, which is 
different for the two gas molecules.
We are perplexed what causes this shift. Was there any change in the new 
version that affects the tpi integration? I will provide the mdp file we used 
below.

The tpi integration is run on basis of the last 10 ns of a 30 ns NVT simulation 
with 'mdrun -rerun'.

Best regards, 
Niels.

#
The mdp file:
#

; VARIOUS PREPROCESSING OPTIONS
cpp  = cpp
include= 
define  = 

; RUN CONTROL PARAMETERS
integrator   = tpi
; Start time and timestep in ps
tinit= 0
dt   = 0.001
nsteps   = 100   
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear

; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps= 

; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
bd-fric  = 0.5
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 100
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 20
; Step size (1/ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep   = 1000
nbfgscorr= 10

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 100  
nstvout  = 0
nstfout  = 0
; Checkpointing helps you continue after crashes
nstcheckpoint= 100
; Output frequency for energies to log file and energy file
nstlog   = 100
nstenergy= 100 
; Output frequency and precision for xtc file
nstxtcout= 0  
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = 
; Selection of energy groups
energygrps   = 

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off
rlist= 0.9
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = pme
rcoulomb-switch  = 0
rcoulomb = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r= 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths   
rvdw-switch  = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0

; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
Tcoupl   = V-rescale  
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 318
; Pressure coupling 
Pcoupl = Parrinello-Rahman
Pcoupltype   = isotropic
; Time

[gmx-users] problem with charmm2gromacs-pvm.py

[Albert]

Hello:

 I am trying to use charmm2gromacs-pvm.py to generate cgenff with comman:

python charmm2gromacs-pvm.py toppar/par_all36_cgenff.prm 
toppar/top_all36_cgenff.rtf


but it always failed with messages:


Creating cgenff-2b7.ff files...
Traceback (most recent call last):
  File "charmm2gromacs-pvm.py", line 283, in 
name = segments[1]
IndexError: list index out of range


thank you very much
Albert
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Re: [gmx-users] TPI Results differ in v4.5.7 and v4.6.1

[João M . Damas]

Niels,

This is very interesting. At our group, a colleague of mine and I have also
identified differences in the TPI integrator between 4.0.X and 4.5.X, but
we still haven't had the time to report it properly, since we are using a
slightly modified version of the TPI algorithm.

Instinctively, we were attributing it to some different behaviours in the
RF that are observed between those versions. We also know that the TPI
algorithm began allowing PME treatment from 4.5.X onwards, so maybe there
are some differences going on the electrostatics level? But, IIRC, no
modifications to the TPI code were on the release notes from 4.5.X to
4.6.X...

We'll try to find some time to report our findings as soon as possible.
Maybe they are related.

Best,
João


On Mon, Jun 24, 2013 at 10:19 AM, Niels Müller  wrote:

> Hi GMX Users,
>
> We are computing the chemical potential of different gas molecules in a
> polymer melt with the tpi integrator.
> The computations are done for CO2 and CH4.
> The previous computations were done with v4.5.5 or 4.5.7 and gave equal
> results.
>
> I recently switched to gromacs version 4.6.1, and the chemical potential
> computed by this version is shifted by a nearly constant factor, which is
> different for the two gas molecules.
> We are perplexed what causes this shift. Was there any change in the new
> version that affects the tpi integration? I will provide the mdp file we
> used below.
>
> The tpi integration is run on basis of the last 10 ns of a 30 ns NVT
> simulation with 'mdrun -rerun'.
>
> Best regards,
> Niels.
>
> #
> The mdp file:
> #
>
> ; VARIOUS PREPROCESSING OPTIONS
> cpp  = cpp
> include=
> define  =
>
> ; RUN CONTROL PARAMETERS
> integrator   = tpi
> ; Start time and timestep in ps
> tinit= 0
> dt   = 0.001
> nsteps   = 100
> ; For exact run continuation or redoing part of a run
> init_step= 0
> ; mode for center of mass motion removal
> comm-mode= Linear
>
> ; number of steps for center of mass motion removal
> nstcomm  = 1
> ; group(s) for center of mass motion removal
> comm-grps=
>
> ; LANGEVIN DYNAMICS OPTIONS
> ; Temperature, friction coefficient (amu/ps) and random seed
> bd-fric  = 0.5
> ld-seed  = 1993
>
> ; ENERGY MINIMIZATION OPTIONS
> ; Force tolerance and initial step-size
> emtol= 100
> emstep   = 0.01
> ; Max number of iterations in relax_shells
> niter= 20
> ; Step size (1/ps^2) for minimization of flexible constraints
> fcstep   = 0
> ; Frequency of steepest descents steps when doing CG
> nstcgsteep   = 1000
> nbfgscorr= 10
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout  = 100
> nstvout  = 0
> nstfout  = 0
> ; Checkpointing helps you continue after crashes
> nstcheckpoint= 100
> ; Output frequency for energies to log file and energy file
> nstlog   = 100
> nstenergy= 100
> ; Output frequency and precision for xtc file
> nstxtcout= 0
> xtc-precision= 1000
> ; This selects the subset of atoms for the xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps =
> ; Selection of energy groups
> energygrps   =
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist  = 5
> ; ns algorithm (simple or grid)
> ns_type  = grid
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc  = xyz
> ; nblist cut-off
> rlist= 0.9
> domain-decomposition = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype  = pme
> rcoulomb-switch  = 0
> rcoulomb = 0.9
> ; Dielectric constant (DC) for cut-off or DC of reaction field
> epsilon-r= 1
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> ; cut-off lengths
> rvdw-switch  = 0
> rvdw = 0.9
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension  = 1
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing   = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> ; EWALD/PME/PPPM parameters
> pme_order= 4
> ewald_rtol   = 1e-05
> ewald_geometry   = 3d
> epsilon_su

[gmx-users] radial distribution function gAB (r, theta)

[neshat haq]

Gromacs manual explains "radial distribution function gAB (r, theta)"
but g_rdf donot have options to directly do this.
Can anyone elaborate this.


-- 
Best regards
Neshatul Haque
PhD, Dpt of Biotechnology
university of hyderabad
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Re: [gmx-users] TPI Results differ in v4.5.7 and v4.6.1

[Niels Müller]

Hi João,

Indeed your instinct seems to be good! When switching the Coulomb-Type to 
Cut-Off, there doesn't seem to be a difference between 4.6 and 4.5.
Apparently its an issue with the PME sum. We will investigate further.


Am 24.06.2013 um 14:42 schrieb João M. Damas :

> Niels,
> 
> This is very interesting. At our group, a colleague of mine and I have also
> identified differences in the TPI integrator between 4.0.X and 4.5.X, but
> we still haven't had the time to report it properly, since we are using a
> slightly modified version of the TPI algorithm.
> 
> Instinctively, we were attributing it to some different behaviours in the
> RF that are observed between those versions. We also know that the TPI
> algorithm began allowing PME treatment from 4.5.X onwards, so maybe there
> are some differences going on the electrostatics level? But, IIRC, no
> modifications to the TPI code were on the release notes from 4.5.X to
> 4.6.X...
> 
> We'll try to find some time to report our findings as soon as possible.
> Maybe they are related.
> 
> Best,
> João
> 
> 
> On Mon, Jun 24, 2013 at 10:19 AM, Niels Müller  wrote:
> 
>> Hi GMX Users,
>> 
>> We are computing the chemical potential of different gas molecules in a
>> polymer melt with the tpi integrator.
>> The computations are done for CO2 and CH4.
>> The previous computations were done with v4.5.5 or 4.5.7 and gave equal
>> results.
>> 
>> I recently switched to gromacs version 4.6.1, and the chemical potential
>> computed by this version is shifted by a nearly constant factor, which is
>> different for the two gas molecules.
>> We are perplexed what causes this shift. Was there any change in the new
>> version that affects the tpi integration? I will provide the mdp file we
>> used below.
>> 
>> The tpi integration is run on basis of the last 10 ns of a 30 ns NVT
>> simulation with 'mdrun -rerun'.
>> 
>> Best regards,
>> Niels.
>> 
>> #
>> The mdp file:
>> #
>> 
>> ; VARIOUS PREPROCESSING OPTIONS
>> cpp  = cpp
>> include=
>> define  =
>> 
>> ; RUN CONTROL PARAMETERS
>> integrator   = tpi
>> ; Start time and timestep in ps
>> tinit= 0
>> dt   = 0.001
>> nsteps   = 100
>> ; For exact run continuation or redoing part of a run
>> init_step= 0
>> ; mode for center of mass motion removal
>> comm-mode= Linear
>> 
>> ; number of steps for center of mass motion removal
>> nstcomm  = 1
>> ; group(s) for center of mass motion removal
>> comm-grps=
>> 
>> ; LANGEVIN DYNAMICS OPTIONS
>> ; Temperature, friction coefficient (amu/ps) and random seed
>> bd-fric  = 0.5
>> ld-seed  = 1993
>> 
>> ; ENERGY MINIMIZATION OPTIONS
>> ; Force tolerance and initial step-size
>> emtol= 100
>> emstep   = 0.01
>> ; Max number of iterations in relax_shells
>> niter= 20
>> ; Step size (1/ps^2) for minimization of flexible constraints
>> fcstep   = 0
>> ; Frequency of steepest descents steps when doing CG
>> nstcgsteep   = 1000
>> nbfgscorr= 10
>> 
>> ; OUTPUT CONTROL OPTIONS
>> ; Output frequency for coords (x), velocities (v) and forces (f)
>> nstxout  = 100
>> nstvout  = 0
>> nstfout  = 0
>> ; Checkpointing helps you continue after crashes
>> nstcheckpoint= 100
>> ; Output frequency for energies to log file and energy file
>> nstlog   = 100
>> nstenergy= 100
>> ; Output frequency and precision for xtc file
>> nstxtcout= 0
>> xtc-precision= 1000
>> ; This selects the subset of atoms for the xtc file. You can
>> ; select multiple groups. By default all atoms will be written.
>> xtc-grps =
>> ; Selection of energy groups
>> energygrps   =
>> 
>> ; NEIGHBORSEARCHING PARAMETERS
>> ; nblist update frequency
>> nstlist  = 5
>> ; ns algorithm (simple or grid)
>> ns_type  = grid
>> ; Periodic boundary conditions: xyz (default), no (vacuum)
>> ; or full (infinite systems only)
>> pbc  = xyz
>> ; nblist cut-off
>> rlist= 0.9
>> domain-decomposition = no
>> 
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> ; Method for doing electrostatics
>> coulombtype  = pme
>> rcoulomb-switch  = 0
>> rcoulomb = 0.9
>> ; Dielectric constant (DC) for cut-off or DC of reaction field
>> epsilon-r= 1
>> ; Method for doing Van der Waals
>> vdw-type = Cut-off
>> ; cut-off lengths
>> rvdw-switch  = 0
>> rvdw = 0.9
>> ; Apply long range dispersion corrections for Energy and Pressure
>> DispCorr = EnerPres
>> ; Extension of the po

Re: [gmx-users] Gromacs GPU system question

[Szilárd Páll]

I strongly suggest that you consider the single-chip GTX cards instead
of a dual-chip one; from the point of view of price/performance you'll
probably get the most from a 680 or 780.

You could ask why, so here are the reasons:
- The current parallelization scheme requires domain-decomposition to
use more than one GPU and the overhead of domain-decomposition is
quite high, so you typically get only 1.5-1.7x when going from one to
two domains (=GPUs, but you'll see that same with running CPUs only as
well);
- GROMACS uses the GPU as a coprocessor and needs to transfer
coordinates to the GPU and forces back; if your PCI-E is shared by two
GPUs which will inherently try to transfer at the same time, you'll
the overhead of transferring will get rather high (15% or more).

Cheers,
--
Szilárd


On Sat, Jun 22, 2013 at 5:31 PM, Mare Libero  wrote:
> Hello,
>
> I am assembling a GPU workstation to run MD simulations, and I was wondering 
> if anyone has any recommendation regarding the GPU/CPU combination.
>
> From what I can see, the GTX690 could be the best bang for my buck in terms 
> of number of cores, memory, clock rate. But being a dual GPU card, I was 
> wondering if  there is any latency issue that could make its performances 
> less favorable with respect to a GTX Titan.
>
> Also, which motherboard, CPU is recommendable for this system.
>
> Thank you in advance for you help,
>
> Al
> --
> 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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Re: [gmx-users] Gromacs GPU system question

[Szilárd Páll]

On Sat, Jun 22, 2013 at 5:55 PM, Mirco Wahab
 wrote:
> On 22.06.2013 17:31, Mare Libero wrote:
>>
>> I am assembling a GPU workstation to run MD simulations, and I was
>> wondering if anyone has any recommendation regarding the GPU/CPU
>> combination.
>>  From what I can see, the GTX690 could be the best bang for my buck in
>> terms of number of cores, memory, clock rate. But being a dual GPU card, I
>> was wondering if  there is any latency issue that could make its
>> performances less favorable with respect to a GTX Titan.
>> Also, which motherboard, CPU is recommendable for this system.
>
>
> The most important aspect to consider (by far) is, in my humble
> opinion, *your specific workload*:
>
>  - Size of the simulation box / number of atoms,
>  - Specific force field/required integrator (verlet?),
>  - Handling of long range electrostatics (pme/RF/coulomb).
>
> Furthermore, the effect of the CPU is, imho, much more
> pronounced. Remember, mdrun-gpu doesn't 'run' on the
> GPU (as, e.g., HOOMD does) but loads work-sets up to
> the GPU, runs them, and loads them back. For example: in
> one box, I  have an AMD FX-8350 and a GTX-660Ti available
> for tests, and I didn't see the GPU load going much over 60%,
> even with millons of atoms. Here, small differences in the

Without DD you should be able to get up to 75-80% CPU-GPU overlap
(slighly less with vsites).

> potential/force field used by the model will probably change
> the performance of the GPU-related parts significantly (due
> to cu-offs and buffering schemes).
>
> Regards
>
> M.
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
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[gmx-users] Re: gmx-users Digest, Vol 110, Issue 114

[Raji Viswanathan]

I am using Red Hat Enterprise Linux 5.5
Raji


On 6/20/13 5:16 PM, "gmx-users-requ...@gromacs.org"
 wrote:

> Send gmx-users mailing list submissions to
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> Today's Topics:
> 
>1. Re: System expansion (Dr. Vitaly Chaban)
>2. Error while using genion (Raji Viswanathan)
>3. Test Particle Insertion (Phan, Anh T.)
>4. Re: Test Particle Insertion (Naga Rajesh Tummala)
>5. Decouple (Hari Pandey)
>6. Re: Error while using genion (Justin Lemkul)
> 
> 
> --
> 
> Message: 1
> Date: Thu, 20 Jun 2013 18:12:16 +0200
> From: "Dr. Vitaly Chaban" 
> Subject: Re: [gmx-users] System expansion
> To: Discussion list for GROMACS users 
> Message-ID:
> 
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Oliver -
> 
> Hmm. Did you try to start from (a little bit) different configurations
> on the problematic machine? Or re-install gromacs there, perhaps?
> 
> Dr. Vitaly Chaban
> 
> 
> 
> 
> 
> On Thu, Jun 20, 2013 at 3:44 PM, Oliver Schillinger
> wrote:
> 
>> Dear Gromacs users,
>> 
>> I experience a very strange problem.
>> I have a well equilibrated system consisting of a protein, a ligand, ions
>> and water. On most machines I run my simulations on, everything is just
>> fine. Except for one compute cluster, where the system undergoes an extreme
>> expansion when I use the md-vv integrator for an NPT-simulation. To give
>> you an impression I uploaded a short video showing the first 100
>> picoseconds of the run to my Dropbox:
>> https://www.dropbox.com/s/**d1ef94bbns0hasr/explode.mpg> om/s/d1ef94bbns0hasr/explode.mpg>
>> 
>> The system expands so heavily that it consists mainly of vacuum.
>> If I switch the integrator from md-vv to md, everything is fine again.
>> The same simulation (same .mdp file, same starting positions and
>> velocities from previous simulation) runs fine with the md-vv integrator on
>> our GPU-cluster.
>> 
>> The .mdp file can be downloaded here:
>> https://www.dropbox.com/s/**k9it6eiqb259o59/explode.mdp> om/s/k9it6eiqb259o59/explode.mdp>
>> 
>> I have no idea if it is me who is doing something wrond, a bug in Gromacs,
>> a problem with the cluster or something else.
>> Any suggestions and ideas are appreciated.
>> 
>> Regards,
>> Oliver
>> 
>> --
>> Oliver Schillinger
>> Master's student
>> 
>> Forschungszentrum Juelich GmbH
>> 52425 Juelich | Germany
>> 
>> Building 5.8v, Room 3010
>> Phone: 02461-61-9532
>> 
>> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
>> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
>> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
>> Prof. Dr. Sebastian M. Schmidt
>> --
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>> 
> 
> 
> --
> 
> Message: 2
> Date: Thu, 20 Jun 2013 17:57:28 +
> From: Raji Viswanathan 
> Subject: [gmx-users] Error while using genion
> To: "gmx-users@gromacs.org" 
> Message-ID:
> 
> Content-Type: text/plain; charset="iso-8859-1"
> 
> I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin
> peptide.  I was going through the steps in the tutorial but got stuck with the
> genion command.  When I am prompted to select a group, I get the error that it
> is not found.  I tried many different ways of specifying this but still get
> the same error.  I would appreciate your help.  I am enclosing the output
> below:
> 
>   GROtesk MACabre and Sinister
> 
> :-)  VERSION 4.5.5  (-:
> 
> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>   Aldert van Buuren, P?r Bjelkmar, Rudi van Drunen, Anton Feenstra,
> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
>Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
> 
>   

Re: [gmx-users] radial distribution function gAB (r, theta)

[Justin Lemkul]

On 6/24/13 9:05 AM, neshat haq wrote:

Gromacs manual explains "radial distribution function gAB (r, theta)"
but g_rdf donot have options to directly do this.
Can anyone elaborate this.



That section probably refers to a feature that was intended to be included but 
was never developed.  Such documentation inconsistencies happen every now and again.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Error while using genion

[Justin Lemkul]

Please do not reply to the entire digest.  It gets hopelessly confusing.

On 6/24/13 10:51 AM, Raji Viswanathan wrote:

I am using Red Hat Enterprise Linux 5.5
Raji


Something about your shell environment is probably hosed.  Do other commands 
that prompt for interactive input work, or just genion?  Does the following work?


echo 13 | genion -s ion.tpr -o fws-b4em.gro -neutral -conc 0.15 -p fws.top -g 
ion.log


-Justin




Message: 2
Date: Thu, 20 Jun 2013 17:57:28 +
From: Raji Viswanathan 
Subject: [gmx-users] Error while using genion
To: "gmx-users@gromacs.org" 
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin
peptide.  I was going through the steps in the tutorial but got stuck with the
genion command.  When I am prompted to select a group, I get the error that it
is not found.  I tried many different ways of specifying this but still get
the same error.  I would appreciate your help.  I am enclosing the output
below:

   GROtesk MACabre and Sinister

 :-)  VERSION 4.5.5  (-:

 Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
   Aldert van Buuren, P?r Bjelkmar, Rudi van Drunen, Anton Feenstra,
 Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
 Michael Shirts, Alfons Sijbers, Peter Tieleman,

Berk Hess, David van der Spoel, and Erik Lindahl.

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2010, The GROMACS development team at
 Uppsala University & The Royal Institute of Technology, Sweden.
 check out http://www.gromacs.org for more information.

  This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 2
  of the License, or (at your option) any later version.

 :-)  genion  (-:

Option Filename  Type Description

   -sion.tpr  InputRun input file: tpr tpb tpa
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
   -n  index.ndx  Input, Opt.  Index file
   -o   fws-b4em.gro  Output   Structure file: gro g96 pdb etc.
   -gion.log  Output   Log file
-potpot.pdb  Output, Opt. Protein data bank file
   -pfws.top  In/Out, Opt! Topology file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint19  Set the nicelevel
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-np  int0   Number of positive ions
-pname   string NA  Name of the positive ion
-pq  int1   Charge of the positive ion
-nn  int0   Number of negative ions
-nname   string CL  Name of the negative ion
-nq  int-1  Charge of the negative ion
-rminreal   0.6 Minimum distance between ions
-[no]random  bool   yes Use random placement of ions instead of based on
 potential. The rmin option should still work
-seedint1993Seed for random number generator
-scale   real   0.001   Scaling factor for the potential for -pot
-concreal   0.15Specify salt concentration (mol/liter). This will
 add sufficient ions to reach up to the specified
 concentration as computed from the volume of the
 cell in the input .tpr file. Overrides the -np
 and -nn options.
-[no]neutral bool   yes This option will add enough ions to neutralize
 the system. In combination with the concentration
 option a neutral system at a given salt
 concentration will be generated.

Reading file ion.tpr, VERSION 4.5.5 (single precision)
Using a coulomb cut-off of 1 nm
Will try to add 12 NA ions and 14 CL ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 12666 elements
Group 1 (Protein) has   495 elements
Group 2 (  Protein-H) has   257 elements
Group 3 (C-alpha) has35 elements
Group 4 (   Backbone) has   105 elements
Group 5 (  MainChain) has   141 elements
Group 6 (   MainChain+Cb) has   171 elements
Group 7 (MainChain+H) has   176 elements
Group 8 (  SideChain) has   319 elements
Group 9 (SideChain-H) has   116 elements
Group10 (Prot-Masses) has

[gmx-users] Re: Error while using genion

[raji_yu]

Yes, that command works and the entry 13 is recognized as 'SOL'




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Re: [gmx-users] Re: Error while using genion

[Justin Lemkul]

On 6/24/13 11:36 AM, raji_yu wrote:

Yes, that command works and the entry 13 is recognized as 'SOL'



OK, then you need to figure out why your shell doesn't understand the difference 
between an input stream and a command, otherwise you have to do all your 
selections via echo, which can be annoying for some commands.  Presumably, 
though, pdb2gmx worked earlier in the tutorial workflow, did it not?  Running 
pdb2gmx requires interactive selections (or a potentially very cumbersome echo 
series).  If other commands work or if genion works in a new terminal window, 
probably some other process is causing the problem.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] TPI Results differ in v4.5.7 and v4.6.1

[Szilárd Páll]

If you have a solid example that reproduced the problem, feel free to
file an issue on redmine.gromacs.org ASAP. Briefly documenting your
experiments and verification process on the issue report page can help
help developers in giving you faster feedback as well as with
accepting the report as a bug and fixing it (if it is one).

Cheers,
--
Szilárd


On Mon, Jun 24, 2013 at 4:40 PM, Niels Müller  wrote:
> Hi João,
>
> Indeed your instinct seems to be good! When switching the Coulomb-Type to 
> Cut-Off, there doesn't seem to be a difference between 4.6 and 4.5.
> Apparently its an issue with the PME sum. We will investigate further.
>
>
> Am 24.06.2013 um 14:42 schrieb João M. Damas :
>
>> Niels,
>>
>> This is very interesting. At our group, a colleague of mine and I have also
>> identified differences in the TPI integrator between 4.0.X and 4.5.X, but
>> we still haven't had the time to report it properly, since we are using a
>> slightly modified version of the TPI algorithm.
>>
>> Instinctively, we were attributing it to some different behaviours in the
>> RF that are observed between those versions. We also know that the TPI
>> algorithm began allowing PME treatment from 4.5.X onwards, so maybe there
>> are some differences going on the electrostatics level? But, IIRC, no
>> modifications to the TPI code were on the release notes from 4.5.X to
>> 4.6.X...
>>
>> We'll try to find some time to report our findings as soon as possible.
>> Maybe they are related.
>>
>> Best,
>> João
>>
>>
>> On Mon, Jun 24, 2013 at 10:19 AM, Niels Müller  wrote:
>>
>>> Hi GMX Users,
>>>
>>> We are computing the chemical potential of different gas molecules in a
>>> polymer melt with the tpi integrator.
>>> The computations are done for CO2 and CH4.
>>> The previous computations were done with v4.5.5 or 4.5.7 and gave equal
>>> results.
>>>
>>> I recently switched to gromacs version 4.6.1, and the chemical potential
>>> computed by this version is shifted by a nearly constant factor, which is
>>> different for the two gas molecules.
>>> We are perplexed what causes this shift. Was there any change in the new
>>> version that affects the tpi integration? I will provide the mdp file we
>>> used below.
>>>
>>> The tpi integration is run on basis of the last 10 ns of a 30 ns NVT
>>> simulation with 'mdrun -rerun'.
>>>
>>> Best regards,
>>> Niels.
>>>
>>> #
>>> The mdp file:
>>> #
>>>
>>> ; VARIOUS PREPROCESSING OPTIONS
>>> cpp  = cpp
>>> include=
>>> define  =
>>>
>>> ; RUN CONTROL PARAMETERS
>>> integrator   = tpi
>>> ; Start time and timestep in ps
>>> tinit= 0
>>> dt   = 0.001
>>> nsteps   = 100
>>> ; For exact run continuation or redoing part of a run
>>> init_step= 0
>>> ; mode for center of mass motion removal
>>> comm-mode= Linear
>>>
>>> ; number of steps for center of mass motion removal
>>> nstcomm  = 1
>>> ; group(s) for center of mass motion removal
>>> comm-grps=
>>>
>>> ; LANGEVIN DYNAMICS OPTIONS
>>> ; Temperature, friction coefficient (amu/ps) and random seed
>>> bd-fric  = 0.5
>>> ld-seed  = 1993
>>>
>>> ; ENERGY MINIMIZATION OPTIONS
>>> ; Force tolerance and initial step-size
>>> emtol= 100
>>> emstep   = 0.01
>>> ; Max number of iterations in relax_shells
>>> niter= 20
>>> ; Step size (1/ps^2) for minimization of flexible constraints
>>> fcstep   = 0
>>> ; Frequency of steepest descents steps when doing CG
>>> nstcgsteep   = 1000
>>> nbfgscorr= 10
>>>
>>> ; OUTPUT CONTROL OPTIONS
>>> ; Output frequency for coords (x), velocities (v) and forces (f)
>>> nstxout  = 100
>>> nstvout  = 0
>>> nstfout  = 0
>>> ; Checkpointing helps you continue after crashes
>>> nstcheckpoint= 100
>>> ; Output frequency for energies to log file and energy file
>>> nstlog   = 100
>>> nstenergy= 100
>>> ; Output frequency and precision for xtc file
>>> nstxtcout= 0
>>> xtc-precision= 1000
>>> ; This selects the subset of atoms for the xtc file. You can
>>> ; select multiple groups. By default all atoms will be written.
>>> xtc-grps =
>>> ; Selection of energy groups
>>> energygrps   =
>>>
>>> ; NEIGHBORSEARCHING PARAMETERS
>>> ; nblist update frequency
>>> nstlist  = 5
>>> ; ns algorithm (simple or grid)
>>> ns_type  = grid
>>> ; Periodic boundary conditions: xyz (default), no (vacuum)
>>> ; or full (infinite systems only)
>>> pbc  = xyz
>>> ; nblist cut-off
>>> rlist= 0.9
>>> domain-decomposition = no
>>>
>>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>>> ; Met

[gmx-users] 1-4 interactions free energy calculations

[Sonia Aguilera]

Hi all!

I have been running a series of simulations for coupling a molecule (free
energy calculations). All my settings and parameters in the mdp file worked
great for one system, but then I change the molecule to a bigger one and I
started to have warnings about 1-4 interactions:

Warning: 1-4 interaction between 1 and 143 at distance 2.579 which is larger
than the 1-4 table size 2.500 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

I made severals tests to find the error: minimization, nvt, mdp and md
without the Free Energy settings and It ran without the warning. So I guess
the warning must be related to the FE implementation. However, I'm clueless
about what can I change to stop having that warning. I already read other
posts but I'm still the same. Should I just ignore it? Also, the initial
structure is the result of a md simulation, so I don't know what can be
wrong in the topology or mdp file.  Should I change the continuation
parameter (continuation=yes) for the minimization and the nvt? 

Energy minimization converged but not to machine precision:

Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 481 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -7.8070088e+05
Maximum force =  7.6036969e+02 on atom 68
Norm of force =  2.3164215e+01


This is the copy of the mdp file (based os Justin Lemluk's tutorial), I'm
using GROMACS 4.5.4.

title= steepest descent energy minimization
; Run control
integrator   = steep
nsteps   = 3
; EM criteria and other stuff
emtol= 100
emstep   = 0.01
niter= 20
nbfgscorr= 10
; Output control
nstlog   = 1
nstenergy= 1
; Neighborsearching and short-range nonbonded interactions
nstlist  = 1
ns_type  = grid
pbc  = xyz
periodic-molecules   = yes
rlist= 1.5
; Electrostatics
coulombtype  = PME
rcoulomb = 1.5
; van der Waals
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PMEPPPM FFT grid
fourierspacing   = 0.12
; EWALDPMEPPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no
; Temperature and pressure coupling are off during EM
tcoupl   = no
pcoupl   = no
; Free energy control stuff
free_energy  = yes
init_lambda  = 1.0
delta_lambda = 0
foreign_lambda   = 0.95
sc-alpha = 0
sc-power = 0
sc-sigma = 0
couple-moltype   = Protein_chain_A   ; name of moleculetype to
decouple
couple-lambda0   = vdw  ;  only vdw interactions
couple-lambda1   = vdw-q; all interactions
couple-intramol  = no
nstdhdl  = 10
; Generate velocities to start
gen_vel  = no
; options for bonds
constraints  = none  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Do not constrain the starting configuration
continuation = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12


Thank you in advance!!

Sonia Aguilera
Graduate assistant
Chemical Engineering Department
Universidad de los Andes




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Re: [gmx-users] 1-4 interactions free energy calculations

[Justin Lemkul]

On 6/24/13 1:07 PM, Sonia Aguilera wrote:

Hi all!

I have been running a series of simulations for coupling a molecule (free
energy calculations). All my settings and parameters in the mdp file worked
great for one system, but then I change the molecule to a bigger one and I
started to have warnings about 1-4 interactions:

Warning: 1-4 interaction between 1 and 143 at distance 2.579 which is larger
than the 1-4 table size 2.500 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

I made severals tests to find the error: minimization, nvt, mdp and md
without the Free Energy settings and It ran without the warning. So I guess
the warning must be related to the FE implementation. However, I'm clueless
about what can I change to stop having that warning. I already read other
posts but I'm still the same. Should I just ignore it? Also, the initial
structure is the result of a md simulation, so I don't know what can be
wrong in the topology or mdp file.  Should I change the continuation
parameter (continuation=yes) for the minimization and the nvt?

Energy minimization converged but not to machine precision:

Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 481 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -7.8070088e+05
Maximum force =  7.6036969e+02 on atom 68
Norm of force =  2.3164215e+01


This is the copy of the mdp file (based os Justin Lemluk's tutorial), I'm
using GROMACS 4.5.4.

title= steepest descent energy minimization
; Run control
integrator   = steep
nsteps   = 3
; EM criteria and other stuff
emtol= 100
emstep   = 0.01
niter= 20
nbfgscorr= 10
; Output control
nstlog   = 1
nstenergy= 1
; Neighborsearching and short-range nonbonded interactions
nstlist  = 1
ns_type  = grid
pbc  = xyz
periodic-molecules   = yes
rlist= 1.5
; Electrostatics
coulombtype  = PME
rcoulomb = 1.5
; van der Waals
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PMEPPPM FFT grid
fourierspacing   = 0.12
; EWALDPMEPPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no
; Temperature and pressure coupling are off during EM
tcoupl   = no
pcoupl   = no
; Free energy control stuff
free_energy  = yes
init_lambda  = 1.0
delta_lambda = 0
foreign_lambda   = 0.95
sc-alpha = 0
sc-power = 0
sc-sigma = 0
couple-moltype   = Protein_chain_A   ; name of moleculetype to
decouple
couple-lambda0   = vdw  ;  only vdw interactions
couple-lambda1   = vdw-q; all interactions
couple-intramol  = no
nstdhdl  = 10
; Generate velocities to start
gen_vel  = no
; options for bonds
constraints  = none  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Do not constrain the starting configuration
continuation = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12



The problem almost certainly comes from the use of "couple-intramol = no," which 
for large molecules can cause issues (which have been reported before).  Larger 
molecules are more flexible, and thus the interaction distances can vary a lot. 
 The manual suggests using "couple-intramol = yes" for large molecules. 
Whether or not this is an appropriate setting for whatever you're trying to do 
is up to you and perhaps table-extension could be increased in this case, as it 
is not likely a crash but also something you cannot simply ignore.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Settles vs. 3 normal constraints (energy conservation problem)

[S. Alireza Bagherzadeh]

Dear All,

I have a box of 3073 tip4p water molecules. I do a 250ps nvt, then 250 ps
npt and finally a 1 ns nve (production run).

I used the opls forcefield and I copied the tip4p.itp to my working
directory (in order to be able to make changes).

In one case I used the [ settles ] directive to constraint water molecules.
.top file:

; Topology for 3087 TIPT4P waters

#include
"/global/software/gromacs/gromacs-4.5.5/share/gromacs/top/oplsaa.ff/forcefield.itp"
;SOL
;---
; water topology - liquid phase
#include "./tip4p.itp"
;
[ system ]
; Name
A box of 216 tip4p for protocol testing

[ molecules ]
; Compound   #mols
SOL  3073


.itp file:
; Note the strange order of atoms to make it faster in gromacs.
;
[ moleculetype ]
; molname   nrexcl
SOL 2

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   opls_1131   SOL  OW 1   0.0
2   opls_1141   SOL HW1 1   0.52
3   opls_1141   SOL HW2 1   0.52
4   opls_1151   SOL  MW 1  -1.04

#ifndef FLEXIBLE
[ settles ]
; OWfunct   dohdhh
1   1   0.095720.15139
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572 502416.0 0.09572502416.0
1   3   1   0.09572 502416.0 0.09572502416.0

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   104.52  628.02  104.52  628.02
#endif

[ exclusions ]
1   2   3   4
2   1   3   4
3   1   2   4
4   1   2   3

; The position of the virtual site is computed as follows:
;
;   O
;
;   D
;
;   H   H
;
; const = distance (OD) / [ cos (angle(DOH))* distance (OH) ]
; 0.015 nm  / [ cos (52.26 deg) * 0.09572 nm]

; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)

[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.128012065 0.128012065

.mdp file:
;-;
;-;
; Run control
integrator   = md   ; Leap-frog algorithm
tinit= 0; starting time [ps]
dt   = 0.001; time step [ps]
nsteps   = 25   ; number of steps
nstcomm  = 100  ; frequency for center of mass motion
removal [steps]
;-;
;-;
; Output control
nstxout  = 0; frequency to write coordinates to
output trajectory file [steps]
nstvout  = 0; frequency to write velocities to
output trajectory file  [steps]
nstfout  = 0; frequency to write forces to output
trajectory file  [steps]
nstlog   = 500  ; frequency to write energies to log
file [steps]
nstenergy= 500  ; frequency to write energies to energy
file [steps]
nstxtcout= 000 ; frequency to write coordinates to xtc
trajectory [steps]
xtc-precision= 1000 ; precision to write to xtc trajectory
[real]
xtc_grps = SOL
energygrps   = SOL
;-;
;-;
; Neighborsearching and short-range nonbonded interactions
nstlist  = 10   ; frequency to update the neighbor list
[steps]
ns_type  = grid ; (grid / simple) search for
neighboring list
pbc  = xyz  ; priodic boundary conditions (xyz / no
/ xy)
rlist= 1.7  ; cut-off distance for the short-range
neighbor list [nm]
;-;
;-;
; Electrostatics
coulombtype  = PME-Switch
rcoulomb_switch  = 1.3  ; where to switch the Coulomb potential
[nm]
rcoulomb = 1.5  ; distance for the Coulomb cut-off [nm]
;-;
;-;
; van der Waals
vdw-type = shift; (the LJ normal out at rvdw_s