Re: [gmx-users] Diffusion/PBC

[Tsjerk Wassenaar]

Hi Debashis,

Makes sure that the anion and receptor are together in the reference
structure you use for trjconv -pbc nojump

Cheers,

Tsjerk


On Tue, Nov 5, 2013 at 8:12 AM, Debashis Sahu wrote:

> Dear All,
>   I have an problem related to jumping trajectory. In my MD
> run, there is a receptor molecule which is binding with an halogen anion in
> water solvent. In the original trajectory, the binding between them looks
> fine but jumping present. To remove the jumping of the system from
> trajectory, I have used 'nojump' as discussed in the forum. Now I got a
> jump-free trajectory, but due to the diffusion here, I have observed that
> the anion and the receptor are far away from each other. I could not fix
> the problem. can any one suggest me?
> Thanks in advance.
> with regards,
> *Debashis Sahu*
> *Central Salt and Marine Chemical Research Institute*
> *Bhavnagar, Gujarat*
> *India, 364002.*
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[gmx-users] Re: Using mpirun on CentOS 6.0

[bharat gupta]

Hi,

I am getting the following error while using the command -

[root@localhost INGT]# mpirun -np 24 mdrun_mpi -v -deffnm npt

Error -

/usr/bin/mpdroot: open failed for root's mpd conf
filempiexec_localhost.localdomain (__init__ 1208): forked process failed;
status=255

I complied gromacs using - ./configure --enable-shared --enable-mpi. I have
installed the mpich package , this is what I get when I check for mpirun
and mpiexec -

[root@localhost /]# which mpirun
/usr/bin/mpirun
[root@localhost /]# which mpiexec
/usr/bin/mpiexec

What could be the problem here ??

Thanks

Bharat
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[gmx-users] free energy

[kiana moghaddam]

Dear GMX Users



I am using parmbsc0 force field to study DNA-ligand interaction but my problem 
is free energy calculation (MMPBSA) for this interaction. How can I calculate 
free energy using MMPBSA approach?

Thank you very much for your time and consideration.


Best Regards
Kiana 
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[gmx-users] extra gro file generation

[sarah k]

Dear all,

I'm going to perform a molecular dynamics simulation on a protein. As a
default the simulation gives one final *.gro file. I need to get a .gro
file after each say 500 ps of my simulation, in addition of the final file.
How can I do so?

Best regards,
Sarah Keshavarz
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Re: [gmx-users] extra gro file generation

[Riccardo Concu]

Dear Sarah,
you have to use the trjconv command with the flags -b -e and -sep.
For example: trjconv -f xxx.trr -s xxx.tpr -o out.gro -b (initial frame
to read in ps) -e (last frame to read in ps) -sep
Regards
El mar, 05-11-2013 a las 01:04 -0800, sarah k escribió:
> Dear all,
> 
> I'm going to perform a molecular dynamics simulation on a protein. As a
> default the simulation gives one final *.gro file. I need to get a .gro
> file after each say 500 ps of my simulation, in addition of the final file.
> How can I do so?
> 
> Best regards,
> Sarah Keshavarz


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Re: [gmx-users] choosing force field

[massimo sandal]

Just out of curiosity -why can you only choose between GROMOS force fields?


2013/11/5 pratibha kapoor 

> Dear all
>
> I would like to carry out unfolding simulations of my dimeric protein and
> would like to know which is the better force field to work with out of
> gromos 96 43 or 53? Also, is gromos 96 43a1 force field redundant?
> When I searched the previous archive, I could see similar question was
> raised for gromos 96 43a3 ff and could make out that 53a6 53a7..have
> entirely different approach in parameterization compared to 43a3 ff. Also
> 43a3 would give more stable structures.
> So is the case with my simulations but with force field 43a1 (instead of
> 43a3). I could see an extra non native helix when I carried out simulations
> with ff 43a1 which is not present with 53a7 ff. I have no experimental
> data/re-sources to confirm this. Also simulations on my system has not been
> done before.
> I would like to know which out of the two simulations should I consider
> more reliable-43a1 or 53a7?
> Thanks in advance.
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Re: [gmx-users] Gromacs-4.6 on two Titans GPUs

[James Starlight]

My suggestions:

1) During compilstion using -march=corei7-avx-i I have obtained error that
somethng now found ( sorry I didnt save log) so I compile gromacs without
this flag

2) I have twice as better performance using just 1 gpu by means of

mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v  -deffnm md_CaM_test

than using of both gpus

mdrun -ntmpi 2 -ntomp 12 -gpu_id 01 -v  -deffnm md_CaM_test

in the last case I have obtained warning

WARNING: Oversubscribing the available 12 logical CPU cores with 24 threads.
 This will cause considerable performance loss!

How it could be fixed?
All gpu are recognized correctly


2 GPUs detected:
  #0: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
compatible
  #1: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
compatible


James


2013/11/4 Szilárd Páll 

> You can use the "-march=native" flag with gcc to optimize for the CPU
> your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge
> CPUs.
> --
> Szilárd Páll
>
>
> On Mon, Nov 4, 2013 at 12:37 PM, James Starlight 
> wrote:
> > Szilárd, thanks for suggestion!
> >
> > What kind of CPU optimisation should I take into account assumint that
> I'm
> > using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as 12
> > nodes in Debian).
> >
> > James
> >
> >
> > 2013/11/4 Szilárd Páll 
> >
> >> That should be enough. You may want to use the -march (or equivalent)
> >> compiler flag for CPU optimization.
> >>
> >> Cheers,
> >> --
> >> Szilárd Páll
> >>
> >>
> >> On Sun, Nov 3, 2013 at 10:01 AM, James Starlight <
> jmsstarli...@gmail.com>
> >> wrote:
> >> > Dear Gromacs Users!
> >> >
> >> > I'd like to compile lattest 4.6 Gromacs with native GPU supporting on
> my
> >> i7
> >> > cpu with dual GeForces Titans gpu mounted. With this config I'd like
> to
> >> > perform simulations using cpu as well as both gpus simultaneously.
> >> >
> >> > What flags besides
> >> >
> >> > cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5
> >> >
> >> >
> >> > should I define to CMAKE for compiling optimized gromacs on such
> >> workstation?
> >> >
> >> >
> >> > Thanks for help
> >> >
> >> > James
> >> > --
> >> > gmx-users mailing listgmx-users@gromacs.org
> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Energy minimization has stopped....

[Kalyanashis Jana]

Hi,
  Whenever I am trying to do position retrained MD run, It has been stopped
at middle of the MD run. I have given the following error. Can you please
suggest me something to resolve this error?
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 100 (whichmay not be possible for your system).
It
stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 20514 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -9.9811250e+06
Maximum force =  6.1228135e+03 on atom 15461
Norm of force =  1.4393512e+01

gcq#322: "The Feeling of Power was Intoxicating, Magic" (Frida Hyvonen)

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Re: [gmx-users] Gromacs-4.6 on two Titans GPUs

[Richard Broadbent]

Dear James,

On 05/11/13 11:16, James Starlight wrote:

My suggestions:

1) During compilstion using -march=corei7-avx-i I have obtained error that
somethng now found ( sorry I didnt save log) so I compile gromacs without
this flag

2) I have twice as better performance using just 1 gpu by means of

mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v  -deffnm md_CaM_test

than using of both gpus

mdrun -ntmpi 2 -ntomp 12 -gpu_id 01 -v  -deffnm md_CaM_test

in the last case I have obtained warning

WARNING: Oversubscribing the available 12 logical CPU cores with 24 threads.
  This will cause considerable performance loss!

here you are requesting 2 thread mpi processes each with 12 openmp 
threads, hence a total of 24 threads however even with hyper threading 
enabled there are only 12 threads on your machine. Therefore, only 
allocate 12. Try


mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v  -deffnm md_CaM_test

or even

mdrun -v  -deffnm md_CaM_test

I believe it should autodetect the GPUs and run accordingly for details 
of how to use gromacs with mpi/thread mpi openmp and GPUs see


http://www.gromacs.org/Documentation/Acceleration_and_parallelization

Which describes how to use these systems

Richard


How it could be fixed?
All gpu are recognized correctly


2 GPUs detected:
   #0: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
compatible
   #1: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
compatible


James


2013/11/4 Szilárd Páll 


You can use the "-march=native" flag with gcc to optimize for the CPU
your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge
CPUs.
--
Szilárd Páll


On Mon, Nov 4, 2013 at 12:37 PM, James Starlight 
wrote:

Szilárd, thanks for suggestion!

What kind of CPU optimisation should I take into account assumint that

I'm

using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as 12
nodes in Debian).

James


2013/11/4 Szilárd Páll 


That should be enough. You may want to use the -march (or equivalent)
compiler flag for CPU optimization.

Cheers,
--
Szilárd Páll


On Sun, Nov 3, 2013 at 10:01 AM, James Starlight <

jmsstarli...@gmail.com>

wrote:

Dear Gromacs Users!

I'd like to compile lattest 4.6 Gromacs with native GPU supporting on

my

i7

cpu with dual GeForces Titans gpu mounted. With this config I'd like

to

perform simulations using cpu as well as both gpus simultaneously.

What flags besides

cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5


should I define to CMAKE for compiling optimized gromacs on such

workstation?



Thanks for help

James
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Re: [gmx-users] extra gro file generation

[Mirco Wahab]

On 05.11.2013 10:04, sarah k wrote:

I'm going to perform a molecular dynamics simulation on a protein. As a
default the simulation gives one final *.gro file. I need to get a .gro
file after each say 500 ps of my simulation, in addition of the final file.
How can I do so?

Riccardo already gave the important hints in another posting,
here are some additional explanations.

# first, generate an empty subdirectory in order to keep
# the simulation directory clean. The rm command is
# important if you repeat these steps

$> mkdir -p GRO/ ; rm -rf GRO/*.gro

# then, decide which part of the system you need:
# 0 - evgerything
# 1 - the protein
# 2 - the cofactor (if any)
# Remember: these numbers correspond to the order of molecules
# named in the .top-file. If your protein is "1" and you
# need only that, do a

echo "1" | trjconv -b 500 -noh -novel -skip 2 -sep -nzero 5 -o GRO/out.gro

# this will dump the system part "1" (the protein or whatever),
# starting from 500 ps (-b) and saving every 2'nd trajectory snapshot.

For each option to "trjconv" (-noh, -novel), please read the manual 
(where all of this can be found).


Regards

M.


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Re: [gmx-users] Gromacs-4.6 on two Titans GPUs

[James Starlight]

Dear Richard,


1)  mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v  -deffnm md_CaM_test
gave me performance about 25ns/day for the explicit solved system consisted
of 68k atoms (charmm ff. 1.0 cutoofs)

gaves slightly worse performation in comparison to the 1)

finally

3) mdrun -deffnm md_CaM_test
running in the same regime as in the 2) so its also gave me 22ns/day for
the same system.

How the efficacy of using of dual-GPUs could be increased?

James


2013/11/5 Richard Broadbent 

> Dear James,
>
>
> On 05/11/13 11:16, James Starlight wrote:
>
>> My suggestions:
>>
>> 1) During compilstion using -march=corei7-avx-i I have obtained error that
>> somethng now found ( sorry I didnt save log) so I compile gromacs without
>> this flag
>>
>> 2) I have twice as better performance using just 1 gpu by means of
>>
>> mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v  -deffnm md_CaM_test
>>
>> than using of both gpus
>>
>> mdrun -ntmpi 2 -ntomp 12 -gpu_id 01 -v  -deffnm md_CaM_test
>>
>> in the last case I have obtained warning
>>
>> WARNING: Oversubscribing the available 12 logical CPU cores with 24
>> threads.
>>   This will cause considerable performance loss!
>>
>>  here you are requesting 2 thread mpi processes each with 12 openmp
> threads, hence a total of 24 threads however even with hyper threading
> enabled there are only 12 threads on your machine. Therefore, only allocate
> 12. Try
>
> mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v  -deffnm md_CaM_test
>
> or even
>
> mdrun -v  -deffnm md_CaM_test
>
> I believe it should autodetect the GPUs and run accordingly for details of
> how to use gromacs with mpi/thread mpi openmp and GPUs see
>
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization
>
> Which describes how to use these systems
>
> Richard
>
>
>  How it could be fixed?
>> All gpu are recognized correctly
>>
>>
>> 2 GPUs detected:
>>#0: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
>> compatible
>>#1: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
>> compatible
>>
>>
>> James
>>
>>
>> 2013/11/4 Szilárd Páll 
>>
>>  You can use the "-march=native" flag with gcc to optimize for the CPU
>>> your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge
>>> CPUs.
>>> --
>>> Szilárd Páll
>>>
>>>
>>> On Mon, Nov 4, 2013 at 12:37 PM, James Starlight >> >
>>> wrote:
>>>
 Szilárd, thanks for suggestion!

 What kind of CPU optimisation should I take into account assumint that

>>> I'm
>>>
 using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as
 12
 nodes in Debian).

 James


 2013/11/4 Szilárd Páll 

  That should be enough. You may want to use the -march (or equivalent)
> compiler flag for CPU optimization.
>
> Cheers,
> --
> Szilárd Páll
>
>
> On Sun, Nov 3, 2013 at 10:01 AM, James Starlight <
>
 jmsstarli...@gmail.com>
>>>
 wrote:
>
>> Dear Gromacs Users!
>>
>> I'd like to compile lattest 4.6 Gromacs with native GPU supporting on
>>
> my
>>>
 i7
>
>> cpu with dual GeForces Titans gpu mounted. With this config I'd like
>>
> to
>>>
 perform simulations using cpu as well as both gpus simultaneously.
>>
>> What flags besides
>>
>> cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5
>>
>>
>> should I define to CMAKE for compiling optimized gromacs on such
>>
> workstation?
>
>>
>>
>> Thanks for help
>>
>> James
>> --
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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>>
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>
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>>
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Re: [gmx-users] Energy minimization has stopped....

[jkrieger]

What does your curve look like? What parameters are you using in the mdp?
How big is your system and what kind of molecules are in there? Providing
this kind of information would help people work out what the problem is.

Then again it may be ok that the minimisation has converged without
reaching the Fmax cutoff. 2 is a large number of steps.

> Hi,
>   Whenever I am trying to do position retrained MD run, It has been
> stopped
> at middle of the MD run. I have given the following error. Can you please
> suggest me something to resolve this error?
> Energy minimization has stopped, but the forces havenot converged to the
> requested precision Fmax < 100 (whichmay not be possible for your system).
> It
> stoppedbecause the algorithm tried to make a new step whose sizewas too
> small, or there was no change in the energy sincelast step. Either way, we
> regard the minimization asconverged to within the available machine
> precision,given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, butthis is often not
> needed for preparing to run moleculardynamics.
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 20514 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  = -9.9811250e+06
> Maximum force =  6.1228135e+03 on atom 15461
> Norm of force =  1.4393512e+01
>
> gcq#322: "The Feeling of Power was Intoxicating, Magic" (Frida Hyvonen)
>
> --
> Kalyanashis Jana
> email: kalyan.chem...@gmail.com
> --
> 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] Energy minimization has stopped....

[Justin Lemkul]

On 11/5/13 6:28 AM, Kalyanashis Jana wrote:

Hi,
   Whenever I am trying to do position retrained MD run, It has been stopped
at middle of the MD run. I have given the following error. Can you please
suggest me something to resolve this error?
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 100 (whichmay not be possible for your system).
It
stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 20514 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -9.9811250e+06
Maximum force =  6.1228135e+03 on atom 15461
Norm of force =  1.4393512e+01



Visualize the output, specifically near atom 15461.  The forces there are too 
high and cannot be resolved further.  Any attempt to use these coordinates for 
dynamics will probably lead to a crash.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] free energy

[Justin Lemkul]

On 11/5/13 3:45 AM, kiana moghaddam wrote:

Dear GMX Users



I am using parmbsc0 force field to study DNA-ligand interaction but my problem 
is free energy calculation (MMPBSA) for this interaction. How can I calculate 
free energy using MMPBSA approach?

Thank you very much for your time and consideration.



An identical question was asked on the list last week, including responses about 
external software that will do these calculations.  Gromacs does not do MM/PBSA, 
but other programs will.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Re: Energy minimization has stopped....

[Kalyanashis]

I have given my .mdp file,
; title =  trp_drg
warning =  10
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  all-bonds
integrator  =  md
dt  =  0.002 ; ps !
nsteps  =  100 ; total 2000.0 ps.
nstcomm =  100
nstxout =  250 ; ouput coordinates every 0.5 ps
nstvout =  1000 ; output velocities every 2.0 ps
nstfout =  0
nstlog  =  100
nstenergy   =  100
nstlist =  100
ns_type =  grid
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
vdwtype =  cut-off
rvdw=  1.0
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  6
ewald_rtol  =  1e-5
optimize_fft=  yes
; Berendsen temparature coupling is on
Tcoupl  =  berendsen
tau_t   =  1.01.0-0.1  1.0   1.0
tc_grps =  SOLNA protein   OMP   CL
ref_t   =  300300300   300   300
; Pressure coupling is on
pcoupl  =  berendsen ; Use Parrinello-Rahman for research work
pcoupltype  =  isotropic ; Use semiisotropic when working with
membranes
tau_p   =  2.0
compressibility =  4.5e-5
ref_p   =  1.0
refcoord-scaling=  all
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp= 300.0
gen_seed= 173529


And It is a large protein system containing drug molecule and the atoms of
whole system is near about 16000.
As I did not get any .gro file, thus the MD run was not properly finished.
Please suggest me the probable source this kind error.
Thank you so much..



On Tue, Nov 5, 2013 at 5:29 PM, jkrie...@mrc-lmb.cam.ac.uk [via GROMACS] <
ml-node+s5086n5012256...@n6.nabble.com> wrote:

> What does your curve look like? What parameters are you using in the mdp?
> How big is your system and what kind of molecules are in there? Providing
> this kind of information would help people work out what the problem is.
>
> Then again it may be ok that the minimisation has converged without
> reaching the Fmax cutoff. 2 is a large number of steps.
>
> > Hi,
> >   Whenever I am trying to do position retrained MD run, It has been
> > stopped
> > at middle of the MD run. I have given the following error. Can you
> please
> > suggest me something to resolve this error?
> > Energy minimization has stopped, but the forces havenot converged to the
> > requested precision Fmax < 100 (whichmay not be possible for your
> system).
> > It
> > stoppedbecause the algorithm tried to make a new step whose sizewas too
> > small, or there was no change in the energy sincelast step. Either way,
> we
> > regard the minimization asconverged to within the available machine
> > precision,given your starting configuration and EM parameters.
> >
> > Double precision normally gives you higher accuracy, butthis is often
> not
> > needed for preparing to run moleculardynamics.
> >
> > writing lowest energy coordinates.
> >
> > Steepest Descents converged to machine precision in 20514 steps,
> > but did not reach the requested Fmax < 100.
> > Potential Energy  = -9.9811250e+06
> > Maximum force =  6.1228135e+03 on atom 15461
> > Norm of force =  1.4393512e+01
> >
> > gcq#322: "The Feeling of Power was Intoxicating, Magic" (Frida Hyvonen)
> >
> > --
> > Kalyanashis Jana
> > email: [hidden email]
> > --
> > gmx-users mailing list[hidden 
> > email]
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to [hidden 
> > email].
>
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> >
>
>
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Re: [gmx-users] Energy minimization has stopped....

[Kalyanashis Jana]

Dear Justin,
  Can you please tell me, how I can solve this problem?? If I will change
the coordinate of atom 15461, will it help me? But you know, I did this
step changing the position of drug molecule and I got same error.


On Tue, Nov 5, 2013 at 5:44 PM, Justin Lemkul  wrote:

>
>
> On 11/5/13 6:28 AM, Kalyanashis Jana wrote:
>
>> Hi,
>>Whenever I am trying to do position retrained MD run, It has been
>> stopped
>> at middle of the MD run. I have given the following error. Can you please
>> suggest me something to resolve this error?
>> Energy minimization has stopped, but the forces havenot converged to the
>> requested precision Fmax < 100 (whichmay not be possible for your system).
>> It
>> stoppedbecause the algorithm tried to make a new step whose sizewas too
>> small, or there was no change in the energy sincelast step. Either way, we
>> regard the minimization asconverged to within the available machine
>> precision,given your starting configuration and EM parameters.
>>
>> Double precision normally gives you higher accuracy, butthis is often not
>> needed for preparing to run moleculardynamics.
>>
>> writing lowest energy coordinates.
>>
>> Steepest Descents converged to machine precision in 20514 steps,
>> but did not reach the requested Fmax < 100.
>> Potential Energy  = -9.9811250e+06
>> Maximum force =  6.1228135e+03 on atom 15461
>> Norm of force =  1.4393512e+01
>>
>>
> Visualize the output, specifically near atom 15461.  The forces there are
> too high and cannot be resolved further.  Any attempt to use these
> coordinates for dynamics will probably lead to a crash.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
>
> --
> 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!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
>
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-- 
Kalyanashis Jana
email: kalyan.chem...@gmail.com
-- 
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Re: [gmx-users] Re: Energy minimization has stopped....

[Justin Lemkul]

On 11/5/13 7:19 AM, Kalyanashis wrote:

I have given my .mdp file,
; title =  trp_drg
warning =  10
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  all-bonds
integrator  =  md
dt  =  0.002 ; ps !
nsteps  =  100 ; total 2000.0 ps.
nstcomm =  100
nstxout =  250 ; ouput coordinates every 0.5 ps
nstvout =  1000 ; output velocities every 2.0 ps
nstfout =  0
nstlog  =  100
nstenergy   =  100
nstlist =  100
ns_type =  grid
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
vdwtype =  cut-off
rvdw=  1.0
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  6
ewald_rtol  =  1e-5
optimize_fft=  yes
; Berendsen temparature coupling is on
Tcoupl  =  berendsen
tau_t   =  1.01.0-0.1  1.0   1.0
tc_grps =  SOLNA protein   OMP   CL
ref_t   =  300300300   300   300


These settings make no sense.  Please read 
http://www.gromacs.org/Documentation/Terminology/Thermostats.



; Pressure coupling is on
pcoupl  =  berendsen ; Use Parrinello-Rahman for research work
pcoupltype  =  isotropic ; Use semiisotropic when working with
membranes
tau_p   =  2.0
compressibility =  4.5e-5
ref_p   =  1.0
refcoord-scaling=  all
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp= 300.0
gen_seed= 173529


And It is a large protein system containing drug molecule and the atoms of
whole system is near about 16000.
As I did not get any .gro file, thus the MD run was not properly finished.
Please suggest me the probable source this kind error.


The run crashes because your energy minimization effectively failed.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Energy minimization has stopped....

[Justin Lemkul]

On 11/5/13 7:31 AM, Kalyanashis Jana wrote:

Dear Justin,
   Can you please tell me, how I can solve this problem?? If I will change
the coordinate of atom 15461, will it help me? But you know, I did this
step changing the position of drug molecule and I got same error.



You should first do what I suggested before.  The reason for a large force is 
either (1) bad atomic clashes that should be apparent upon visual inspection or 
(2) bad topology for the drug.


-Justin



On Tue, Nov 5, 2013 at 5:44 PM, Justin Lemkul  wrote:




On 11/5/13 6:28 AM, Kalyanashis Jana wrote:


Hi,
Whenever I am trying to do position retrained MD run, It has been
stopped
at middle of the MD run. I have given the following error. Can you please
suggest me something to resolve this error?
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 100 (whichmay not be possible for your system).
It
stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 20514 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -9.9811250e+06
Maximum force =  6.1228135e+03 on atom 15461
Norm of force =  1.4393512e+01



Visualize the output, specifically near atom 15461.  The forces there are
too high and cannot be resolved further.  Any attempt to use these
coordinates for dynamics will probably lead to a crash.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==

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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] mdrun

[MUSYOKA THOMMAS]

Dear Users,
I am running MD simulations of a protein-ligand system. Sometimes when i do
an mdrun, be it for the energy minimization or during the nvt and npt
equillibration  or the actual md run step, sometimes the output files are
named in a very odd way (strange extensions) e.g em.gro.tprr or md.tpr.cpt,
md.tpr.xtc.

Can anyone explain the cause of this?

Thanks
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Re: [gmx-users] mdrun

[Justin Lemkul]

On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote:

Dear Users,
I am running MD simulations of a protein-ligand system. Sometimes when i do
an mdrun, be it for the energy minimization or during the nvt and npt
equillibration  or the actual md run step, sometimes the output files are
named in a very odd way (strange extensions) e.g em.gro.tprr or md.tpr.cpt,
md.tpr.xtc.

Can anyone explain the cause of this?



You are issuing the command in a way that you probably don't want.  I suspect 
what you are doing is:


mdrun -deffnm md.tpr

The -deffnm option is for the base file name and should not include an 
extension.  mdrun is only doing what you tell it; you're saying, "all my files 
are named md.tpr, and you can put whatever the necessary extension is on them."


What you want is:

mdrun -deffnm md

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] free energy

[Kieu Thu Nguyen]

Dear Kiana,

You can contact with Paissoni Cristina (email: paissoni.crist...@hsr.it) to
get tool using MM/PBSA with GROMACS.
Hope it help :)

Cheers,
Kieu Thu


On Tue, Nov 5, 2013 at 7:18 PM, Justin Lemkul  wrote:

>
>
> On 11/5/13 3:45 AM, kiana moghaddam wrote:
>
>> Dear GMX Users
>>
>>
>>
>> I am using parmbsc0 force field to study DNA-ligand interaction but my
>> problem is free energy calculation (MMPBSA) for this interaction. How can I
>> calculate free energy using MMPBSA approach?
>>
>> Thank you very much for your time and consideration.
>>
>>
> An identical question was asked on the list last week, including responses
> about external software that will do these calculations.  Gromacs does not
> do MM/PBSA, but other programs will.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
> --
> 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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> interface or send it to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] mdrun

[MUSYOKA THOMMAS]

Dear Dr Justin,
Much appreciation. You nailed it.
Kind regards.


On Tue, Nov 5, 2013 at 2:41 PM, Justin Lemkul  wrote:

>
>
> On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote:
>
>> Dear Users,
>> I am running MD simulations of a protein-ligand system. Sometimes when i
>> do
>> an mdrun, be it for the energy minimization or during the nvt and npt
>> equillibration  or the actual md run step, sometimes the output files are
>> named in a very odd way (strange extensions) e.g em.gro.tprr or
>> md.tpr.cpt,
>> md.tpr.xtc.
>>
>> Can anyone explain the cause of this?
>>
>>
> You are issuing the command in a way that you probably don't want.  I
> suspect what you are doing is:
>
> mdrun -deffnm md.tpr
>
> The -deffnm option is for the base file name and should not include an
> extension.  mdrun is only doing what you tell it; you're saying, "all my
> files are named md.tpr, and you can put whatever the necessary extension is
> on them."
>
> What you want is:
>
> mdrun -deffnm md
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 

*MUSYOKA THOMMAS MUTEMIMob nos **+27844846540*
*B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science
(Nagasaki University)*

*PhD Student-Bioinformatics (Rhodes University)*Skype ID- MUSYOKA THOMMAS
MUTEMI
Alternative email - thom...@sia.co.ke








*"Do all the good you can, By all the means you can, In all the ways you
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[gmx-users] CHARMM .mdp settings for GPU

[rajat desikan]

Dear All,
I intend to run a membrane-protein system in GPU. I am slightly confused
about the .mdp settings

Non-gpu settings (according to original CHARMM FF paper):

rlist  = 1.0
rlistlong= 1.4
rvdw_switch  = 0.8
vdwtype= Switch
coulombtype  = pme
DispCorr= EnerPres ;only usefull with reaction-field
and pme or pppm
rcoulomb   = 1.0
rcoulomb_switch= 0.0
rvdw = 1.2

For cutoff-scheme = Verlet , shouldn't rvdw=rcoulomb? How should the above
settings be modified?

Thank you.


-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] Gromacs-4.6 on two Titans GPUs

[Mark Abraham]

On Tue, Nov 5, 2013 at 12:55 PM, James Starlight wrote:

> Dear Richard,
>
>
> 1)  mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v  -deffnm md_CaM_test
> gave me performance about 25ns/day for the explicit solved system consisted
> of 68k atoms (charmm ff. 1.0 cutoofs)
>
> gaves slightly worse performation in comparison to the 1)
>
>
Richard suggested

mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v  -deffnm md_CaM_test,

which looks correct to me. -ntomp 6 is probably superfluous

Mark


> finally
>
> 3) mdrun -deffnm md_CaM_test
> running in the same regime as in the 2) so its also gave me 22ns/day for
> the same system.
>
> How the efficacy of using of dual-GPUs could be increased?
>
> James
>
>
> 2013/11/5 Richard Broadbent 
>
> > Dear James,
> >
> >
> > On 05/11/13 11:16, James Starlight wrote:
> >
> >> My suggestions:
> >>
> >> 1) During compilstion using -march=corei7-avx-i I have obtained error
> that
> >> somethng now found ( sorry I didnt save log) so I compile gromacs
> without
> >> this flag
> >>
> >> 2) I have twice as better performance using just 1 gpu by means of
> >>
> >> mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v  -deffnm md_CaM_test
> >>
> >> than using of both gpus
> >>
> >> mdrun -ntmpi 2 -ntomp 12 -gpu_id 01 -v  -deffnm md_CaM_test
> >>
> >> in the last case I have obtained warning
> >>
> >> WARNING: Oversubscribing the available 12 logical CPU cores with 24
> >> threads.
> >>   This will cause considerable performance loss!
> >>
> >>  here you are requesting 2 thread mpi processes each with 12 openmp
> > threads, hence a total of 24 threads however even with hyper threading
> > enabled there are only 12 threads on your machine. Therefore, only
> allocate
> > 12. Try
> >
> > mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v  -deffnm md_CaM_test
> >
> > or even
> >
> > mdrun -v  -deffnm md_CaM_test
> >
> > I believe it should autodetect the GPUs and run accordingly for details
> of
> > how to use gromacs with mpi/thread mpi openmp and GPUs see
> >
> > http://www.gromacs.org/Documentation/Acceleration_and_parallelization
> >
> > Which describes how to use these systems
> >
> > Richard
> >
> >
> >  How it could be fixed?
> >> All gpu are recognized correctly
> >>
> >>
> >> 2 GPUs detected:
> >>#0: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
> >> compatible
> >>#1: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
> >> compatible
> >>
> >>
> >> James
> >>
> >>
> >> 2013/11/4 Szilárd Páll 
> >>
> >>  You can use the "-march=native" flag with gcc to optimize for the CPU
> >>> your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge
> >>> CPUs.
> >>> --
> >>> Szilárd Páll
> >>>
> >>>
> >>> On Mon, Nov 4, 2013 at 12:37 PM, James Starlight <
> jmsstarli...@gmail.com
> >>> >
> >>> wrote:
> >>>
>  Szilárd, thanks for suggestion!
> 
>  What kind of CPU optimisation should I take into account assumint that
> 
> >>> I'm
> >>>
>  using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as
>  12
>  nodes in Debian).
> 
>  James
> 
> 
>  2013/11/4 Szilárd Páll 
> 
>   That should be enough. You may want to use the -march (or equivalent)
> > compiler flag for CPU optimization.
> >
> > Cheers,
> > --
> > Szilárd Páll
> >
> >
> > On Sun, Nov 3, 2013 at 10:01 AM, James Starlight <
> >
>  jmsstarli...@gmail.com>
> >>>
>  wrote:
> >
> >> Dear Gromacs Users!
> >>
> >> I'd like to compile lattest 4.6 Gromacs with native GPU supporting
> on
> >>
> > my
> >>>
>  i7
> >
> >> cpu with dual GeForces Titans gpu mounted. With this config I'd like
> >>
> > to
> >>>
>  perform simulations using cpu as well as both gpus simultaneously.
> >>
> >> What flags besides
> >>
> >> cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5
> >>
> >>
> >> should I define to CMAKE for compiling optimized gromacs on such
> >>
> > workstation?
> >
> >>
> >>
> >> Thanks for help
> >>
> >> James
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> * Please search the archive at
> >>
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >
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> >> www interface or send it to gmx-users-requ...@gromacs.org.
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> >>
> > --
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[gmx-users] Re: Replacing atom

[J Alizadeh]

Hi,
I need to replace an atom with another in the considered system.
I'd like to know if it is possible and if so what changes I need to do.

thanks
j.rahrow


On Thu, Oct 31, 2013 at 12:47 PM, J Alizadeh  wrote:

> Hi,
>   I need to replace an atom with another in the considered system.
>   I'd like to know if it is possible and if so what changes I need to do.
>
> thanks
> j.rahrow
>
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Re: [gmx-users] Re: Hardware for best gromacs performance?

[Timo Graen]

29420 Atoms with a some tuning of the write out and communication intervals:
nodes again: 2 x Xeon E5-2680v2 + 2 x NVIDIA K20X GPGPUs @ 4fs vsites
1 node   212 ns/day
2 nodes  295 ns/day
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Re: [gmx-users] extra gro file generation

[sarah k]

Dear Riccardo Concu and Mirco Wahab,

Thanks for your perfect responses.

Regards,
Sarah
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Re: [gmx-users] Re: Replacing atom

[Justin Lemkul]

On 11/5/13 10:34 AM, J Alizadeh wrote:

Hi,
I need to replace an atom with another in the considered system.
I'd like to know if it is possible and if so what changes I need to do.



The coordinate file replacement is trivial.  Just open the file in a text editor 
and repname the atom.  The topology is trickier, because you need a whole new 
set of parameters.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Gentle heating with implicit solvent

[Gianluca Interlandi]

I wonder whether increasing the surface tension parameter 
sa-surface-tension might solve the problem with the protein unfolding.


Thanks,

 Gianluca

On Mon, 4 Nov 2013, Gianluca Interlandi wrote:


Hi Justin,

We are using infinite cutoffs (all vs all). Here is the mdp file for the 
heating (please note that -DPOSRES is commented out) and the time step is 1 
fs:


; VARIOUS PREPROCESSING OPTIONS =
title=
cpp  = /lib/cpp
include  =
;define   = -DPOSRES

; RUN CONTROL PARAMETERS =
integrator   = md
; start time and timestep in ps =
tinit= 0
dt   = 0.001
nsteps   = 20
; 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-temp  = 300
bd-fric  = 0
ld_seed  = 1993

; IMPLICIT SOLVENT OPTIONS =
implicit-solvent = GBSA
gb-algorithm = OBC
rgbradii = 0

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

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 0
nstvout  = 0
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 100
nstenergy= 100
; Output frequency and precision for xtc file =
nstxtcout= 1000
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  = 0
; ns algorithm (simple or grid) =
ns_type  = simple
; Periodic boundary conditions: xyz or no =
pbc  = no
; nblist cut-off =
rlist= 0
;rlistlong= 1.8
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = Cut-off
rcoulomb_switch  = 0
rcoulomb = 0
; 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
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing   = 0.1
; 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

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
Tcoupl   = V-rescale
; Groups to couple separately =
tc_grps  = Protein
; Time constant (ps) and reference temperature (K) =
tau_t= 0.1
ref_t= 300
; Pressure coupling  =
Pcoupl   = no
Pcoupltype   = isotropic
refcoord_scaling = All
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

; SIMULATED ANNEALING CONTROL =
annealing= single
; Number of time points to use for specifying annealing in each group
annealing_npoints = 21
; List of times at the annealing points for each group
annealing_time= 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 
150 160 170 180 190 200

; Temp. at each annealing point, for each group
annealing_temp= 5 30 30 60 60 90 90 120 120 150 150 180 180 210 
210 240 240 270 270 300 300


; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = yes
gen_temp = 5
gen_seed = 173529

; OPTIONS FOR BONDS =
constraints  = none
; Type of constraint algorithm =
;constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start  = no
; Use successive overrelaxation to red

Re: [gmx-users] Re: Using gromacs on Rocks cluster

[Mark Abraham]

You need to configure your MPI environment to do so (so read its docs).
GROMACS can only do whatever that makes available.

Mark


On Tue, Nov 5, 2013 at 2:16 AM, bharat gupta wrote:

> Hi,
>
> I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having
> 32 processors (cpu). But while running the nvt equilibration step, it uses
> only 1 cpu and the others remain idle. I have complied the Gromacs using
> enable-mpi option. How can make the mdrun use all the 32 processors ??
>
> --
> Bharat
> --
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Re: [gmx-users] Re: Hardware for best gromacs performance?

[Szilárd Páll]

Timo,

Have you used the default settings, that is one rank/GPU? If that is
the case, you may want to try using multiple ranks per GPU, this can
often help when you have >4-6 cores/GPU. Separate PME ranks are not
switched on by default with GPUs, have you tried using any?

Cheers,
--
Szilárd Páll


On Tue, Nov 5, 2013 at 3:29 PM, Timo Graen  wrote:
> 29420 Atoms with a some tuning of the write out and communication intervals:
> nodes again: 2 x Xeon E5-2680v2 + 2 x NVIDIA K20X GPGPUs @ 4fs vsites
> 1 node   212 ns/day
> 2 nodes  295 ns/day
>
> --
> 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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[gmx-users] Re: Gromacs-4.6 on two Titans GPUs

[Dwey]

Hi Mike,


I have similar configurations except a cluster of AMD-based linux
platforms with 2 GPU cards.

Your  suggestion works. However, the performance of 2 GPU  discourages
me  because , for example,  with 1 GPU, our computer node can easily
obtain a  simulation of 31ns/day for a protein of 300 amino acids but
with 2 GPUs, it goes as far as 38 ns/day. I am very curious as to  why
 the performance of 2 GPUs is under expectation. Is there any overhead
that we should pay attention to ?  Note that these 2GPU cards are
linked by a SLI bridge within the same node.

Since the computer nodes of our cluster have at least one GPU  but
they are connected by slow network cards ( 1GB/sec), unfortunately, I
reasonably doubt that the performance will not be proportional to the
total number of  GPU cards.  I am wondering if you have any suggestion
about a cluster of GPU nodes.   For example, will a infiniband
networking help increase a final performance when we execute a mpi
task ? or what else ?  or forget about mpi and use single GPU instead.

Any suggestion is highly appreciated.
Thanks.

Dwey

> Date: Tue, 5 Nov 2013 16:20:39 +0100
> From: Mark Abraham 
> Subject: Re: [gmx-users] Gromacs-4.6 on two Titans GPUs
> To: Discussion list for GROMACS users 
> Message-ID:
> 
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Tue, Nov 5, 2013 at 12:55 PM, James Starlight 
> wrote:
>
>> Dear Richard,
>>
>>
>> 1)  mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v  -deffnm md_CaM_test
>> gave me performance about 25ns/day for the explicit solved system consisted
>> of 68k atoms (charmm ff. 1.0 cutoofs)
>>
>> gaves slightly worse performation in comparison to the 1)
>>
>>
> Richard suggested
>
> mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v  -deffnm md_CaM_test,
>
> which looks correct to me. -ntomp 6 is probably superfluous
>
> Mark
>
>
>> finally
>>
>> 3) mdrun -deffnm md_CaM_test
>> running in the same regime as in the 2) so its also gave me 22ns/day for
>> the same system.
>>
>> How the efficacy of using of dual-GPUs could be increased?
>>
>> James
>>
>>
>> 2013/11/5 Richard Broadbent 
>>
>> > Dear James,
>> >
>> >
>> > On 05/11/13 11:16, James Starlight wrote:
>> >
>> >> My suggestions:
>> >>
>> >> 1) During compilstion using -march=corei7-avx-i I have obtained error
>> that
>> >> somethng now found ( sorry I didnt save log) so I compile gromacs
>> without
>> >> this flag
>> >>
>> >> 2) I have twice as better performance using just 1 gpu by means of
>> >>
>> >> mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v  -deffnm md_CaM_test
>> >>
>> >> than using of both gpus
>> >>
>> >> mdrun -ntmpi 2 -ntomp 12 -gpu_id 01 -v  -deffnm md_CaM_test
>> >>
>> >> in the last case I have obtained warning
>> >>
>> >> WARNING: Oversubscribing the available 12 logical CPU cores with 24
>> >> threads.
>> >>   This will cause considerable performance loss!
>> >>
>> >>  here you are requesting 2 thread mpi processes each with 12 openmp
>> > threads, hence a total of 24 threads however even with hyper threading
>> > enabled there are only 12 threads on your machine. Therefore, only
>> allocate
>> > 12. Try
>> >
>> > mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v  -deffnm md_CaM_test
>> >
>> > or even
>> >
>> > mdrun -v  -deffnm md_CaM_test
>> >
>> > I believe it should autodetect the GPUs and run accordingly for details
>> of
>> > how to use gromacs with mpi/thread mpi openmp and GPUs see
>> >
>> > http://www.gromacs.org/Documentation/Acceleration_and_parallelization
>> >
>> > Which describes how to use these systems
>> >
>> > Richard
>> >
>> >
>> >  How it could be fixed?
>> >> All gpu are recognized correctly
>> >>
>> >>
>> >> 2 GPUs detected:
>> >>#0: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
>> >> compatible
>> >>#1: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
>> >> compatible
>> >>
>> >>
>> >> James
>> >>
>> >>
>> >> 2013/11/4 Szilárd Páll 
>> >>
>> >>  You can use the "-march=native" flag with gcc to optimize for the CPU
>> >>> your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge
>> >>> CPUs.
>> >>> --
>> >>> Szilárd Páll
>> >>>
>> >>>
>> >>> On Mon, Nov 4, 2013 at 12:37 PM, James Starlight <
>> jmsstarli...@gmail.com
>> >>> >
>> >>> wrote:
>> >>>
>>  Szilárd, thanks for suggestion!
>> 
>>  What kind of CPU optimisation should I take into account assumint that
>> 
>> >>> I'm
>> >>>
>>  using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as
>>  12
>>  nodes in Debian).
>> 
>>  James
>> 
>> 
>>  2013/11/4 Szilárd Páll 
>> 
>>   That should be enough. You may want to use the -march (or equivalent)
>> > compiler flag for CPU optimization.
>> >
>> > Cheers,
>> > --
>> > Szilárd Páll
>> >
>> >
>> > On Sun, Nov 3, 2013 at 10:01 AM, James Starlight <
>> >
>>  jmsstarli...@gmail.com>
>> >>>
>>  wrote:
>> >
>> >> Dear Gromacs Users!
>> >>
>> >> I'd like to compile lattest 4.6 

[gmx-users] Re: Hardware for best gromacs performance?

[Dwey Kauffman]

Hi Timo,

  Can you provide a benchmark with  "1"  Xeon E5-2680 with   "1"  Nvidia
k20x GPGPU on the same test of 29420 atoms ?

Are these two GPU cards (within the same node) connected by a SLI (Scalable
Link Interface) ? 

Thanks,
Dwey

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Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs

[Szilárd Páll]

Hi Dwey,

First and foremost, make sure to read the
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
page, in particular the "Multiple MPI ranks per GPU" section which
applies in your case.

Secondly, please do post log files (pastebin is your friend), the
performance table at the end of the log tells much the performance
story and based on that I/we can make suggestions.

Using multiple GPU requires domain-decomposition which does have a
considerable overhead, especially comparing no DD with DD (i.e. 1 GPU
run with 2 GPU run). However, in your case I suspect that the
bottleneck is multi-threaded scaling on the AMD CPUs and you should
probably decrease the number of threads per MPI rank and share GPUs
between 2-4 ranks.

Regarding scaling across nodes, you can't expect much from gigabit
ethernet - especially not from the cheaper cards/switches, in my
experience even reaction field runs don't scale across nodes with 10G
ethernet if you have more than 4-6 ranks per node trying to
communicate (let alone with PME). However, on infiniband clusters we
have seen scaling to 100 atoms/core (at peak).

Cheers,
--
Szilárd

On Tue, Nov 5, 2013 at 9:29 PM, Dwey  wrote:
> Hi Mike,
>
>
> I have similar configurations except a cluster of AMD-based linux
> platforms with 2 GPU cards.
>
> Your  suggestion works. However, the performance of 2 GPU  discourages
> me  because , for example,  with 1 GPU, our computer node can easily
> obtain a  simulation of 31ns/day for a protein of 300 amino acids but
> with 2 GPUs, it goes as far as 38 ns/day. I am very curious as to  why
>  the performance of 2 GPUs is under expectation. Is there any overhead
> that we should pay attention to ?  Note that these 2GPU cards are
> linked by a SLI bridge within the same node.
>
> Since the computer nodes of our cluster have at least one GPU  but
> they are connected by slow network cards ( 1GB/sec), unfortunately, I
> reasonably doubt that the performance will not be proportional to the
> total number of  GPU cards.  I am wondering if you have any suggestion
> about a cluster of GPU nodes.   For example, will a infiniband
> networking help increase a final performance when we execute a mpi
> task ? or what else ?  or forget about mpi and use single GPU instead.
>
> Any suggestion is highly appreciated.
> Thanks.
>
> Dwey
>
>> Date: Tue, 5 Nov 2013 16:20:39 +0100
>> From: Mark Abraham 
>> Subject: Re: [gmx-users] Gromacs-4.6 on two Titans GPUs
>> To: Discussion list for GROMACS users 
>> Message-ID:
>> 
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> On Tue, Nov 5, 2013 at 12:55 PM, James Starlight 
>> wrote:
>>
>>> Dear Richard,
>>>
>>>
>>> 1)  mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v  -deffnm md_CaM_test
>>> gave me performance about 25ns/day for the explicit solved system consisted
>>> of 68k atoms (charmm ff. 1.0 cutoofs)
>>>
>>> gaves slightly worse performation in comparison to the 1)
>>>
>>>
>> Richard suggested
>>
>> mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v  -deffnm md_CaM_test,
>>
>> which looks correct to me. -ntomp 6 is probably superfluous
>>
>> Mark
>>
>>
>>> finally
>>>
>>> 3) mdrun -deffnm md_CaM_test
>>> running in the same regime as in the 2) so its also gave me 22ns/day for
>>> the same system.
>>>
>>> How the efficacy of using of dual-GPUs could be increased?
>>>
>>> James
>>>
>>>
>>> 2013/11/5 Richard Broadbent 
>>>
>>> > Dear James,
>>> >
>>> >
>>> > On 05/11/13 11:16, James Starlight wrote:
>>> >
>>> >> My suggestions:
>>> >>
>>> >> 1) During compilstion using -march=corei7-avx-i I have obtained error
>>> that
>>> >> somethng now found ( sorry I didnt save log) so I compile gromacs
>>> without
>>> >> this flag
>>> >>
>>> >> 2) I have twice as better performance using just 1 gpu by means of
>>> >>
>>> >> mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v  -deffnm md_CaM_test
>>> >>
>>> >> than using of both gpus
>>> >>
>>> >> mdrun -ntmpi 2 -ntomp 12 -gpu_id 01 -v  -deffnm md_CaM_test
>>> >>
>>> >> in the last case I have obtained warning
>>> >>
>>> >> WARNING: Oversubscribing the available 12 logical CPU cores with 24
>>> >> threads.
>>> >>   This will cause considerable performance loss!
>>> >>
>>> >>  here you are requesting 2 thread mpi processes each with 12 openmp
>>> > threads, hence a total of 24 threads however even with hyper threading
>>> > enabled there are only 12 threads on your machine. Therefore, only
>>> allocate
>>> > 12. Try
>>> >
>>> > mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v  -deffnm md_CaM_test
>>> >
>>> > or even
>>> >
>>> > mdrun -v  -deffnm md_CaM_test
>>> >
>>> > I believe it should autodetect the GPUs and run accordingly for details
>>> of
>>> > how to use gromacs with mpi/thread mpi openmp and GPUs see
>>> >
>>> > http://www.gromacs.org/Documentation/Acceleration_and_parallelization
>>> >
>>> > Which describes how to use these systems
>>> >
>>> > Richard
>>> >
>>> >
>>> >  How it could be fixed?
>>> >> All gpu are recognized correctly
>>> >>
>>> >>
>>> >> 2 GPUs detected:
>

Re: [gmx-users] Re: Hardware for best gromacs performance?

[Szilárd Páll]

On Tue, Nov 5, 2013 at 9:55 PM, Dwey Kauffman  wrote:
> Hi Timo,
>
>   Can you provide a benchmark with  "1"  Xeon E5-2680 with   "1"  Nvidia
> k20x GPGPU on the same test of 29420 atoms ?
>
> Are these two GPU cards (within the same node) connected by a SLI (Scalable
> Link Interface) ?

Note that SLI has no use for compute, only for graphics.

--
Szilárd
>
> Thanks,
> Dwey
>
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/Hardware-for-best-gromacs-performance-tp5012124p5012276.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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[gmx-users] Re: Gromacs-4.6 on two Titans GPUs

[Dwey Kauffman]

Hi Szilard,

   Thanks for your suggestions. I am  indeed aware of this page. In a 8-core
AMD with 1GPU, I am very happy about its performance. See below. My
intention is to obtain a even better one because we have multiple nodes.

### 8 core AMD with  1 GPU,
Force evaluation time GPU/CPU: 4.006 ms/2.578 ms = 1.554
For optimal performance this ratio should be close to 1!


NOTE: The GPU has >20% more load than the CPU. This imbalance causes
  performance loss, consider using a shorter cut-off and a finer PME
grid.

   Core t (s)   Wall t (s)(%)
   Time:   216205.51027036.812  799.7
 7h30:36
 (ns/day)(hour/ns)
Performance:   31.9560.751

### 8 core AMD with 2 GPUs

   Core t (s)   Wall t (s)(%)
   Time:   178961.45022398.880  799.0
 6h13:18
 (ns/day)(hour/ns)
Performance:   38.5730.622
Finished mdrun on node 0 Sat Jul 13 09:24:39 2013


>However, in your case I suspect that the 
>bottleneck is multi-threaded scaling on the AMD CPUs and you should 
>probably decrease the number of threads per MPI rank and share GPUs 
>between 2-4 ranks.


OK but can you give a example of mdrun command ? given a 8 core AMD with 2
GPUs.
I will try to run it again.


>Regarding scaling across nodes, you can't expect much from gigabit 
>ethernet - especially not from the cheaper cards/switches, in my 
>experience even reaction field runs don't scale across nodes with 10G 
>ethernet if you have more than 4-6 ranks per node trying to 
>communicate (let alone with PME). However, on infiniband clusters we 
>have seen scaling to 100 atoms/core (at peak). 

>From your comments, it sounds like a cluster of AMD cpus is difficult to
scale across nodes in our current setup.

Let's assume we install Infiniband (20 or 40GB/s) in the same system of 16
nodes of 8 core AMD with 1 GPU only. Considering the same AMD system, what
is a good way to obtain better performance  when we run a task across nodes
? in other words, what dose mudrun_mpi look like ?

Thanks,
Dwey




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[gmx-users] Re: Hardware for best gromacs performance?

[Dwey Kauffman]

Hi Szilard,

 Thanks.

>From Timo's benchmark, 
1  node142 ns/day 
2  nodes FDR14 218 ns/day 
4  nodes FDR14 257 ns/day 
8  nodes FDR14 326 ns/day 


It looks like a infiniband network is "required" in order to scale up when
running a task across nodes. Is it correct ?   


Dwey


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RE: [gmx-users] RE: Gibbs Energy Calculation and charges

[Dallas Warren]

Thank you for the pointer Michael.

couple-intramol = no
What a diff of the output from gmxdump of the two tpr files shows is in both of 
these cases (normal and double charged), when:
lambda is set to 1.0 (atoms within both molecules will have zero charge)
lambda is set to 0.00 and 0.50, respectively (both will have the same 
charge)
There are the following differences:
functype[] = LJC14_Q, qi and qj are set to the original charges, not 
the ones scaled by lambda
functype[] = LJC_NB, qi and qj are set to the original charges, not the 
ones scaled by lambda
atom[] = q is set to the original charges, not the ones scaled by 
lambda

So this explains why I do not see the two topologies giving the same value at 
the same atomic charges, since the topologies being simulated are not the same. 
 The 1-4 charge interactions are still at the original charges, as are the 1-5 
and beyond.

What is the reason that the charges are being left untouched here with changing 
lambda?  I can understand when we are dealing with LJ/van der Waals, since the 
1-4 are important for the proper dihedrals, but what is the reason for charges 
being left untouched?  Having thought this through, answered it myself, it is 
because here we are interested in molecule - external environment interactions 
being turned off, we are moving the entire molecule from full interacting with 
its external environment to non-interacting.  The molecule itself should be 
left alone.

Turning to the side issue of turning couple-intramol on -

couple-intramol = yes
diff of the equivalent files, there are the following differences:
functype[] = LJC14_Q, qi and qj are set to the original charges, not 
the ones scaled by lambda
atom[] = q is set to the original charges, not the ones scaled by 
lambda

Which confirms what Michael mentioned earlier about couple-intramol only 
affecting those 1-5 and beyond i.e. LJC_NB

Which then begs the question, why does the value of dH/dl change so 
dramatically when this option is turned on, as I observed at 
http://ozreef.org/stuff/gromacs/couple-intramol.png  The only thing being 
changed is the fact that LJC_NB is now being scaled with lambda.

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
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 


> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Michael Shirts
> Sent: Thursday, 31 October 2013 1:52 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] RE: Gibbs Energy Calculation and charges
> 
> I likely won't have much time to look at it tonight, but you can see
> exactly what the option is doing to the topology.  run gmxdump on the
> tpr.  All of the stuff that couple-intramol does is in grompp, so the
> results will show up in the detailed listings of the interactions, and
> which ones have which values set for the A and B states.
> 
> On Wed, Oct 30, 2013 at 5:36 PM, Dallas Warren
>  wrote:
> > Michael, thanks for taking the time to comment and have a look.
> >
> > The real issue I am having is a bit deeper into the topic than that,
> my last reply was just an observation on something else.  Will
> summarise what I have been doing etc.
> >
> > I have a molecule that are calculating the Gibbs energy of hydration
> and solvation (octanol).  In a second topology the only difference is
> that the atomic charges have been doubled.  Considering that charges
> are scaled linearly with lambda, the normal charge values of dH/dl from
> lambda 0 to 1 obtained should reproduce that of the double charged
> molecule from lambda 0.5 to 1.0.  Is that a correct interpretation?
> Since the only difference should be that charge of the atoms and over
> that range the charge will be identical.
> >
> > I was using couple-intramol = no and the following are the results
> from those simulations.
> >
> > For the OE atom within the molecule, I have plotted the following
> graphs of dH/dl versus charge of that atom for both of the topologies.
> > octanol - http://ozreef.org/stuff/octanol.gif
> > water - http://ozreef.org/stuff/water.gif
> > mdp file - http://ozreef.org/stuff/gromacs/mdout.mdp
> >
> > The mismatch between the two topologies is the real issue that I am
> having.  I was hoping to get the two to overlap.
> >
> > My conclusion based on this is that there is actually something else
> being changed with the topology by GROMACS when the simulations are
> being run.  The comments in the manual allude to that, but not entirely
> sure what is going on.
> >
> >> From the manual:
> >>
> >>couple-intramol:
> >>
> >>no
> >> All intra-molecular non-bonded interac

[gmx-users] RE: Gibbs Energy Calculation and charges

[Dallas Warren]

Thanks for the suggestion Chris.  Had a quick look and can't see easily how to 
do this, but I think I am at a point now where it is not an issue and don't 
have to actually do this.

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
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 


> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Christopher Neale
> Sent: Saturday, 2 November 2013 3:50 AM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Gibbs Energy Calculation and charges
> 
> Dear Dallas:
> 
> Seems like you could test Michael's idea by removing all 1-4 NB
> interactions from your topology. It won't produce any biologically
> useful results, but might be a worthwhile check to see if indeed this
> is the issue.
> 
> To do this, I figure you would set gen-pairs to "no" in the [ defaults
> ] directive of forcefield.itp, remove the [ pairtypes ] section from
> ffnonbonded.itp, and remove the [ pairs ] section from your molecular
> .itp file. (You can quickly check that the 1-4 energy is zero in all
> states to ensure that this works).
> 
> If that gives you the result that you expect, then you could go on to
> explicitely state the 1-4 interactions for the A and B states (I
> presume that this is possible). Of course, you should be able to jump
> directly to this second test, but the first test might be useful
> because it rules out the possibility that you make a typo somewhere.
> 
> Chris.
> 
> -- original message --
> 
> I think the grammar got a little garbled there, so I'm not sure quite
> what you are claiming.
> 
> One important thing to remember; 1-4 interactions are treated as
> bonded interactions right now FOR COUPLE intramol (not for lambda
> dependence of the potential energy function), so whether
> couple-intramol is set to yes or no does not affect these interactions
> at all.  It only affects the nonbondeds with distances greater than
> 1-5.  At least to me, this is nonintuitive (and we're coming up with a
> better scheme for 5.0), but might that explain what you are getting?
> 
> On Tue, Oct 29, 2013 at 9:44 PM, Dallas Warren  monash.edu> wrote:
> > Just want this to make another pass, just in case those in the know
> missed it.
> >
> > Using couple-intrmol = yes the resulting dH/dl plot actually looks
> like that at lamba = 1 it is actually equal to couple-intramol = no
> with lambda = 0.
> >
> > Should that be the case?
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> --
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[gmx-users] Re: gmx-users Digest, Vol 115, Issue 16

[Stephanie Teich-McGoldrick]

Message: 5
Date: Mon, 04 Nov 2013 13:32:52 -0500
From: Justin Lemkul 
Subject: Re: [gmx-users] Analysis tools and triclinic boxes
To: Discussion list for GROMACS users 
Message-ID: <5277e854.9000...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Justin,

Thanks for the response. My question was prompted by line 243 in
gmx_cluster.c which states "/* Should use pbc_dx when analysing multiple
molecueles,but the box is not stored for every frame.*/" I just wanted to
verify that analysis tools are written for any box shape.

Cheers,
Stephanie



On 11/4/13 1:29 PM, Stephanie Teich-McGoldrick wrote:
> Dear all,
>
> I am using gromacs 4.6.3 with a triclinic box. Based on the manual and
mail
> list, it is my understanding that the default box shape in gromacs in a
> triclinic box. Can I assume that all the analysis tools also work for a
> triclinic box.
>

All analysis tools should work correctly for all box types.  Is there a
specific
issue you are having, or just speculation?

-Justin

--
==


Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==


On Mon, Nov 4, 2013 at 12:28 PM,  wrote:

> Send gmx-users mailing list submissions to
> gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
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>
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> gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: Re: Installation Gromacs 4.5.7 on rocluster cluster   with
>   centos 6.0 (Mark Abraham)
>2. Analysis tools and triclinic boxes (Stephanie Teich-McGoldrick)
>3. Group protein not found in indexfile (Steve Seibold)
>4. Re: Group protein not found in indexfile (Justin Lemkul)
>5. Re: Analysis tools and triclinic boxes (Justin Lemkul)
>6. Re: TFE-water simulation (Archana Sonawani-Jagtap)
>7. Re: Gentle heating with implicit solvent (Gianluca Interlandi)
>
>
> --
>
> Message: 1
> Date: Mon, 4 Nov 2013 17:05:36 +0100
> From: Mark Abraham 
> Subject: Re: [gmx-users] Re: Installation Gromacs 4.5.7 on rocluster
> cluster with centos 6.0
> To: Discussion list for GROMACS users 
> Message-ID:
>  s_uzbyw8uf...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Mon, Nov 4, 2013 at 12:01 PM, bharat gupta  >wrote:
>
> > Hi,
> >
> > I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works
> > fine till .configure command, but I am getting error at the make command
> :-
> >
> > Error:
> > 
> > [root@cluster gromacs-4.5.7]# make
> >
>
> These is no need to run make as root - doing so guarantees you have almost
> no knowledge of the final state of your entire machine.
>
>
> > /bin/sh ./config.status --recheck
> > running CONFIG_SHELL=/bin/sh /bin/sh ./configure  --enable-mpi
> > LDFLAGS=-L/opt/rocks/lib CPPFLAGS=-I/opt/rocks/include  --no-create
> > --no-recursion
> > checking build system type... x86_64-unknown-linux-gnu
> > checking host system type... x86_64-unknown-linux-gnu
> > ./configure: line 2050: syntax error near unexpected token `tar-ustar'
> > ./configure: line 2050: `AM_INIT_AUTOMAKE(tar-ustar)'
> > make: *** [config.status] Error 2
> >
>
> Looks like the system has an archaic autotools setup. Probably you can
> comment out the line with tar-ustar from the original configure script, or
> remove tar-ustar. Or use the CMake build.
>
>
> >
> >
> > I have another query regarding the gromacs that comes with the Rocks
> > cluster distribution. The mdrun of that gromacs has been complied without
> > mpi option. How can I recomplie with mpi option. As I need the .configure
> > file which is not there in the installed gromacs folder of the rocks
> > cluster ...
> >
>
> The 4.5-era GROMACS installation instructions are up on the website.
> Whatever's distributed with Rocks is more-or-less irrelevant.
>
> Mark
>
>
> >
> >
> > Thanks in advance for help
> >
> >
> >
> >
> > Regards
> > 
> > Bharat
> > --
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[gmx-users] Re: Hardware for best gromacs performance?

[david.chalm...@monash.edu]

Hi Szilárd and all,

Thanks very much for the information.  I am more interested in getting
single simulations to go as fast as possible (within reason!) rather than
overall throughput.  Would you expect that the more expensive dual
Xeon/Titan systems would perform better in this respect? 

Cheers

David

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Re: [gmx-users] Re: Hardware for best gromacs performance?

[Mark Abraham]

Yes, that has been true for GROMACS for a few years. Low-latency
communication is essential if you want a whole MD step to happen in around
1ms wall time.

Mark
On Nov 5, 2013 11:24 PM, "Dwey Kauffman"  wrote:

> Hi Szilard,
>
>  Thanks.
>
> >From Timo's benchmark,
> 1  node142 ns/day
> 2  nodes FDR14 218 ns/day
> 4  nodes FDR14 257 ns/day
> 8  nodes FDR14 326 ns/day
>
>
> It looks like a infiniband network is "required" in order to scale up when
> running a task across nodes. Is it correct ?
>
>
> Dwey
>
>
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Re: [gmx-users] Diffusion/PBC

[Trayder Thomas]

Your best bet is probably to center everything on the receptor. That will
prevent jumping of the receptor only, which is hopefully all you need.

-Trayder


On Tue, Nov 5, 2013 at 7:14 PM, Tsjerk Wassenaar  wrote:

> Hi Debashis,
>
> Makes sure that the anion and receptor are together in the reference
> structure you use for trjconv -pbc nojump
>
> Cheers,
>
> Tsjerk
>
>
> On Tue, Nov 5, 2013 at 8:12 AM, Debashis Sahu  >wrote:
>
> > Dear All,
> >   I have an problem related to jumping trajectory. In my MD
> > run, there is a receptor molecule which is binding with an halogen anion
> in
> > water solvent. In the original trajectory, the binding between them looks
> > fine but jumping present. To remove the jumping of the system from
> > trajectory, I have used 'nojump' as discussed in the forum. Now I got a
> > jump-free trajectory, but due to the diffusion here, I have observed that
> > the anion and the receptor are far away from each other. I could not fix
> > the problem. can any one suggest me?
> > Thanks in advance.
> > with regards,
> > *Debashis Sahu*
> > *Central Salt and Marine Chemical Research Institute*
> > *Bhavnagar, Gujarat*
> > *India, 364002.*
> > --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] g_lie and ligand only simulation

[Kavyashree M]

Dear users,

When the simulation was carried out with PME
rcoulomb was set equal to rlist. But when I need to
to ligand-water simulation without PME (with RF-0)
then it requires rlist greater by 0.1-0.3 than rcoulomb.
So if I rerun protein-ligand-water simulation there
could be more differences in the energies isnt it?

Thank you
Regards
Kavya


On Sat, Nov 2, 2013 at 9:51 PM, Kavyashree M  wrote:

> Ok thank you. I thought it was for protein-ligand-water
> that needs to be rerun without PME.
>
> Thanks
> Regards
> Kavya
>
>
>
> On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 11/2/13 12:14 PM, Kavyashree M wrote:
>>
>>> Sir,
>>>
>>> Thank you. Should the ligand-water MD be done without PME?
>>>
>>>
>> I already answered this.  Please read my previous reply again.
>>
>> -Justin
>>
>>
>>  Thank you
>>> Regards
>>>
>>> Kavya
>>>
>>>
>>> On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul  wrote:
>>>
>>>

 On 11/2/13 1:22 AM, Kavyashree M wrote:

  Dear Users,
>
> Its mentioned in the list that it would be
> wrong to use g_lie on a simulation which
> uses PME.
>
> So kindly suggest any other way available
> to get the free energy of ligand binding other
> using g_lie?
>
>
>  The original simulation should be done with PME, then the energies
 recalculated using mdrun -rerun without PME.  More detailed methods are
 available in the list archive; this topic gets discussed a lot.


 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow

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

 jalem...@outerbanks.umaryland.edu | (410) 706-7441

 ==
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>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>
>> ==
>> --
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>
>
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