Re: [gmx-users] need help

[Mark Abraham]

- Original Message -
From: Anamika Awasthi 
Date: Thursday, August 12, 2010 16:41
Subject: [gmx-users] need help
To: gmx-users@gromacs.org

> Dear gromacs user,
> 
>   I want to install gromacs new version on my linux system. can u all please 
> guide me,

The GROMACS installation guide can be found on the GROMACS webpage :-) There's 
a ton of other useful information there, please be sure to search it and the 
rest of the web before asking questions. You'll make much faster progress that 
way! :-)

Mark

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[gmx-users] need help

[Anamika Awasthi]

Dear gromacs user,

  I want to install gromacs new version on my linux system. can u all please
guide me,


 Thanking u in advance

 Anamika
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Re: [gmx-users] mdrun : error

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello,
I am trying to do equilibration for my system (solvent + solute). I am
geting the following error. If I run solvent and solute molecules
separately, its run well. For mixture I am getting following error.
What this error means.

Fatal error:
1 of the 22334 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck



Search the list archive.  This has been asked and answered several times, so 
you'll likely find something useful.  Also, take mdrun's advice and read about 
the options it's telling you.


-Justin


NIlesh



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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] mdrun : error

[Nilesh Dhumal]

Hello,
I am trying to do equilibration for my system (solvent + solute). I am
geting the following error. If I run solvent and solute molecules
separately, its run well. For mixture I am getting following error.
What this error means.

Fatal error:
1 of the 22334 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck

NIlesh

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[gmx-users] g_rms question

[udi]

Hi gromacs users,

I'm simulating a protein that consists of 5 domains. I have calculated the
whole protein's backbone RMSD by entering '4' twice.

Now, I would like to calculate the contribution of every domain i.e. if the
whole protein's RMSD in the first frame is  1nm, then how is this 1nm
distributed between the 5 domains.

I have created 5 groups in the index file of the backbone of every domain
and calculated the RMSD by first entering '4' in order to fit the whole
backbone and entered the domains backbone groups in the second entry. (5
different calculations). The problem is that the values I get from the
domains do not add up to the whole backbone RMSD values!!! What am doing
wrong? 

 

Thanks from advanced

Chears

 

Udi 

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Re: [gmx-users] New beta release: 4.5-beta3

[Da-Wei Li]

According to our HPC manage, our MVAPICH2's version is 1.0.3.

thanks for the information.

dawei

On Wed, Aug 11, 2010 at 2:52 PM, Roland Schulz  wrote:
> MVAPICH2 >=1.4.1 should be fine. Did you use a version <1.4.1?
> On Wed, Aug 11, 2010 at 2:45 PM, Da-Wei Li  wrote:
>>
>> Yes it is. Now everything is fine with openmpi instead of mvapich2.
>>
>> dawei
>>
>> On Wed, Aug 11, 2010 at 12:59 AM, Mark Abraham 
>> wrote:
>> >
>> >
>> > - Original Message -
>> > From: Da-Wei Li 
>> > Date: Wednesday, August 11, 2010 6:23
>> > Subject: Re: [gmx-users] New beta release: 4.5-beta3
>> > To: Discussion list for GROMACS users 
>> >
>> >> Hi,all
>> >>
>> >> Unfortunately, it still crash. Here it is the output of mdrun. Both
>> >> Gromacs-4.0.7 and non-parallel 4.5b3 work fine on this system. I use
>> >> mvapich2 and intel compiler.
>> >
>> > MPICH variants are known to cause problems. Try OpenMPI.
>> >
>> > Mark
>> >
>> >> ***
>> >> Getting Loaded...
>> >> Reading file em.tpr, VERSION 4.5-beta3 (single precision)
>> >> Loaded with Money
>> >>
>> >>
>> >> Will use 9 particle-particle and 7 PME only nodes
>> >> This is a guess, check the performance at the end of the log file
>> >> Making 1D domain decomposition 9 x 1 x 1
>> >>
>> >> Back Off! I just backed up em.trr to ./#em.trr.4#
>> >>
>> >> Back Off! I just backed up em.edr to ./#em.edr.4#
>> >>
>> >> Steepest Descents:
>> >>    Tolerance (Fmax)   =  1.0e+03
>> >>    Number of steps
>> >> =    5
>> >> rank 9 in job 1  hpc-8-6.local_58777   caused
>> >> collective abort of all ranks
>> >>   exit status of rank 9: killed by signal 9
>> >>
>> >> ***
>> >>
>> >> dawei
>> >>
>> >> On Tue, Aug 10, 2010 at 3:24 PM, Rossen Apostolov
>> >>  wrote:
>> >> >
>> >> > New beta release of gromacs is available for testing:
>> >> > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz.
>> >> >
>> >> > Many bugs have been fixed in this release, mainly double
>> >> precision support
>> >> > with icc compilers, SSE2. Have a look at the release note on
>> >> the website for
>> >> > more details. There are still some issues on Windows platofrms
>> >> that will be
>> >> > resolved before the final release.
>> >> >
>> >> > Please try it out and see if it works as expected! Hopefully
>> >> there won't be
>> >> > many more betas :))
>> >> >
>> >> > Rossen
>> >> > --
>> >> > gmx-users mailing list    gmx-us...@gromacs.org
>> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> > Please search the archive at http://www.gromacs.org/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.
>> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >> >
>> >> --
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>
>
>
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Re: [gmx-users] broken links

[Rossen Apostolov]

 Hi Alan,

Those links were pointing to the old wiki. I fixed them and now they 
refer directly to the original resources. Let us know if the page needs 
updating.


Rossen

On 08/11/2010 06:59 PM, Alan wrote:

Hi there,

I cannot download from 
http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM 
any file and link to Gamess-UK seems to be broken as well.


Alan

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80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28 <<


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[gmx-users] Units of k1 in the pulling code

[XUEMING TANG]

Hi there

The units for pull_k1 = $$ kJ/mol/nm. If this force is applied to a cluster,
the "/mol" in the units of force means per atom in the cluster, or single
molecule composed of several atoms? Sorry, I don't know the default value of
mol in gromacs. Does that mean per molecule? Besides, the force is applied
to the COM of cluster, but in the real pulling process, the force is applied
to each of the molecule in the cluster, or each of the atom in the cluster?

Thanks in advance!

Best!
Xueming
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Re: [gmx-users] New beta release: 4.5-beta3

[Roland Schulz]

MVAPICH2 >=1.4.1 should be fine. Did you use a version <1.4.1?

On Wed, Aug 11, 2010 at 2:45 PM, Da-Wei Li  wrote:

> Yes it is. Now everything is fine with openmpi instead of mvapich2.
>
> dawei
>
> On Wed, Aug 11, 2010 at 12:59 AM, Mark Abraham 
> wrote:
> >
> >
> > - Original Message -
> > From: Da-Wei Li 
> > Date: Wednesday, August 11, 2010 6:23
> > Subject: Re: [gmx-users] New beta release: 4.5-beta3
> > To: Discussion list for GROMACS users 
> >
> >> Hi,all
> >>
> >> Unfortunately, it still crash. Here it is the output of mdrun. Both
> >> Gromacs-4.0.7 and non-parallel 4.5b3 work fine on this system. I use
> >> mvapich2 and intel compiler.
> >
> > MPICH variants are known to cause problems. Try OpenMPI.
> >
> > Mark
> >
> >> ***
> >> Getting Loaded...
> >> Reading file em.tpr, VERSION 4.5-beta3 (single precision)
> >> Loaded with Money
> >>
> >>
> >> Will use 9 particle-particle and 7 PME only nodes
> >> This is a guess, check the performance at the end of the log file
> >> Making 1D domain decomposition 9 x 1 x 1
> >>
> >> Back Off! I just backed up em.trr to ./#em.trr.4#
> >>
> >> Back Off! I just backed up em.edr to ./#em.edr.4#
> >>
> >> Steepest Descents:
> >>Tolerance (Fmax)   =  1.0e+03
> >>Number of steps
> >> =5
> >> rank 9 in job 1  hpc-8-6.local_58777   caused
> >> collective abort of all ranks
> >>   exit status of rank 9: killed by signal 9
> >>
> >> ***
> >>
> >> dawei
> >>
> >> On Tue, Aug 10, 2010 at 3:24 PM, Rossen Apostolov
> >>  wrote:
> >> >
> >> > New beta release of gromacs is available for testing:
> >> > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz.
> >> >
> >> > Many bugs have been fixed in this release, mainly double
> >> precision support
> >> > with icc compilers, SSE2. Have a look at the release note on
> >> the website for
> >> > more details. There are still some issues on Windows platofrms
> >> that will be
> >> > resolved before the final release.
> >> >
> >> > Please try it out and see if it works as expected! Hopefully
> >> there won't be
> >> > many more betas :))
> >> >
> >> > Rossen
> >> > --
> >> > gmx-users mailing listgmx-users@gromacs.org
> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> > Please search the archive at http://www.gromacs.org/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.
> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >> >
> >> --
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> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search
> >> before posting!
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Re: [gmx-users] New beta release: 4.5-beta3

[Da-Wei Li]

Yes it is. Now everything is fine with openmpi instead of mvapich2.

dawei

On Wed, Aug 11, 2010 at 12:59 AM, Mark Abraham  wrote:
>
>
> - Original Message -
> From: Da-Wei Li 
> Date: Wednesday, August 11, 2010 6:23
> Subject: Re: [gmx-users] New beta release: 4.5-beta3
> To: Discussion list for GROMACS users 
>
>> Hi,all
>>
>> Unfortunately, it still crash. Here it is the output of mdrun. Both
>> Gromacs-4.0.7 and non-parallel 4.5b3 work fine on this system. I use
>> mvapich2 and intel compiler.
>
> MPICH variants are known to cause problems. Try OpenMPI.
>
> Mark
>
>> ***
>> Getting Loaded...
>> Reading file em.tpr, VERSION 4.5-beta3 (single precision)
>> Loaded with Money
>>
>>
>> Will use 9 particle-particle and 7 PME only nodes
>> This is a guess, check the performance at the end of the log file
>> Making 1D domain decomposition 9 x 1 x 1
>>
>> Back Off! I just backed up em.trr to ./#em.trr.4#
>>
>> Back Off! I just backed up em.edr to ./#em.edr.4#
>>
>> Steepest Descents:
>>    Tolerance (Fmax)   =  1.0e+03
>>    Number of steps
>> =    5
>> rank 9 in job 1  hpc-8-6.local_58777   caused
>> collective abort of all ranks
>>   exit status of rank 9: killed by signal 9
>>
>> ***
>>
>> dawei
>>
>> On Tue, Aug 10, 2010 at 3:24 PM, Rossen Apostolov
>>  wrote:
>> >
>> > New beta release of gromacs is available for testing:
>> > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz.
>> >
>> > Many bugs have been fixed in this release, mainly double
>> precision support
>> > with icc compilers, SSE2. Have a look at the release note on
>> the website for
>> > more details. There are still some issues on Windows platofrms
>> that will be
>> > resolved before the final release.
>> >
>> > Please try it out and see if it works as expected! Hopefully
>> there won't be
>> > many more betas :))
>> >
>> > Rossen
>> > --
>> > gmx-users mailing list    gmx-us...@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at http://www.gromacs.org/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.
>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >
>> --
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Re: [gmx-users] RE: log files

[Justin A. Lemkul]

Nimesh Jain wrote:
Well, no. I got a 20GB log file when nstlog was 1000. When I changed it 
to 1, the log file was about 1 MB after a few minutes of simulation 
which means that it will be in GBs in a few days.




Then look at what it's writing.  Is it giving the output you expect?  Are all 
replicas written to the same log file?  I haven't used REMD since Gromacs 3.x, 
when replicas were written to separate logs, I don't know if it's changed.  I'd 
be far more concerned with outputting full precision coordinates and velocities 
every 10 ps - that will likely occupy huge amounts of disk space.


And as an aside, when you directly say a certain .mdp file produces a 20 GB log 
file, the users of this list will expect that to be accurate.  If you're not 
telling the whole truth, then it makes it hard to diagnose any issues and 
discourages people from helping you.  Accurate reporting makes for faster 
resolution.


-Justin

On Wed, Aug 11, 2010 at 10:49 AM, Gaurav Goel > wrote:


You've set the frequency of writing to log file as
'nstlog   = 10'.
Given that 'nsteps   = 1', you're writing to
the log file only 1000 times. Do you get a 20GB md.log file with
these settings?

-Gaurav

On Wed, Aug 11, 2010 at 10:52 AM, Nimesh Jain
mailto:nimeshjain2...@u.northwestern.edu>> wrote:

Hi,

I am having some problem in my simulations related to log files.
The file sizes are enormous, its like after 3 days of simulation
I had a 20 GB md.log file. One of my grompps looks like this:
[tau_t is very low because I am using bd and it doesn't work
otherwise]. [I am doing a replica exchange with 10,000 as
exchange frequency]


include  =
define   =
integrator   = bd
tinit= 0
dt   = 0.001
nsteps   = 1 ;10
simulation_part  = 1
init_step= 0
comm-mode= Angular
nstcomm  = 1
comm-grps=


emtol= 0.01
emstep   = 1.5

nstxout  = 1
nstvout  = 1
nstfout  = 1

nstlog   = 10
nstenergy= 1000

nstxtcout= 1000
xtc-precision= 1000

xtc-grps =
energygrps   =

ns_type  = grid
pbc  = xyz
periodic_molecules   = no

rlist= 8.95

coulombtype  = user
rcoulomb-switch  = 0
rcoulomb = 8.95

epsilon-r= 1

vdw-type = user  ;cutoff
rvdw-switch  = 0
rvdw = 8.95
DispCorr = No
table-extension  = 1
; Seperate tables between energy group pairs
energygrps   = A T G C P260 SA SB

energygrp_table  = A A  A T  A G  A C  A P260  A SA  A
SB  T T  T G  T C  T P260  T S
A  T SB  G G  G C  G P260  G SA  G SB  C C  C P260  C SA  C SB 
P260 P260  P260 SA  P260 SB

SA SA  SA SB  SB SB

; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.10

Tcoupl   = Nose-Hoover
tc-grps  = System
tau_t= 0.0001
ref_t= 260.00

Pcoupl   = No

andersen_seed= 815131

gen_vel  = yes
gen_temp = 260.
gen_seed = 1993

; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions
are excluded
energygrp_excl   =



Please let me know if anyone knows whats the problem.

Thanks,
Nimesh

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Re: [gmx-users] Unsubscribe

[Justin A. Lemkul]

Peter Wilczynski wrote:

Could you unsubscribe me from this email chain?

Thanks for all your help!



Per the header of the message to which you replied:

To subscribe or unsubscribe via the World Wide Web, visit 
http://lists.gromacs.org/mailman/listinfo/gmx-users


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] RE: log files

[Nimesh Jain]

Well, no. I got a 20GB log file when nstlog was 1000. When I changed it to
1, the log file was about 1 MB after a few minutes of simulation which
means that it will be in GBs in a few days.

On Wed, Aug 11, 2010 at 10:49 AM, Gaurav Goel wrote:

> You've set the frequency of writing to log file as
> 'nstlog   = 10'.
> Given that 'nsteps   = 1', you're writing to the
> log file only 1000 times. Do you get a 20GB md.log file with these settings?
>
> -Gaurav
>
> On Wed, Aug 11, 2010 at 10:52 AM, Nimesh Jain <
> nimeshjain2...@u.northwestern.edu> wrote:
>
>> Hi,
>>
>> I am having some problem in my simulations related to log files. The file
>> sizes are enormous, its like after 3 days of simulation I had a 20 GB md.log
>> file. One of my grompps looks like this:
>> [tau_t is very low because I am using bd and it doesn't work otherwise].
>> [I am doing a replica exchange with 10,000 as exchange frequency]
>>
>>
>> include  =
>> define   =
>> integrator   = bd
>> tinit= 0
>> dt   = 0.001
>> nsteps   = 1 ;10
>> simulation_part  = 1
>> init_step= 0
>> comm-mode= Angular
>> nstcomm  = 1
>> comm-grps=
>>
>>
>> emtol= 0.01
>> emstep   = 1.5
>>
>> nstxout  = 1
>> nstvout  = 1
>> nstfout  = 1
>>
>> nstlog   = 10
>> nstenergy= 1000
>>
>> nstxtcout= 1000
>> xtc-precision= 1000
>>
>> xtc-grps =
>> energygrps   =
>>
>> ns_type  = grid
>> pbc  = xyz
>> periodic_molecules   = no
>>
>> rlist= 8.95
>>
>> coulombtype  = user
>> rcoulomb-switch  = 0
>> rcoulomb = 8.95
>>
>> epsilon-r= 1
>>
>> vdw-type = user  ;cutoff
>> rvdw-switch  = 0
>> rvdw = 8.95
>> DispCorr = No
>> table-extension  = 1
>> ; Seperate tables between energy group pairs
>> energygrps   = A T G C P260 SA SB
>>
>> energygrp_table  = A A  A T  A G  A C  A P260  A SA  A SB  T T  T
>> G  T C  T P260  T S
>> A  T SB  G G  G C  G P260  G SA  G SB  C C  C P260  C SA  C SB  P260 P260
>> P260 SA  P260 SB
>> SA SA  SA SB  SB SB
>>
>> ; Spacing for the PME/PPPM FFT grid
>> fourierspacing   = 0.10
>>
>> Tcoupl   = Nose-Hoover
>> tc-grps  = System
>> tau_t= 0.0001
>> ref_t= 260.00
>>
>> Pcoupl   = No
>>
>> andersen_seed= 815131
>>
>> gen_vel  = yes
>> gen_temp = 260.
>> gen_seed = 1993
>>
>> ; ENERGY GROUP EXCLUSIONS
>> ; Pairs of energy groups for which all non-bonded interactions are
>> excluded
>> energygrp_excl   =
>>
>>
>>
>> Please let me know if anyone knows whats the problem.
>>
>> Thanks,
>> Nimesh
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>
>
> --
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-- 
Nimesh Jain
Graduate Student
Biomedical Engineering
Northwestern University
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[gmx-users] broken links

[Alan]

Hi there,

I cannot download from
http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMMany
file and link to Gamess-UK seems to be broken as well.

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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[gmx-users] gromacs from git failed with cmake on Mac SL and fftw from Fink

[Alan]

Hi there,

I am using gromacs from git source with cmake on Mac SL with Fink.

~/Programmes/gromacs% git show
commit 86226a1a075a071920b0413aa7030545f8e6e282
Merge: b8f35b9 c903375
Author: Berk Hess 
Date:   Wed Aug 11 12:57:53 2010 +0200

Merge remote branch 'origin/release-4-5-patches'


If using the old way (after bootstrapping), everything goes fine with:

./configure CPPFLAGS=-I/sw/include LDFLAGS=-L/sw/lib --with-gsl --with-x

With cmake (cmake -D BUILD_SHARED_LIBS=ON or OFF), although CMakeCache.txt
seems to be correct, for example, I see:

//Path to a file.
FFTW3F_INCLUDE_DIR:PATH=/sw/include

//Path to a library.
FFTW3F_LIBRARIES:FILEPATH=/sw/lib/libfftw3f.dylib

(But have no idea if using gsl libs)

I got this error:

[ skip ]
Scanning dependencies of target grompp
[ 77%] Building C object src/kernel/CMakeFiles/grompp.dir/grompp.c.o
Linking C executable grompp
[ 77%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_lie.c.o
Undefined symbols:
  "_fftwf_plan_many_dft_r2c", referenced from:
  _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  "_fftwf_plan_dft_r2c_2d", referenced from:
  _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  "_fftwf_plan_dft_r2c_3d", referenced from:
  _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  "_fftwf_malloc", referenced from:
  _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o)
  "_fftwf_execute_dft_c2r", referenced from:
  _gmx_fft_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  "_fftwf_free", referenced from:
  _gmx_fft_destroy in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o)
  _gmx_fft_init_many_1d in libmd.a(gmx_fft_

[gmx-users] gromacs from git, using cmake, where's gsl option?

[Alan]

Hi list,

I am giving a try with gromacs from git source using cmake. It seems to get
everything right in my system (Mac SL 64 bits) but I have no idea if it's
using gsl lib as I would do if using the old method ./configure --with-gsl
etc.

Can someone please make it clear here? Many thanks in advance,

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
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[gmx-users] Unsubscribe

[Peter Wilczynski]

> ; ENERGY MINIMIZATION OPTIONS =
> ; Force tolerance and initial step-size =
> emtol= 100
> emstep   = 0.01
> ; Max number of iterations in relax_shells =
> niter= 20
> ; Number of correction steps to use for L-BFGS minimization
> nbfgscorr= 10
> ; NEIGHBORSEARCHING PARAMETERS =
> ; nblist update frequency =
> nstlist  = 1
> ; ns algorithm (simple or grid) =
> ns_type  = grid
> ; Periodic boundary conditions: xyz or none =
> pbc  = xyz
> ; nblist cut-off =
> rlist= 1.0
> 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 = switch
> ; cut-off lengths=
> rvdw-switch  = 0.8
> rvdw = 0.9
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr  = EnerPres
> ; 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    = 6
> ewald_rtol   = 1e-06
> epsilon_surface  = 0
> optimize_fft = no
> ; Free energy control stuff
> free_energy  = yes
> init_lambda  = 0.0
> delta_lambda = 0
> sc_alpha =0.5
> sc-power =1.0
> sc-sigma = 0.3
> --
> 
> Can anybody suggest whether the mdp file has some error or I can use
> the one with the warning.
> 
> 
> Thanks in advance,
> Vivek
> -- next part --
> An HTML attachment was scrubbed...
> URL: 
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100811/d1a2fc77/attachment-0001.html
> 
> --
> 
> Message: 4
> Date: Wed, 11 Aug 2010 14:59:13 +1000
> From: Mark Abraham 
> Subject: Re: [gmx-users] New beta release: 4.5-beta3
> To: Discussion list for GROMACS users 
> Message-ID: 
> Content-Type: text/plain; charset="us-ascii"
> 
> 
> 
> - Original Message -
> From: Da-Wei Li 
> Date: Wednesday, August 11, 2010 6:23
> Subject: Re: [gmx-users] New beta release: 4.5-beta3
> To: Discussion list for GROMACS users 
> 
>> Hi,all
>> 
>> Unfortunately, it still crash. Here it is the output of mdrun. Both
>> Gromacs-4.0.7 and non-parallel 4.5b3 work fine on this system. I use
>> mvapich2 and intel compiler.
> 
> MPICH variants are known to cause problems. Try OpenMPI.
> 
> Mark
> 
>> ***
>> Getting Loaded...
>> Reading file em.tpr, VERSION 4.5-beta3 (single precision)
>> Loaded with Money
>> 
>> 
>> Will use 9 particle-particle and 7 PME only nodes
>> This is a guess, check the performance at the end of the log file
>> Making 1D domain decomposition 9 x 1 x 1
>> 
>> Back Off! I just backed up em.trr to ./#em.trr.4#
>> 
>> Back Off! I just backed up em.edr to ./#em.edr.4#
>> 
>> Steepest Descents:
>>   Tolerance (Fmax)   =  1.0e+03
>>   Number of steps
>> =5
>> rank 9 in job 1  hpc-8-6.local_58777   caused 
>> collective abort of all ranks
>>  exit status of rank 9: killed by signal 9
>> 
>> ***
>> 
>> dawei
>> 
>> On Tue, Aug 10, 2010 at 3:24 PM, Rossen Apostolov
>>  wrote:
>>> 
>>> New beta release of gromacs is available for testing:
>>> ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz.
>>> 
>>> Many bugs have been fixed in this release, mainly double 
>> precision support
>>> with icc compilers, SSE2. Have a look at the release note on 
>> the website for
>>> more details. There are still some issues on Windows platofrms 
>> that will be
>>> resolved before the final release.
>>> 
>>> Please try it out and see if it works as expected! Hopefully 
>> there won't be
>>> many more betas :))
>>> 
>>> Rossen
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] RE: log files

[Gaurav Goel]

You've set the frequency of writing to log file as 'nstlog
= 10'.
Given that 'nsteps   = 1', you're writing to the log
file only 1000 times. Do you get a 20GB md.log file with these settings?

-Gaurav

On Wed, Aug 11, 2010 at 10:52 AM, Nimesh Jain <
nimeshjain2...@u.northwestern.edu> wrote:

> Hi,
>
> I am having some problem in my simulations related to log files. The file
> sizes are enormous, its like after 3 days of simulation I had a 20 GB md.log
> file. One of my grompps looks like this:
> [tau_t is very low because I am using bd and it doesn't work otherwise]. [I
> am doing a replica exchange with 10,000 as exchange frequency]
>
>
> include  =
> define   =
> integrator   = bd
> tinit= 0
> dt   = 0.001
> nsteps   = 1 ;10
> simulation_part  = 1
> init_step= 0
> comm-mode= Angular
> nstcomm  = 1
> comm-grps=
>
>
> emtol= 0.01
> emstep   = 1.5
>
> nstxout  = 1
> nstvout  = 1
> nstfout  = 1
>
> nstlog   = 10
> nstenergy= 1000
>
> nstxtcout= 1000
> xtc-precision= 1000
>
> xtc-grps =
> energygrps   =
>
> ns_type  = grid
> pbc  = xyz
> periodic_molecules   = no
>
> rlist= 8.95
>
> coulombtype  = user
> rcoulomb-switch  = 0
> rcoulomb = 8.95
>
> epsilon-r= 1
>
> vdw-type = user  ;cutoff
> rvdw-switch  = 0
> rvdw = 8.95
> DispCorr = No
> table-extension  = 1
> ; Seperate tables between energy group pairs
> energygrps   = A T G C P260 SA SB
>
> energygrp_table  = A A  A T  A G  A C  A P260  A SA  A SB  T T  T
> G  T C  T P260  T S
> A  T SB  G G  G C  G P260  G SA  G SB  C C  C P260  C SA  C SB  P260 P260
> P260 SA  P260 SB
> SA SA  SA SB  SB SB
>
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing   = 0.10
>
> Tcoupl   = Nose-Hoover
> tc-grps  = System
> tau_t= 0.0001
> ref_t= 260.00
>
> Pcoupl   = No
>
> andersen_seed= 815131
>
> gen_vel  = yes
> gen_temp = 260.
> gen_seed = 1993
>
> ; ENERGY GROUP EXCLUSIONS
> ; Pairs of energy groups for which all non-bonded interactions are excluded
> energygrp_excl   =
>
>
>
> Please let me know if anyone knows whats the problem.
>
> Thanks,
> Nimesh
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
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[gmx-users] RE: log files

[Nimesh Jain]

Hi,

I am having some problem in my simulations related to log files. The file
sizes are enormous, its like after 3 days of simulation I had a 20 GB md.log
file. One of my grompps looks like this:
[tau_t is very low because I am using bd and it doesn't work otherwise]. [I
am doing a replica exchange with 10,000 as exchange frequency]


include  =
define   =
integrator   = bd
tinit= 0
dt   = 0.001
nsteps   = 1 ;10
simulation_part  = 1
init_step= 0
comm-mode= Angular
nstcomm  = 1
comm-grps=


emtol= 0.01
emstep   = 1.5

nstxout  = 1
nstvout  = 1
nstfout  = 1

nstlog   = 10
nstenergy= 1000

nstxtcout= 1000
xtc-precision= 1000

xtc-grps =
energygrps   =

ns_type  = grid
pbc  = xyz
periodic_molecules   = no

rlist= 8.95

coulombtype  = user
rcoulomb-switch  = 0
rcoulomb = 8.95

epsilon-r= 1

vdw-type = user  ;cutoff
rvdw-switch  = 0
rvdw = 8.95
DispCorr = No
table-extension  = 1
; Seperate tables between energy group pairs
energygrps   = A T G C P260 SA SB

energygrp_table  = A A  A T  A G  A C  A P260  A SA  A SB  T T  T G
T C  T P260  T S
A  T SB  G G  G C  G P260  G SA  G SB  C C  C P260  C SA  C SB  P260 P260
P260 SA  P260 SB
SA SA  SA SB  SB SB

; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.10

Tcoupl   = Nose-Hoover
tc-grps  = System
tau_t= 0.0001
ref_t= 260.00

Pcoupl   = No

andersen_seed= 815131

gen_vel  = yes
gen_temp = 260.
gen_seed = 1993

; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl   =



Please let me know if anyone knows whats the problem.

Thanks,
Nimesh
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Re: [gmx-users] about do_dssp

[Justin A. Lemkul]

babu gokul wrote:

dear all
I am analyzing  a collagen dynamics i would like to analysis the 
collagen structure in and its parameter ? what is the difference between 
beta bridge and beta strand.




I would suggest you have a look at the DSSP paper.

http://www.gromacs.org/Developer_Zone/Programming_Guide/DSSP

-Justin

thank you 
E R azhagiya singam




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MILES-IGERT Trainee
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] GMXRC missing

[Ondrej Marsalek]

Hi,

thanks for the fix.

Best,
Ondrej


On Wed, Aug 11, 2010 at 08:46, Rossen Apostolov
 wrote:
>  Hi,
>
> I commited a patch in the latest git.
>
> Thanks for reporting,
> Rossen
>
> On 8/10/10 4:13 PM, Ondrej Marsalek wrote:
>>
>> Dear all,
>>
>> I have installed 4.5 beta2 using cmake and it seems that the GMXRC
>> files are missing in the installation. Can anyone confirm this?
>>
>> Best,
>> Ondrej
>
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[gmx-users] about do_dssp

[babu gokul]

dear all
I am analyzing  a collagen dynamics i would like to analysis the collagen 
structure in and its parameter ? what is the difference between beta bridge and 
beta strand.

thank you 
E R azhagiya singam

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Re: [gmx-users] New beta release: 4.5-beta3

[Jussi Lehtola]

On Wed, 11 Aug 2010 15:19:06 +0200
Rossen Apostolov  wrote:

>   Hi,
> > > I can't compile using CMake - I get undefined references to GSL
> > > functions when compiling do_dssp. -lgsl seems to be missing from
> > > the linker line.
> > >
> GSL libraries support has been removed from the CMake system, you can 
> use autoconf for now. The GSL and Gromacs licenses are not compatible 
> for binary releases.

Now how would that be possible? GSL is licensed under the GPL, so is
Gromacs. Or, to be more exact:

Gromacs 4.5 beta3: GPLv2+, LGPLv2+, and 3 clause BSD => linking
produces GPLv2+

GSL 1.14: GPLv3+

So, compiling Gromacs with GSL included results in a GPLv3+ binary.
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Fysiikan laitos, Helsingin Yliopisto
jussi.leht...@helsinki.fi, p. 191 50632
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Department of Physics, University of Helsinki, Finland
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Re: [gmx-users] New beta release: 4.5-beta3

[Rossen Apostolov]

 Hi,

> I can't compile using CMake - I get undefined references to GSL
> functions when compiling do_dssp. -lgsl seems to be missing from the
> linker line.
>
GSL libraries support has been removed from the CMake system, you can 
use autoconf for now. The GSL and Gromacs licenses are not compatible 
for binary releases.

> Another issue is that the CMake build scripts do not seem to honor
> CFLAGS. The string "-fomit-frame-pointer -finline-functions
> -funroll-all-loops  -O3 -DNDEBUG" is added to the end of
> the flags,
> which causes a problem since the optimization settings are overruled.
>
Sander just commited a patch that will honour the CFLAGS/CXXFLAGS 
environmental variables, if they are set. However, the CMake system 
provides a few build types such as Debug and Release, and they come with 
predefined set of flags which will be appended to your custom settings. 
In Gromacs the default "Release" comes with -O3 etc.(what you see above).



If you want more control over the flags then you can use:
* cmake -i
* ccmake
* cmake-gui
* manually modify CMakeCache.txt (and run $ cmake /path/to/gromacs after 
without other arguments)


Pay attention that variables are called CMAKE_C_FLAGS, 
CMAKE_C_FLAGS_RELEASE, CMAKE_CXX_FLAGS etc., and those are the ones that 
you have to modify.


I'll extend the section on custom flags on the website.


> Plus, I think there should be some kind of minimal readme for usage
> with CMake.

Agreed - I asked for that a while ago, and Rossen put some info here 
http://www.gromacs.org/Developer_Zone/Cmake
I added a new INSTALL.cmake file in the source tree, it will be 
available in the next release.


Rossen
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Re: [gmx-users] GMXRC missing

[Rossen Apostolov]

 Hi,

I commited a patch in the latest git.

Thanks for reporting,
Rossen

On 8/10/10 4:13 PM, Ondrej Marsalek wrote:

Dear all,

I have installed 4.5 beta2 using cmake and it seems that the GMXRC
files are missing in the installation. Can anyone confirm this?

Best,
Ondrej


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Re: [gmx-users] New beta release: 4.5-beta3

[Mark Abraham]

- Original Message -
From: Jussi Lehtola 
Date: Wednesday, August 11, 2010 21:04
Subject: Re: [gmx-users] New beta release: 4.5-beta3
To: gmx-users@gromacs.org

> On Tue, 10 Aug 2010 21:24:50 +0200
> Rossen Apostolov  wrote:
> 
> > 
> > New beta release of gromacs is available for testing: 
> > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz.
> > 
> > Many bugs have been fixed in this release, mainly double 
> precision 
> > support with icc compilers, SSE2. Have a look at the release 
> note on
> > the website for more details. There are still some issues on 
> Windows 
> > platofrms that will be resolved before the final release.
> > 
> > Please try it out and see if it works as expected! Hopefully there
> > won't be many more betas :))
> 
> I can't compile using CMake - I get undefined references to GSL
> functions when compiling do_dssp. -lgsl seems to be missing from the
> linker line.
> 
> Another issue is that the CMake build scripts do not seem to honor
> CFLAGS. The string "-fomit-frame-pointer -finline-functions
> -funroll-all-loops  -O3 -DNDEBUG" is added to the end of 
> the flags,
> which causes a problem since the optimization settings are overruled.
> 
> Plus, I think there should be some kind of minimal readme for usage
> with CMake.

Agreed - I asked for that a while ago, and Rossen put some info here 
http://www.gromacs.org/Developer_Zone/Cmake

Mark

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[gmx-users] umbrella histograms

[Gavin Melaugh]

Hi all

 I am generating a potential of mean force curve for the interaction
between two cage molecules using umbrella sampling. The system is
composed of only the two molecules in question, using no pbc and no
cut-offs. Umbrella sampling is performed at 25 different distances
(between COMs) between 0.75 and 2.75 nm.  The histogram generated form
g_wham shows very good overlap between the histogram between 0.75 nm and
2 nm. The shapes of the histogram and the width of the distribution are
all well in this region. Above 2nm the histograms show two peaks and
therefore the shape and distribution at these distances is poor. Has
anyone ever come across this sort of behaviour before? Also can you use
different force constants for the harmonic potential at different
distances ?

Cheers

Gavin

p.s Here is a copy of the mdp file that I am using

title   = Pull test
cpp =
include =
define  =
integrator  = md
nsteps  = 5000
dt  = 0.002
nstxout = 25
nstvout = 25
nstlog  = 25
nstenergy   = 5000
nstfout = 25
pbc = no
nstlist = 10
ns_type = simple
vdwtype = cut-off
rlist   = 0
rvdw_switch = 0
rvdw= 0
coulombtype = cut-off
rcoulomb= 0
tcoupl  = nose-hoover
tc_grps = system
tau_t   = 0.1
ref_t   = 600
gen_vel = no
gen_temp=
constraints = none
comm_mode   = angular
pull= umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = no
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_init1 = 2.59
pull_rate1 = 0.0
pull_k1 = 1000
pull_nstxout = 1000
pull_nstfout = 1000

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Re: [gmx-users] New beta release: 4.5-beta3

[Jussi Lehtola]

On Tue, 10 Aug 2010 21:24:50 +0200
Rossen Apostolov  wrote:

> 
> New beta release of gromacs is available for testing: 
> ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz.
> 
> Many bugs have been fixed in this release, mainly double precision 
> support with icc compilers, SSE2. Have a look at the release note on
> the website for more details. There are still some issues on Windows 
> platofrms that will be resolved before the final release.
> 
> Please try it out and see if it works as expected! Hopefully there
> won't be many more betas :))

I can't compile using CMake - I get undefined references to GSL
functions when compiling do_dssp. -lgsl seems to be missing from the
linker line.

Another issue is that the CMake build scripts do not seem to honor
CFLAGS. The string "-fomit-frame-pointer -finline-functions
-funroll-all-loops  -O3 -DNDEBUG" is added to the end of the flags,
which causes a problem since the optimization settings are overruled.

Plus, I think there should be some kind of minimal readme for usage
with CMake.
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--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.leht...@helsinki.fi, p. 191 50632
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.leht...@helsinki.fi
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RE: [gmx-users] Replica Exchange problem in gmx-4.5 beta3

[Berk Hess]

Hi,

This could be due to problems with MPICH.
Could you please try openmpi and report back?

Thanks,

Berk

From: sht_yc...@hotmail.com
To: gmx-users@gromacs.org
Date: Wed, 11 Aug 2010 18:09:00 +0900
Subject: [gmx-users] Replica Exchange problem in gmx-4.5 beta3 








Hello!
I'm doing a simple REMD test with 4 
replicas.
Time step : 2 fs
Exchange : every 500fs
 
md_0.tpr md_1.tpr md_2.tpr md_3.tpr 
 
mpiexec(or mpirun) -np 4 mdrun_mpi_d -deffnm md_ 
-multi 4 -replex 200
 I got a error message.
 
##error##
100 steps,   2000.0 ps.
step 600 rank 
3 in job 10  localhost.localdomain_50305   caused collective 
abort of all ranks
  exit status of rank 3: killed by signal 11 
rank 
2 in job 10  localhost.localdomain_50305   caused collective 
abort of all ranks
  exit status of rank 2: killed by signal 11 

 
Using gmx4.0.7 , It works fine.
Is this bug in gmx-4.5 beta ?
In log files, no error message were 
found.
gmx-4.5 beta3 was compiled with icc 11.0
and mpich2-1.2.1p1.



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[gmx-users] Replica Exchange problem in gmx-4.5 beta3

[Changwon Yang]

Hello!
I'm doing a simple REMD test with 4 replicas.
Time step : 2 fs
Exchange : every 500fs

md_0.tpr md_1.tpr md_2.tpr md_3.tpr 

mpiexec(or mpirun) -np 4 mdrun_mpi_d -deffnm md_ -multi 4 -replex 200
 I got a error message.

##error##
100 steps,   2000.0 ps.
step 600 rank 3 in job 10  localhost.localdomain_50305   caused collective 
abort of all ranks
  exit status of rank 3: killed by signal 11 
rank 2 in job 10  localhost.localdomain_50305   caused collective abort of all 
ranks
  exit status of rank 2: killed by signal 11 

Using gmx4.0.7 , It works fine.
Is this bug in gmx-4.5 beta ?
In log files, no error message were found.
gmx-4.5 beta3 was compiled with icc 11.0
and mpich2-1.2.1p1.

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Re: [gmx-users] gromacs-4.5-beta2 implicit solvent lincs errors

[Mark Abraham]

- Original Message -
From: Elio Cino 
Date: Wednesday, August 11, 2010 4:33
Subject: [gmx-users] gromacs-4.5-beta2 implicit solvent lincs errors
To: gmx-users@gromacs.org

> Hello. I have tested GBSA in 4.5 beta2 on 3 different machines: OSX 10.6 w/ 
> core2duo, Centos5.5 w/ dual socket quad core Xenon, and another Linux machine 
> (unsure of OS) w/ quad socket hexacore AMD Istambul. I tested the same tpr on 
> all machines and only the core2duo runs the job successfully. The other 
> machines give lincs errors and segmentation fault during position restrain 
> dynamics. Normal runs (with solvent) seem fine on all machines.  I am unsure 
> if there is a known issue with implicit solvent on certain machines so I 
> though I would post this for testing purposes. Also, I tested the latest git 
> with the same results. 

Just as with explicit solvent MD, if the starting configuration is a bit 
unhappy, then you can run into integration problems, and these will vary with 
things like the architecture and compiler version. Try a gentler 
EM-equilibration regime.

Mark

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Re: [gmx-users] Error while trying free energy calculation

[Mark Abraham]

The tutorial was written for a very old version of GROMACS that didn't warn 
when the user was doing something that had the potential to fail to conserve 
energy (viz, PME + LJ-switch/shift. It is just a warning, so you could go ahead 
and ignore it on the implicit advice of the tutorial author. Or you could ask 
them :-)

Mark

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Re: [gmx-users] dimer simulation

[Mark Abraham]

- Original Message -
From: sanja...@iitb.ac.in
Date: Wednesday, August 11, 2010 15:31
Subject: [gmx-users] dimer simulation
To: gmx-users@gromacs.org

> Dear gmx-users
> I want to simulate a protein which biological function defined 
> by dimer
> formation. I need to simulate this protein in dimer as well as in
> monomeric form to solve my objectives. I am using Gromacs-4.0.4 for
> simulation. I have a doubt, is there any specific parameters for dimer
> simulation or we have to use similar parameters like monomer protein
> simulation. I read some literature's on dimer simulation but 
> they are
> using similar parameters like monomer.

Making ad hoc changes to force fields just asks for trouble. Needing to ask 
whether you should make changes to force fields guarantees it :-) See 
http://www.gromacs.org/Documentation/Terminology/Force_Fields

There's nothing magic about protein dimerization by comparison with any other 
protein-protein intra- or inter-molecular interaction. The same model physics 
should cope with them all.

Mark

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