Re: [gmx-users] problem with icc compiler

[Erik Brandt]

Hi,
I have reported this problem to Bugzilla some months ago:

  http://bugzilla.gromacs.org/show_bug.cgi?id=378

I don't exactly know what the problem is, but it is definitely related
to the MKL FFTs, which can be seen by switching from PME to cutoff, and
the problem should go away.

I have reproduced this behavior on several computers, as I have written
in the bugzilla report.

/ Erik Brandt

tor 2010-03-11 klockan 01:34 +0100 skrev Mark Abraham:

> On 11/03/2010 3:04 AM, Thomas Schlesier wrote:
> > Gromacs was compiled on a xeon (woodcrest). for the simulations i used
> > an old xeon (don't know what chip, but also 64bit system) and a i7.
> 
> Well, don't do that. IMO, dynamic linking should work in that kind of 
> scenario, but something is clearly broken.
> 
> > About static / dynamic libraries:
> > I used there default settings. At the end of the configure command it
> > tells me the following:
> > * On most platforms you can save 10X space with dynamic libraries,
> > although the binaries might be less portable. Why not try --enable-shared?
> > So i think the libraries are static.
> 
> Your internal GROMACS linking is static, which you could change with 
> --enable-shared. You will need to kick the linker harder than that to 
> force it to link statically to system libraries also.
> 
> > I tried Mark's suggestion and compiled a new version, where i change
> > '--with-fft=mkl' with '--enable-fft=fftpack' (the restr of the configure
> > command was the same then before). With that, the error didn't appear.
> > Does that mean that the linking to mkl did not work for mdrun, but
> > worked for mdrun_mpi (because there the temperature was right)?
> 
> Yep, that is strong evidence for my hypothesis. Either compile GROMACS 
> on the target execution system (even submit a cluster job for the 
> compilation!), or (if the former doesn't work) get the MKL documentation 
> and read it about how to enforce static linking. There may be some 
> cunning linker option for that, or you may need to explicitly cite the 
> static versions of the libraries. Or, get FFTW installed and link to 
> that. I have found near-negligible performance differences between MKL 
> and FFTW on my machine.
> 
> > One thing for the temperature jump:
> > Temperature starts at around 300 K (from 'gen_temp') then goes in 1-2ps
> > up to around 425 K and then stays there. the simulation was 100ps long,
> > in the end i had an average value of about 425 K (from log file).
> >
> > Here are the first 20ps from g_energy
> > 0.00 305.240509
> > 1.00 381.614166
> > 2.00 410.572906
> > 3.00 434.954956
> > 4.00 414.660400
> > 5.00 394.799591
> > 6.00 389.087128
> > 7.00 414.893982
> > 8.00 449.444183
> > 9.00 417.877472
> > 10.00 442.470306
> > 11.01 446.170258
> > 12.01 448.844666
> > 13.01 412.847473
> > 14.01 454.549744
> > 15.01 447.908478
> > 16.00 404.607422
> > 17.00 404.629944
> > 18.00 441.559448
> > 19.00 396.328400
> > 20.00 421.386017
> 
> That's broken all right!
> 
> Mark
> 
> > and:
> > Energy Average RMSD Fluct. Drift Tot-Drift
> > 
> > Temperature 424.625 21.7645 21.6696 0.0703201 7.03215
> >
> >
> >
> >>
> >> On 10/03/2010 12:21 AM, Thomas Schlesier wrote:
> >>> Could anybody reproduce that error or has an idea what is happening?
> >>> Or i am alone with that problem?
> >>
> >> Nothing looks obviously wrong, but it's hard to be sure in the absence
> >> of information about your hardware. The most likely issue is some kind
> >> of dynamically-linked library mismatch. This can happen if your
> >> execution environment differs from your linking environment. Try forcing
> >> linking to static versions of the libraries, which will prevent this.
> >>
> >> Also try disabling things until you get sensible behaviour in all cases,
> >> like --enable-fft=fftpack. That would reveal that the problem was with
> >> linking to mkl.
> >>
> >> Also 1-2ps is a bit too short to expect convergence of temperature -
> >> check the plot of T against t with g_energy.
> >>
> >> Mark
> >>
>  Date: Fri, 5 Mar 2010 23:11:45 +0100
>  From: Thomas Schlesier 
>  Subject: [gmx-users] problem with icc compiler
>  To: "gmx-users@gromacs.org" 
>  Message-ID: <4b9181a1.7060...@uni-mainz.de>
>  Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
> 
>  Hi,
>  i observed the following problem. if i simulate water (spc or tip4p)
>  with gromacs 4.0.5 i get with v-rescale or berendsen thermostat the
>  wrong temperature (ref_t = 300K -> average around 425K, in about
>  1-2ps),
>  but only in serial, not in parallel runs.
>  non-water molecules or nose-hoover thermostat make no problems.
>  see also
>  http://lists.gromacs.org/pipermail/gmx-users/2010-March/049248.html
>  for mdp and log file.
> 
>  gromacs was compiled with the followin

[gmx-users] huge field.xvg output

[Dmitri Dubov]

Dear GMX'ers,

I'm watching electric field effect to small systems (~20 atoms). Simulations 
are rather long, about 200 ns, and the output is infrequent. Without electric 
fiels all is right. But when applying small field by the line in mdp-file:

E-x = 1 0.1 0.1

my output includes huge (more than 60Gb) file "field.xvg". I failed to find its 
description in manual. What is the purpose of this output, and how can I reduce 
its size?

Thanks, 
-- 
 Dmitri  mailto:ddu...@ngs.ru-- 
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RE: [gmx-users] rdf problem

[Dallas B. Warren]

If you have aggregation and a small box size, then the rdf will not be
able to asymptote to one.

 

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Antonia V.
Sent: Thursday, 11 March 2010 2:18 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] rdf problem

 

Dear all,

I am simulating a binary system of two non mixing components (5CB and
water using version 4-0-3; the whole equilibrated trajectory is about
300ns). 
I want to calculate the rdf of the centers of mass of 5CB using the
command 
g_rdf -f traj300.xtc -rdf mol_com  -o rdf_com_300.xvg -noxvgr.
The problem is that the rdf I am getting does not approach one at long
distances. Is there a way to correct that? 
I have the same problem, with all rdfs, and also when I compute the rdfs
for a lipid bilayer (DPPC-water)... I think it has to do with the way
that the normalization is done, 
because the ones that are calculated for a one component system (i.e.
bulk 5CB) are normal (they do approach one). 

Thank you,
Antonia



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Re: [gmx-users] problem with icc compiler

[Mark Abraham]

On 11/03/2010 3:04 AM, Thomas Schlesier wrote:

Gromacs was compiled on a xeon (woodcrest). for the simulations i used
an old xeon (don't know what chip, but also 64bit system) and a i7.


Well, don't do that. IMO, dynamic linking should work in that kind of 
scenario, but something is clearly broken.



About static / dynamic libraries:
I used there default settings. At the end of the configure command it
tells me the following:
* On most platforms you can save 10X space with dynamic libraries,
although the binaries might be less portable. Why not try --enable-shared?
So i think the libraries are static.


Your internal GROMACS linking is static, which you could change with 
--enable-shared. You will need to kick the linker harder than that to 
force it to link statically to system libraries also.



I tried Mark's suggestion and compiled a new version, where i change
'--with-fft=mkl' with '--enable-fft=fftpack' (the restr of the configure
command was the same then before). With that, the error didn't appear.
Does that mean that the linking to mkl did not work for mdrun, but
worked for mdrun_mpi (because there the temperature was right)?


Yep, that is strong evidence for my hypothesis. Either compile GROMACS 
on the target execution system (even submit a cluster job for the 
compilation!), or (if the former doesn't work) get the MKL documentation 
and read it about how to enforce static linking. There may be some 
cunning linker option for that, or you may need to explicitly cite the 
static versions of the libraries. Or, get FFTW installed and link to 
that. I have found near-negligible performance differences between MKL 
and FFTW on my machine.



One thing for the temperature jump:
Temperature starts at around 300 K (from 'gen_temp') then goes in 1-2ps
up to around 425 K and then stays there. the simulation was 100ps long,
in the end i had an average value of about 425 K (from log file).

Here are the first 20ps from g_energy
0.00 305.240509
1.00 381.614166
2.00 410.572906
3.00 434.954956
4.00 414.660400
5.00 394.799591
6.00 389.087128
7.00 414.893982
8.00 449.444183
9.00 417.877472
10.00 442.470306
11.01 446.170258
12.01 448.844666
13.01 412.847473
14.01 454.549744
15.01 447.908478
16.00 404.607422
17.00 404.629944
18.00 441.559448
19.00 396.328400
20.00 421.386017


That's broken all right!

Mark


and:
Energy Average RMSD Fluct. Drift Tot-Drift

Temperature 424.625 21.7645 21.6696 0.0703201 7.03215





On 10/03/2010 12:21 AM, Thomas Schlesier wrote:

Could anybody reproduce that error or has an idea what is happening?
Or i am alone with that problem?


Nothing looks obviously wrong, but it's hard to be sure in the absence
of information about your hardware. The most likely issue is some kind
of dynamically-linked library mismatch. This can happen if your
execution environment differs from your linking environment. Try forcing
linking to static versions of the libraries, which will prevent this.

Also try disabling things until you get sensible behaviour in all cases,
like --enable-fft=fftpack. That would reveal that the problem was with
linking to mkl.

Also 1-2ps is a bit too short to expect convergence of temperature -
check the plot of T against t with g_energy.

Mark


Date: Fri, 5 Mar 2010 23:11:45 +0100
From: Thomas Schlesier 
Subject: [gmx-users] problem with icc compiler
To: "gmx-users@gromacs.org" 
Message-ID: <4b9181a1.7060...@uni-mainz.de>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed

Hi,
i observed the following problem. if i simulate water (spc or tip4p)
with gromacs 4.0.5 i get with v-rescale or berendsen thermostat the
wrong temperature (ref_t = 300K -> average around 425K, in about
1-2ps),
but only in serial, not in parallel runs.
non-water molecules or nose-hoover thermostat make no problems.
see also
http://lists.gromacs.org/pipermail/gmx-users/2010-March/049248.html
for mdp and log file.

gromacs was compiled with the following comands:
and in the file 'configure' all '-lmkl' were deleted (don't ask me why,
i don't really understand that stuff, the command were from our
previous
phd student).

./configure CC="icc"
CPPFLAGS="-I/share/apps/intel/mkl/10.0.011/include"
LDFLAGS="-L/share/apps/intel/mkl/10.0.011/lib/em64t
-lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64
-lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-fft=mkl
--prefix="/share/apps/gromacs/4.0.5"
make
make install
make clean
./configure CC="icc"
CPPFLAGS="-I/share/apps/intel/mkl/10.0.011/include"
LDFLAGS="-L/share/apps/intel/mkl/10.0.011/lib/em64t
-lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64
-lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-fft=mkl
--prefix="/share/apps/gromacs/4.0.5" --enable-mpi --disable-nice
--program-suffix=_mpi
make mdrun
make install-mdrun

for gromacs 4.0.5 i used the icc 

[gmx-users] Steered MD: Gromacs 4.0

[chris . neale]

Dear Matt:

pull_vec1 = -31.07-15.37 9.89
is not equal to
pull_vec1 = -31.07 -15.37 9.89

There could be other problems, but I would start there.

-- original message --

Hi,

I am having some trouble using the COM pulling code (Gromacs 4.0). I  
will try to describe the problem as
best I can and hopefully someone will be able to point me in the right  
direction!


Basically what I would like to do is pull a ligand (LIG) along a specified
path from the interior of a protein to the exterior (Steered MD simulation).
Using the following .mdp file I was able to pull the ligand, but it  
did not travel
along the path that I thought it would (ie along the vector specified  
in pull_vec1).


Pull section of my md.mdp file:

pull= umbrella
pull_geometry = position
pull_dim = Y Y Y

pull_r1 = 1
pull_r0 = 1.5
pull_constr_tol= 1e-06
pull_start = no
pull_nstxout = 10
pull_nstfout = 1
pull_ngroups = 1

pull_group0 =
pull_weights0 =
pull_pbcatom0 = 0
pull_group1 = LIG
pull_weights1 =
pull_pbcatom1 = 0
pull_vec1 = -31.07-15.37 9.89
pull_init1 = 43.416 66.914 40.125
pull_rate1 = 0.001
pull_k1 = 500
pull_kB1=


I specified pull_vec1 as the vector I would like to pull the ligand  
along (ie -x,-y,+z).
Looking at the simulation in VMD the ligand traveled in the (+x, +y,  
+z) direction.


In this trial I specified pull_init1 as the point I would like the  
spring to be attached to the ligand.


I have read the gromacs 4.0 manual and many of the posts online, but I  
still cannot seem to figure out what values are required in the  
parameter file.
I know the following pieces of information, but I don't know how/if  
they fit into the parameter file:


1. The point where I would like the spring to be attached to the ligand
2. The vector along which I would like the ligand to travel
3. The distance between a reference atom in the protein and the  
desired spring attachment point on the ligand



Anyone have any ideas of what i am missing or doing wrong?  Or if I am  
missing some fundamental concept here?


Thanks,
Matt Danielson


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Re: [gmx-users] Steered MD: Gromacs 4.0

[Justin A. Lemkul]

Matthew L. Danielson wrote:

Hi,
I am having some trouble using the COM pulling code (Gromacs 4.0). I 
will try to describe the problem as best I can and hopefully someone 
will be able to point me in the right direction!


Basically what I would like to do is pull a ligand (LIG) along a 
specified path from the interior of a protein to the exterior (Steered 
MD simulation). Using the following .mdp file I was able to pull the 
ligand, but it did not travel along the path that I thought it would (ie 
along the vector specified in pull_vec1).

Pull section of my md.mdp file:

pull= umbrella
pull_geometry = position
pull_dim = Y Y Y

pull_r1 = 1
pull_r0 = 1.5
pull_constr_tol= 1e-06
pull_start = no
pull_nstxout = 10
pull_nstfout = 1
pull_ngroups = 1

pull_group0 = pull_weights0 =
pull_pbcatom0 = 0
pull_group1 = LIG pull_weights1 =
pull_pbcatom1 = 0
pull_vec1 = -31.07-15.37 9.89
pull_init1 = 43.416 66.914 40.125
pull_rate1 = 0.001
pull_k1 = 500
pull_kB1=


I specified pull_vec1 as the vector I would like to pull the ligand 
along (ie -x,-y,+z).  Looking at the simulation in VMD the ligand 
traveled in the (+x, +y, +z) direction.
In this trial I specified pull_init1 as the point I would like the 
spring to be attached to the ligand.


I have read the gromacs 4.0 manual and many of the posts online, but I 
still cannot seem to figure out what values are required in the 
parameter file. I know the following pieces of information, but I don't 
know how/if they fit into the parameter file:


1. The point where I would like the spring to be attached to the ligand


I don't think that can be specified.


2. The vector along which I would like the ligand to travel


That's pull_vec1.

3. The distance between a reference atom in the protein and the desired 
spring attachment point on the ligand




Again, the spring attachment isn't something you set, but the initial distance 
is something you can set with pull_init1 or pull_start.




Anyone have any ideas of what i am missing or doing wrong?  Or if I am 
missing some fundamental concept here?




Are your units appropriate?  Is your box really that large?  Gromacs specifies 
all distances in nm, not Angstrom.  It may also be worthwhile to upgrade to the 
latest version (4.0.7); there have been several fixes for overall stability of 
the code since version 4.0, some of them pertinent to the pull code.  See the 
revision history on the Gromacs site for this important information.


-Justin


Thanks,
Matt Danielson



--


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] Steered MD: Gromacs 4.0

[Matthew L. Danielson]

Hi, 

I am having some trouble using the COM pulling code (Gromacs 4.0). I will try to describe the problem as 
best I can and hopefully someone will be able to point me in the right direction!


Basically what I would like to do is pull a ligand (LIG) along a specified 
path from the interior of a protein to the exterior (Steered MD simulation). 
Using the following .mdp file I was able to pull the ligand, but it did not travel 
along the path that I thought it would (ie along the vector specified in pull_vec1). 


Pull section of my md.mdp file:

pull= umbrella
pull_geometry   = position
pull_dim= Y Y Y

pull_r1 = 1
pull_r0 = 1.5
pull_constr_tol = 1e-06
pull_start  = no
pull_nstxout= 10
pull_nstfout= 1
pull_ngroups= 1

pull_group0 		= 
pull_weights0 		=

pull_pbcatom0   = 0
pull_group1 		= LIG 
pull_weights1 		=

pull_pbcatom1   = 0
pull_vec1   = -31.07-15.37 9.89
pull_init1  = 43.416 66.914 40.125
pull_rate1  = 0.001
pull_k1 = 500
pull_kB1=


I specified pull_vec1 as the vector I would like to pull the ligand along (ie -x,-y,+z).  
Looking at the simulation in VMD the ligand traveled in the (+x, +y, +z) direction. 


In this trial I specified pull_init1 as the point I would like the spring to be 
attached to the ligand.

I have read the gromacs 4.0 manual and many of the posts online, but I still cannot seem to figure out what values are required in the parameter file. 
I know the following pieces of information, but I don't know how/if they fit into the parameter file:


1. The point where I would like the spring to be attached to the ligand
2. The vector along which I would like the ligand to travel
3. The distance between a reference atom in the protein and the desired spring 
attachment point on the ligand


Anyone have any ideas of what i am missing or doing wrong?  Or if I am missing 
some fundamental concept here?

Thanks,
Matt Danielson

--

Matthew L. Danielson

Graduate Student of Medicinal Chemistry & Molecular Pharmacology
College of Pharmacy, Nursing, and Health Sciences
Purdue University
MCMP RHPH 504c
575 Stadium Mall Drive
West Lafayette, IN 47907-2091

(765)496-6643 office 


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Re: [gmx-users] topolbuild 1.3, revision to topolbuild that incorporates OPLS-AA support

[Bruce D. Ray]

On Wed, March 10, 2010 at 3:35 PM, Joe Joe  wrote:

 

> This is great. I was able to easily make a molecule that runs with
> OPLS-AA. Would it be possible to add a feature which creates an
>*.rtp
entry? It would be really useful for making non standard
>amino acids
and incorporating it with pdb2gmx.

I've been working on something to do that.  Because of some
differences that require use of names given in defines, this
would be a separate program from topolbuild despite sharing
some component subroutines.  Other research, plus my age
tend to make this a slow process.


Sincerely,


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273



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Re: [gmx-users] topolbuild 1.3, revision to topolbuild that incorporates OPLS-AA support

[Joe Joe]

Bruce,

This is great. I was able to easily make a molecule that runs with OPLS-AA.
Would it be possible to add a feature which creates an *.rtp entry? It would
be really useful for making non standard amino acids and incorporating it
with pdb2gmx.

Thanks,

Ilya


On Wed, Mar 10, 2010 at 11:07 AM, Bruce D. Ray  wrote:

> I have uploaded to the user contributed software at gromacs.org a
> further revision of topolbuild that includes support for OPLS-AA as
> file topolbuild1_3.tgz
>
> topolbuild 1.3
> Reads a syntactically correct Tripos .mol2 file with charges to generate
> something approximating gromacs *.gro, *.top, and *.itp files from it
> based on selected force field parameters. This version adds support for
> oplsaa. Includes tables to support amber, gaff, glycam, oplsaa, and gmx
> type force fields. Requires that the *.mol2 file have syntactically correct
> Tripos atom types and absolutely will not work with other input atom
> types.  Includes capability of pruning dihedral angles to a possibly more
> reasonable set.  Note that the standard for a syntactically correct mol2
> file is the Tripos Toolkit Utilities Manual.
>
> Revisions include:
>   1.  Added OPLS-AA support, atom definition files, and force field
>   data tables.  Best results for pruning of dihedral angles will
>   probably be with -purge 0
>   2.  Corrected errors in setting some categories of rings
>   3.  Corrected Makefile to be compatible with more variants of make
>   4.  Increased initial estimate of maximum number of rings for ring
>   detection
>   5.  Added lines to log, topology, and include files to give version
>   and command line of invocation
>   6.  Made internal rearrangements to ease addition of and handling
>   of other force fields
>   7.  Set default prune of excess dihedral angles equivalent to -purge 1
>   8.  Added option to translate molecule coordinates to center of
>   mass when renumbering is not requested
>   9.  Added elements to internal atomic masses / numbers table
> 10.  Revised method of correction of Tripos out of plane pyramid
>height improper force constants to cosine function force constants
> 11.  Altered setting of dihedral phases for Tripos force field
> 12.  Changed error messages in mol2 file reading to give clearer
>statement of problems
> 13.  Changed error for not ending the bonds section of the mol2 file
>with @ from fatal error to warning because mol2 files
>supplied by some databases lack correct termination
> 14.  Added atom type default entries to the amber atom type definition
>tables
> 15.  Corrected errors in gromacs topology defaults line settings.
> 16.  Changed preferences in dihedral angles purge to choose the
>maximum number of heavy atoms possible for dihedrals retained
>for topology output.
> 17.  Modified renaming.
> 18.  Use of distances and angles measured from structure no
>longer affects dihedral values.
> 19.  Added -charge option to permit assignment of atom charges
>based on atom type charges from force field.  Currently only
>OPLS-AA tables support this option.
>
> Special Processing Used for oplsaa Force Fields
> With the exception of van der Waals parameters and default atom
> charges, oplsaa is designed such that force field parameters are
> associated with atom types from a modified and amplified version
> of the Kollman atom types. However, oplsaa also uses a much richer
> set of atom types to determine van der Waals parameters and default
> atom charges. Therefore, generation of an oplsaa topology requires
> double determination of atom types.  A first determination of atom
> types is performed with the expanded version of the Kollman atom
> types. This assignment is used to assign force constants, bond lengths,
> angles, dihedral angles, and improper angles. A second determination
> of atom types is performed to assign final oplsaa atom types to match
> the atom types in ffoplsaanb.itp from the gromacs distribution. A
> major problem of this double conversion is that topolbuild does not
> always select the exact same atom type for a residue listed in
> ffoplsaa.rtp. The following table gives some of the differences
> discovered:
>  residueatomrtp value   topolbuild  usage
>HISA ND1 opls_503 opls_557imidazole N1
>HISA HD1 opls_504 opls_562imidazole H1
>HISA HE1 opls_146 opls_563imidazole H2
>HISB HD2 opls_146 opls_565imidazole H5
>HISB HE1 opls_146 opls_563imidazole H2
>HISB NE2 opls_503 opls_557imidazole N1
>HISB HE2 opls_504 opls_562imidazole H1
>TRP  HD1 opls_146 opls_597indole H2
>TRP  CE3 opls_145 opls_590indole C4
>TRP  HE3 opls_146 opls_599indole H4
>TRP  CZ2 opls_145 opls_593

Re: [gmx-users] On the new web site, how does one make a user contribution?

[Bruce D. Ray]

On Tue, March 9, 2010 at 8:30 PM, Rossen Apostolov  
wrote:

> On 03/09/2010 09:15 PM, Bruce D. Ray wrote:
>> I went to the new web site to make a user contribution,
>> and I was not able to find the method to do that.
>> In fact, I even had to create my user ID again that I
>> had on the old web site.  With this new web site, how
>> does one go submitting user contributed software?
>>
>  Hi Бруце,
> 
> Many users who registered on the old wiki were given a default
> status of  "viewers" after the transition to the new site. I changed
> your status and now you should be able to edit pages across the
> site.

Thank-you very much, both for the assistance and for rendering
my name in Cyrillic.


Sincerely,

-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273



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Re: [gmx-users] On the new web site, how does one make a user contribution?

[Bruce D. Ray]

On Tue, March 9, 2010 at 4:08, Justin A. Lemkul  wrote:
> Bruce D. Ray wrote:
>> I went to the new web site to make a user contribution,
>> and I was not able to find the method to do that.
>> In fact, I even had to create my user ID again that I
>> had on the old web site.  With this new web site, how
>> does one go submitting user contributed software?
>>
> You
should be able to click "Attach file or image" on the
> contributed
software page, which will prompt a popup where
> you select the file and
write the description.

That's what I thought, but at the time that was not working.
Since the message from Rossen Spostolov, it is working.
Thank-you very much.

Sincerely,

 -- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273



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[gmx-users] topolbuild 1.3, revision to topolbuild that incorporates OPLS-AA support

[Bruce D. Ray]

I have uploaded to the user contributed software atgromacs.org a
further revision of topolbuild that includes support for OPLS-AA as
file topolbuild1_3.tgz 


topolbuild 1.3
Reads a syntactically correct Tripos .mol2 file with charges to generate
something approximating gromacs *.gro, *.top, and *.itp files from it
based on selected force field parameters. This version adds support for
oplsaa. Includes tables to support amber, gaff, glycam, oplsaa, and gmx
type force fields. Requires that the *.mol2 file have syntactically correct
Tripos atom types and absolutely will not work with other input atom
types.  Includes capability of pruning dihedral angles to a possibly more
reasonable set.  Note that the standard for a syntactically correct mol2
file is the Tripos Toolkit Utilities Manual.

Revisions include:
  1.  Added OPLS-AA support, atom definition files, and force field
  data tables.  Best results for pruning of dihedral angles will
  probably be with -purge 0
  2.  Corrected errors in setting some categories of rings
  3.  Corrected Makefile to be compatible with more variants of make
  4.  Increased initial estimate of maximum number of rings for ring
  detection
  5.  Added lines to log, topology, and include files to give version
  and command line of invocation
  6.  Made internal rearrangements to ease addition of and handling
  of other force fields
  7.  Set default prune of excess dihedral angles equivalent to -purge 1
  8.  Added option to translate molecule coordinates to center of
  mass when renumbering is not requested
  9.  Added elements to internal atomic masses / numbers table
10.  Revised method of correction of Tripos out of plane pyramid
   height improper force constants to cosine function force constants
11.  Altered setting of dihedral phases for Tripos force field
12.  Changed error messages in mol2 file reading to give clearer
   statement of problems
13.  Changed error for not ending the bonds section of the mol2 file
   with @ from fatal error to warning because mol2 files
   supplied by some databases lack correct termination
14.  Added atom type default entries to the amber atom type definition
   tables
15.  Corrected errors in gromacs topology defaults line settings.
16.  Changed preferences in dihedral angles purge to choose the
   maximum number of heavy atoms possible for dihedrals retained
   for topology output.
17.  Modified renaming.
18.  Use of distances and angles measured from structure no
   longer affects dihedral values.
19.  Added -charge option to permit assignment of atom charges
   based on atom type charges from force field.  Currently only
   OPLS-AA tables support this option. 

Special Processing Used for oplsaa Force Fields
With the exception of van der Waals parameters and default atom
charges, oplsaa is designed such that force field parameters are
associated with atom types from a modified and amplified version
of the Kollman atom types. However, oplsaa also uses a much richer
set of atom types to determine van der Waals parameters and default
atom charges. Therefore, generation of an oplsaa topology requires
double determination of atom types.  A first determination of atom
types is performed with the expanded version of the Kollman atom
types. This assignment is used to assign force constants, bond lengths,
angles, dihedral angles, and improper angles. A second determination
of atom types is performed to assign final oplsaa atom types to match
the atom types in ffoplsaanb.itp from the gromacs distribution. A
major problem of this double conversion is that topolbuild does not
always select the exact same atom type for a residue listed in
ffoplsaa.rtp. The following table gives some of the differences
discovered:
 residueatomrtp value   topolbuild  usage
   HISA ND1 opls_503 opls_557imidazole N1
   HISA HD1 opls_504 opls_562imidazole H1
   HISA HE1 opls_146 opls_563imidazole H2
   HISB HD2 opls_146 opls_565imidazole H5
   HISB HE1 opls_146 opls_563imidazole H2
   HISB NE2 opls_503 opls_557imidazole N1
   HISB HE2 opls_504 opls_562imidazole H1
   TRP  HD1 opls_146 opls_597indole H2
   TRP  CE3 opls_145 opls_590indole C4
   TRP  HE3 opls_146 opls_599indole H4
   TRP  CZ2 opls_145 opls_593indole C7
   TRP  HZ2 opls_146 opls_602indole H7
   TRP  CZ3 opls_145 opls_591indole C5
   TRP  HZ3 opls_146 opls_600indole H5
   TRP  CH2 opls_145 opls_592indole C6
   TRP  HH2 opls_146 opls_601indole H6

Because of the manner in which oplsaa constants were developed
originally, in all of these cases the same bond, angle, dihedral, and
improper constants are assigned. The

Re: [gmx-users] g_dist and vsites

[Joe Joe]

I think I know the problem. I looked through gmx_dist and the distance is
calculated using the center of mass of the group. Since I am using Vsite the
mass of CB in ALA is set to zero. Is that correct?

Thanks,

Ilya


On Tue, Mar 9, 2010 at 11:44 AM, David van der Spoel
wrote:

> On 2010-03-09 20.01, Joe Joe wrote:
>
>> I also just tried on a different ALA and got the same problem.
>>
>
> can you please submit a bugzilla and upload files to reproduce the problem?
>
>
>> Ilya
>>
>>
>> On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe > > wrote:
>>
>>I am looking the the gmxdump output and everything seems consistent.
>>The only difference is that the numbering in the index file starts
>>at 1 whereas in the gmxdump the arrays are indexed starting at 0.
>>The coordinates look just fine.
>>
>>Thanks,
>>
>>Ilya
>>
>>
>>
>>On Tue, Mar 9, 2010 at 10:30 AM, Joe Joe >> wrote:
>>
>>I  trjconv/ed xtc to pdb and loaded into vmd. The coordinates
>>looked fine.
>>
>>I also
>>
>>tpbconv/ed topol.tpr to topol_subset.tpr.
>>
>>then I
>>
>>editconf/ed topol_subset.tpr to gro and looked at the
>>coordinates. Index file matched and structure looked whole in vmd.
>>
>>I will try the gmxdump
>>
>>Thanks,
>>
>>Ilya
>>
>>
>>
>>
>>On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel
>>mailto:sp...@xray.bmc.uu.se>> wrote:
>>
>>On 2010-03-09 19.16, Joe Joe wrote:
>>
>>yep.
>>
>>Have you gmxdump/ed the xtc to check the coordinates are right?
>>
>>
>>On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
>>mailto:sp...@xray.bmc.uu.se>
>>>>> wrote:
>>
>>On 2010-03-09 19.09, Joe Joe wrote:
>>
>>Hi I am trying to post process and xtc
>>trajectory using g_dist. I am
>>trying to calculate the CA-CB distance of an
>>Alanine residue but
>>I get
>>NAN in all the distance columns. It works for
>>the other residues
>>I've
>>tried (i.e. SER, VAL). I am using vsites in my
>>simulation and I
>>think it
>>may have some thing to do with the way gromacs
>>outputs the CB
>>positions
>>in the xtc file when the CB is part of the vsite
>>network. Any
>>thoughs?
>>
>>Thanks,
>>
>>Ilya
>>
>>Are you sure your index file matches the xtc/tpr?
>>
>>--
>>David van der Spoel, Ph.D., Professor of Biology
>>Dept. of Cell & Molec. Biol., Uppsala University.
>>Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>sp...@xray.bmc.uu.se 
>>> >>
>>
>>
>>http://folding.bmc.uu.se
>>--
>>gmx-users mailing list gmx-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
>>
>>
>>
>>
>>--
>>David van der Spoel, Ph.D., Professor of Biology
>>Dept. of Cell & Molec. Biol., Uppsala University.
>>Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>sp...@xray.bmc.uu.se 
>>http://folding.bmc.uu.se
>>--
>>gmx-users mailing list gmx-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 in

Re: [gmx-users] simulating several proteins

[Justin A. Lemkul]

Cristiano De Michele wrote:

ok but after I generated two .gro files using genconf (or editconf I guess)
containing two identical proteins in different positions/orientations
how can I concatenate these two files in order to supply a unique .gro 
file to grompp?




If you run genconf correctly, then it should give you a proper .gro file, i.e.:

genconf -f oneprotein.gro -o twoprotein.gro -nbox 2 1 1

The above command will give two replicates of your protein aligned along the x 
axis.

If you have two unique orientations that you want to align, you can simply use 
editconf to assign their position within a box (with -center and -box 
simultaneously), and simply use the Unix 'cat' command to concatenate them. 
Then you have to update the second line of the .gro file to reflect the proper 
number of atoms and remove the superfluous headers and box vectors in the middle 
of the file.


-Justin


thanks Cristiano

Il giorno 10/mar/10, alle ore 16:27, Mark Abraham ha scritto:




- Original Message -
From: Cristiano De Michele 
Date: Thursday, March 11, 2010 2:25
Subject: [gmx-users] simulating several proteins
To: gmx-users@gromacs.org


Dear all,
is it possible to simulate more than one protein with GROMACS?
I would like to simulate two lysozyme proteins not solvated and
I tried changing number of proteins in topology file (attached) and
then I used this modified .top file to generate a .gro configuration
with genbox, but I always end up getting just one protein
in the simulation box...


genbox doesn't take input from the .top file to guide its output.

Use genconf on your original structure file to multiply it. Then edit 
your .top by hand to match.


Mark
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Cristiano De Michele, Ph.D.
Department of Physics Tel.  :  +390649913524
University of Rome  "La Sapienza"Fax  :  +39064463158
Piazzale Aldo Moro, 2
I-00185 Roma - Italy
homepage: http://pacci.phys.uniroma1.it/
--
"Shoot for the moon. Even if you miss, you'll land among the stars."







--


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] protein in dppc

[Justin A. Lemkul]

edmund lee wrote:

Dear all and Justin,
 
I have try with the KALP-15 in DPPC tutorials..it was successfully done 
until Inflategro step.
then I tried with my own protein, I still having the same problems, 
while i wanna do the energy minimization after inflategro.


3 DPPC removed during inflategro...and i updated the number of molecules 
of DPPC lipid in topology..



here is how the strong_posre.itp file look like

 [ position_restraints ]
 ; i funct fcx fcy fcz
 1 1 10 10 10
 2 1 10 10 10
 3 1 10 10 10
 4 1 10 10 10
 5 1 10 10 10
 .
 
 
3483 1 10 10 10
3484 1 10 10 10
3485 1 10 10 10
3486 1 10 10 10

ONLY protein included in the strong_posre.itp file(this protein has 
3486 atoms..)


then again i updated my topology...


; Include forcefield parameters
#include "ffG53a6_lipid.itp"


; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif

; Include DPPC chain topology
#include "dppc.itp"

; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"

; Include water topology
#include "spc.itp"


#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
protein in dppc



[ molecules ]
; Compound#mols
Protein_A   1
Protein_B   1
DPPC   125


 and I also add in the "define" line in the energyminimization.mdp file
 
 here is my em.mdp file 
 
 define =-DSTRONG_POSRES

 integrator = steep
 nsteps = 200
 constraints = none
 emtol = 1000.0
 nstcgsteep = 10 ; do a steep every 10 steps of cg
 emstep = 0.01 ; used with steep
 nstcomm = 1
 coulombtype = PME
 ns_type = grid
 rlist = 1.0
 rcoulomb = 1.0
 rvdw = 1.4
 Tcoupl = no
 Pcoupl = no
 gen_vel = no
 nstxout = 0 ; write coords every # step
 optimize_fft = yes
 
 
 HOWEVER, I still get this error when I proceed to the grompp step.


 
 Fatal error:

Syntax error - File strong_posre.itp, line 3
 Last line read:
 '[ position_restraints ]'
 Invalid order for directive position_restraints
 

as Justin commented, only Protein is selected in strong posre, ( yea..i 
only selected the protein)


 Can anyone guide me in this?
 Yr comments and advices are appreciated.



As the error message indicates, your topology is completely out of order.  See 
the examples on the "Errors" page of the Gromacs wiki:


http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_defaults

Specifically, you are defining position restraints in the topology before you 
have defined any molecules, so grompp doesn't know what to do with them.  The 
examples of "WRONG" and "RIGHT" on the above page should illustrate this principle.


-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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[gmx-users] protein in dppc

[edmund lee]

Dear all and Justin, I have try with the KALP-15 in DPPC tutorials..it was 
successfully done until Inflategro step.then I tried with my own protein, I 
still having the same problems, while i wanna do the energy minimization after 
inflategro.
3 DPPC removed during inflategro...and i updated the number of molecules of 
DPPC lipid in topology..

here is how the strong_posre.itp file look like
 [ position_restraints ] ; i funct fcx fcy fcz 1 1 10 10 10 2 1 
10 10 10 3 1 10 10 10 4 1 10 10 10 5 1 
10 10 10 .  3483 1 10 10 103484 1 10 
10 103485 1 10 10 103486 1 10 10 10
ONLY protein included in the strong_posre.itp file(this protein has 3486 
atoms..)
then again i updated my topology...

; Include forcefield parameters#include "ffG53a6_lipid.itp"

; Include Position restraint file#ifdef POSRES#include "posre.itp"#endif
; Strong position restraints for InflateGRO#ifdef STRONG_POSRES#include 
"strong_posre.itp"#endif
; Include DPPC chain topology#include "dppc.itp"
; Include chain topologies#include "topol_A.itp"#include "topol_B.itp"
; Include water topology#include "spc.itp"

#ifdef POSRES_WATER; Position restraint for each water oxygen[ 
position_restraints ];  i funct   fcxfcyfcz   11   
1000   1000   1000#endif
; Include generic topology for ions#include "ions.itp"
[ system ]; Nameprotein in dppc


[ molecules ]; Compound#molsProtein_A   1Protein_B   
1DPPC   125

 and I also add in the "define" line in the energyminimization.mdp file  here 
is my em.mdp file   define =-DSTRONG_POSRES integrator = steep nsteps = 200 
constraints = none emtol = 1000.0 nstcgsteep = 10 ; do a steep every 10 steps 
of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = 
grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no 
nstxout = 0 ; write coords every # step optimize_fft = yes   HOWEVER, I still 
get this error when I proceed to the grompp step.  Fatal error:Syntax error - 
File strong_posre.itp, line 3 Last line read: '[ position_restraints ]' Invalid 
order for directive position_restraints 
as Justin commented, only Protein is selected in strong posre, ( yea..i only 
selected the protein) Can anyone guide me in this? Yr comments and advices are 
appreciated.








edmund lee wrote:> > Dear Justin and all..> > > > I have been struggled for the 
pass few weeks...> > I follow the KALP-15 in DPPC tutorials but I am using my 
own protein > > instead.> > > > I had successfully reached the step INFLATEGRO 
where 2 lipid removed > > from the upper layer n 2 lipids removed from the 
lower layer. Then i > > updated my topology with deducted 4 number of molecule 
of lipid.> > > > then I generated the strong_porse.itp using the following 
command:> > > > genrestr -f 1_newbox.gro -o strong_posre.itp -fc 10 10 
10> > > > here is how the strong_posre.itp file look like> > [ 
position_restraints ]> > ; i funct fcx fcy fcz> > 1 1 10 10 10> > 2 
1 10 10 10> > 3 1 10 10 10> > 4 1 10 10 10> 
> 5 1 10 10 10> > .> > > > > > ...> > 3483 1 10 
10 10> > 3484 1 10 10 10> > 3485 1 10 10 10> > 
3486 1 10 10 10> > > > then i updated the topology (as shown 
below)> > > > ; Include Position restraint file> > #ifdef POSRES> > #include 
"posre.itp"> > #endif> > > > ; Strong position restraints for InflateGRO> > 
#ifdef STRONG_POSRES> > #include "strong_posre.itp"> > #endif> > > > ; Include 
DPPC chain topology> > #include "dppc.itp"> > > > ; Include water topology> > 
#include "spc.itp"> > > > ; System specifications> > [ system ]> > 128-Lipid 
DPPC Bilayer > > > > [ molecules ]> > ; molecule name nr.> > DPP 124> > SOL 
3655> > > > > > > > > > and I also add in the "define" line in the 
energyminimization.mdp file> > > > here is my em.mdp file > > > > define 
=-DSTRONG_POSRES> > integrator = steep> > nsteps = 200> > constraints = none> > 
emtol = 1000.0> > nstcgsteep = 10 ; do a steep every 10 steps of cg> > emstep = 
0.01 ; used with steep> > nstcomm = 1> > coulombtype = PME> > ns_type = grid> > 
rlist = 1.0> > rcoulomb = 1.0> > rvdw = 1.4> > Tcoupl = no> > Pcoupl = no> > 
gen_vel = no> > nstxout = 0 ; write coords every # step> > optimize_fft = yes> 
> > > > > HOWEVER, I get this error when I proceed to the grompp step.> > > > 
Fatal error:> > Syntax error - File strong_posre.itp, line 3> > Last line 
read:> > '[ position_restraints ]'> > Invalid order for directive 
position_restraints> > > > Can anyone guide me in this?> > Yr comments and 
advices are appreciated.> > > > You have several problems:> > 1. Your 
[molecules] directive makes no reference to the protein that should be > 
present.> 2. Your "strong_posre.itp" file looks like it refers to the whole 
system; it > sho

Re: [gmx-users] problems with non pbc simulations in parallel

[Gavin Melaugh]

Hi Berk

Cheers for your help

Gavin

Berk Hess wrote:
> Hi,
>
> This is a silly bug with nose-hoover and pbc=no.
> I fixed it for 4.0.8 (if we will ever release that).
>
> To fix it you only need to move a brace up 4 lines in src/mdlib/init.c
> Or you can use the v-rescale thermostat.
>
> Berk
>
> --- a/src/mdlib/init.c
> +++ b/src/mdlib/init.c
> @@ -119,9 +119,9 @@ static void set_state_entries(t_state
> *state,t_inputrec *ir,
> int nnodes)
>  if (ir->epc != epcNO) {
>state->flags |= (1<  }
> -if (ir->etc == etcNOSEHOOVER) {
> -  state->flags |= (1< -}
> +  }
> +  if (ir->etc == etcNOSEHOOVER) {
> +state->flags |= (1<}
>if (ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) {
>  state->flags |= (1<
>
> > Date: Wed, 10 Mar 2010 14:16:38 +
> > From: gmelaug...@qub.ac.uk
> > To: gmx-users@gromacs.org
> > Subject: [gmx-users] problems with non pbc simulations in parallel
> >
> > Hi all
> >
> > I have installed gromacs-4.0.7-parallel with open mpi. I have
> > successfully ran a few short simulations on 2,3 and 4 nodes using pbc. I
> > am now interested in simulating a cluster of 32 molecules with no pbc in
> > parallel and the simulation doe not proceed. I have set by box vectors
> > to 0 0 0 in the conf.gro file, pbc = no in the mdp file, and use
> > dparticle decomposition. The feedback I get from the following command
> >
> > nohup mpirun -np 2 /local1/gromacs-4.0.7-parallel/bin/mdrun -pd -s &
> >
> > is
> >
> > Back Off! I just backed up md.log to ./#md.log.1#
> > Reading file topol.tpr, VERSION 4.0.7 (single precision)
> > starting mdrun 'test of 32 hexylcage molecules'
> > 1000 steps, 0.0 ps.
> > [emerald:22662] *** Process received signal ***
> > [emerald:22662] Signal: Segmentation fault (11)
> > [emerald:22662] Signal code: Address not mapped (1)
> > [emerald:22662] Failing at address: (nil)
> > [emerald:22662] [ 0] /lib64/libpthread.so.0 [0x7fbc17eefa90]
> > [emerald:22662] [ 1]
> > /local1/gromacs-4.0.7-parallel/bin/mdrun(nosehoover_tcoupl+0x74)
> [0x436874]
> > [emerald:22662] [ 2]
> > /local1/gromacs-4.0.7-parallel/bin/mdrun(update+0x171) [0x4b2311]
> > [emerald:22662] [ 3]
> > /local1/gromacs-4.0.7-parallel/bin/mdrun(do_md+0x2608) [0x42dd38]
> > [emerald:22662] [ 4]
> > /local1/gromacs-4.0.7-parallel/bin/mdrun(mdrunner+0xe33) [0x430973]
> > [emerald:22662] [ 5]
> > /local1/gromacs-4.0.7-parallel/bin/mdrun(main+0x5b8) [0x431128]
> > [emerald:22662] [ 6] /lib64/libc.so.6(__libc_start_main+0xe6)
> > [0x7fbc17ba6586]
> > [emerald:22662] [ 7] /local1/gromacs-4.0.7-parallel/bin/mdrun [0x41e1e9]
> > [emerald:22662] *** End of error message ***
> >
> --
> > mpirun noticed that process rank 1 with PID 22662 on node emerald exited
> > on signal 11 (Segmentation fault).
> >
> > p.s I have ran several of these non pbc simulations with the same system
> > in serial and have never experienced a problem. Has anyone ever come
> > across this sort of problem before? and if so could you please provide
> > some advice.
> >
> > Many Thanks
> >
> > Gavin
> >
> > --
> > gmx-users mailing list gmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/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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Re: [gmx-users] problem with icc compiler

[Thomas Schlesier]

Gromacs was compiled on a xeon (woodcrest). for the simulations i used 
an old xeon (don't know what chip, but also 64bit system) and a i7.


About static / dynamic libraries:
I used there default settings. At the end of the configure command it 
tells me the following:
* On most platforms you can save 10X space with dynamic libraries, 
although the binaries might be less portable. Why not try --enable-shared?

So i think the libraries are static.

I tried Mark's suggestion and compiled a new version, where i change 
'--with-fft=mkl' with '--enable-fft=fftpack' (the restr of the configure 
command was the same then before). With that, the error didn't appear.
Does that mean that the linking to mkl did not work for mdrun, but 
worked for mdrun_mpi (because there the temperature was right)?


One thing for  the temperature jump:
Temperature starts at around 300 K (from 'gen_temp') then goes in 1-2ps 
up to around 425 K and then stays there. the simulation was 100ps long, 
in the end i had an average value of about 425 K (from log file).


Here are the first 20ps from g_energy
0.00  305.240509
1.00  381.614166
2.00  410.572906
3.00  434.954956
4.00  414.660400
5.00  394.799591
6.00  389.087128
7.00  414.893982
8.00  449.444183
9.00  417.877472
   10.00  442.470306
   11.01  446.170258
   12.01  448.844666
   13.01  412.847473
   14.01  454.549744
   15.01  447.908478
   16.00  404.607422
   17.00  404.629944
   18.00  441.559448
   19.00  396.328400
   20.00  421.386017
and:
Energy   Average   RMSD Fluct.  Drift  Tot-Drift

Temperature  424.62521.764521.6696  0.07032017.03215





On 10/03/2010 12:21 AM, Thomas Schlesier wrote:

Could anybody reproduce that error or has an idea what is happening?
Or i am alone with that problem?


Nothing looks obviously wrong, but it's hard to be sure in the absence
of information about your hardware. The most likely issue is some kind
of dynamically-linked library mismatch. This can happen if your
execution environment differs from your linking environment. Try forcing
linking to static versions of the libraries, which will prevent this.

Also try disabling things until you get sensible behaviour in all cases,
like --enable-fft=fftpack. That would reveal that the problem was with
linking to mkl.

Also 1-2ps is a bit too short to expect convergence of temperature -
check the plot of T against t with g_energy.

Mark


Date: Fri, 5 Mar 2010 23:11:45 +0100
From: Thomas Schlesier 
Subject: [gmx-users] problem with icc compiler
To: "gmx-users@gromacs.org" 
Message-ID: <4b9181a1.7060...@uni-mainz.de>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed

Hi,
i observed the following problem. if i simulate water (spc or tip4p)
with gromacs 4.0.5 i get with v-rescale or berendsen thermostat the
wrong temperature (ref_t = 300K -> average around 425K, in about 1-2ps),
but only in serial, not in parallel runs.
non-water molecules or nose-hoover thermostat make no problems.
see also
http://lists.gromacs.org/pipermail/gmx-users/2010-March/049248.html
for mdp and log file.

gromacs was compiled with the following comands:
and in the file 'configure' all '-lmkl' were deleted (don't ask me why,
i don't really understand that stuff, the command were from our previous
phd student).

./configure CC="icc" CPPFLAGS="-I/share/apps/intel/mkl/10.0.011/include"
LDFLAGS="-L/share/apps/intel/mkl/10.0.011/lib/em64t
-lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64
-lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-fft=mkl
--prefix="/share/apps/gromacs/4.0.5"
make
make install
make clean
./configure CC="icc" CPPFLAGS="-I/share/apps/intel/mkl/10.0.011/include"
LDFLAGS="-L/share/apps/intel/mkl/10.0.011/lib/em64t
-lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64
-lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-fft=mkl
--prefix="/share/apps/gromacs/4.0.5" --enable-mpi --disable-nice
--program-suffix=_mpi
make mdrun
make install-mdrun

for gromacs 4.0.5 i used the icc 9.1.046 compiler.

i also tried gromacs 4.0.7 with icc 9.1.046 and icc 10.1.008 with spc
water, v-rescale thermostat.
-> serial: too high temperature 425K iso 300K
-> parallel: no problems
with non-water (mesitylene) i have no problem in serial.

the problem does not come from grompp because i can use same tpr-file
for serial and parallel runs with the above results.

if someone needs more informations about this please tell me.

greetings
thomas


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RE: [gmx-users] problems with non pbc simulations in parallel

[Berk Hess]

Hi,

This is a silly bug with nose-hoover and pbc=no.
I fixed it for 4.0.8 (if we will ever release that).

To fix it you only need to move a brace up 4 lines in src/mdlib/init.c
Or you can use the v-rescale thermostat.

Berk

--- a/src/mdlib/init.c
+++ b/src/mdlib/init.c
@@ -119,9 +119,9 @@ static void set_state_entries(t_state *state,t_inputrec *ir,
int nnodes)
 if (ir->epc != epcNO) {
   state->flags |= (1flags |= (1flags |= (1etc == etcVRESCALE) {
 state->flags |= (1< Date: Wed, 10 Mar 2010 14:16:38 +
> From: gmelaug...@qub.ac.uk
> To: gmx-users@gromacs.org
> Subject: [gmx-users] problems with non pbc simulations in parallel
> 
> Hi all
> 
> I have installed gromacs-4.0.7-parallel with open mpi. I have
> successfully ran a few short simulations on 2,3 and 4 nodes using pbc. I
> am now interested in simulating a cluster of 32 molecules with no pbc in
> parallel and the simulation doe not proceed. I have set by box vectors
> to 0 0 0 in the conf.gro file, pbc = no in the mdp file, and use
> dparticle decomposition. The feedback I get from the following command
> 
> nohup mpirun -np 2 /local1/gromacs-4.0.7-parallel/bin/mdrun -pd -s &
> 
> is
> 
> Back Off! I just backed up md.log to ./#md.log.1#
> Reading file topol.tpr, VERSION 4.0.7 (single precision)
> starting mdrun 'test of 32 hexylcage molecules'
> 1000 steps,  0.0 ps.
> [emerald:22662] *** Process received signal ***
> [emerald:22662] Signal: Segmentation fault (11)
> [emerald:22662] Signal code: Address not mapped (1)
> [emerald:22662] Failing at address: (nil)
> [emerald:22662] [ 0] /lib64/libpthread.so.0 [0x7fbc17eefa90]
> [emerald:22662] [ 1]
> /local1/gromacs-4.0.7-parallel/bin/mdrun(nosehoover_tcoupl+0x74) [0x436874]
> [emerald:22662] [ 2]
> /local1/gromacs-4.0.7-parallel/bin/mdrun(update+0x171) [0x4b2311]
> [emerald:22662] [ 3]
> /local1/gromacs-4.0.7-parallel/bin/mdrun(do_md+0x2608) [0x42dd38]
> [emerald:22662] [ 4]
> /local1/gromacs-4.0.7-parallel/bin/mdrun(mdrunner+0xe33) [0x430973]
> [emerald:22662] [ 5]
> /local1/gromacs-4.0.7-parallel/bin/mdrun(main+0x5b8) [0x431128]
> [emerald:22662] [ 6] /lib64/libc.so.6(__libc_start_main+0xe6)
> [0x7fbc17ba6586]
> [emerald:22662] [ 7] /local1/gromacs-4.0.7-parallel/bin/mdrun [0x41e1e9]
> [emerald:22662] *** End of error message ***
> --
> mpirun noticed that process rank 1 with PID 22662 on node emerald exited
> on signal 11 (Segmentation fault).
> 
> p.s I have ran several of these non pbc simulations with the same system
> in serial and have never experienced a problem. Has anyone ever come
> across this sort of problem before? and if so could you please provide
> some advice.
> 
> Many Thanks
> 
> Gavin
> 
> -- 
> 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!
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Re: [gmx-users] simulating several proteins

[Cristiano De Michele]

ok but after I generated two .gro files using genconf (or editconf I  
guess)

containing two identical proteins in different positions/orientations
how can I concatenate these two files in order to supply a unique .gro  
file to grompp?


thanks Cristiano

Il giorno 10/mar/10, alle ore 16:27, Mark Abraham ha scritto:




- Original Message -
From: Cristiano De Michele 
Date: Thursday, March 11, 2010 2:25
Subject: [gmx-users] simulating several proteins
To: gmx-users@gromacs.org


Dear all,
is it possible to simulate more than one protein with GROMACS?
I would like to simulate two lysozyme proteins not solvated and
I tried changing number of proteins in topology file (attached) and
then I used this modified .top file to generate a .gro configuration
with genbox, but I always end up getting just one protein
in the simulation box...


genbox doesn't take input from the .top file to guide its output.

Use genconf on your original structure file to multiply it. Then  
edit your .top by hand to match.


Mark
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Cristiano De Michele, Ph.D.
Department of Physics Tel.  :  +390649913524
University of Rome  "La Sapienza"Fax  :  +39064463158
Piazzale Aldo Moro, 2
I-00185 Roma - Italy
homepage: http://pacci.phys.uniroma1.it/
--
"Shoot for the moon. Even if you miss, you'll land among the stars."





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Re: [gmx-users] simulating several proteins

[Mark Abraham]

- Original Message -
From: Cristiano De Michele 
Date: Thursday, March 11, 2010 2:25
Subject: [gmx-users] simulating several proteins
To: gmx-users@gromacs.org

> Dear all,
> is it possible to simulate more than one protein with GROMACS?
> I would like to simulate two lysozyme proteins not solvated and
> I tried changing number of proteins in topology file (attached) and
> then I used this modified .top file to generate a .gro configuration
> with genbox, but I always end up getting just one protein
> in the simulation box...

genbox doesn't take input from the .top file to guide its output.

Use genconf on your original structure file to multiply it. Then edit your .top 
by hand to match.

Mark
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[gmx-users] simulating several proteins

[Cristiano De Michele]

Dear all,
is it possible to simulate more than one protein with GROMACS?
I would like to simulate two lysozyme proteins not solvated and
I tried changing number of proteins in topology file (attached) and
then I used this modified .top file to generate a .gro configuration
with genbox, but I always end up getting just one protein
in the simulation box...

thanks,
Cristiano

Cristiano De Michele, Ph.D.
Department of Physics Tel.  :  +390649913524
University of Rome  "La Sapienza"Fax  :  +39064463158
Piazzale Aldo Moro, 2
I-00185 Roma - Italy
homepage: http://pacci.phys.uniroma1.it/
--
"Shoot for the moon. Even if you miss, you'll land among the stars."





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[gmx-users] rdf problem

[Antonia V .]

Dear all,

I am simulating a binary system of two non mixing components (5CB and water 
using version 4-0-3; the whole equilibrated trajectory is about 300ns). 
I want to calculate the rdf of the centers of mass of 5CB using the command 
g_rdf -f traj300.xtc -rdf mol_com  -o rdf_com_300.xvg -noxvgr.
The problem is that the rdf I am getting does not approach one at long 
distances. Is there a way to correct that? 
I have the same problem, with all rdfs, and also when I compute the rdfs for a 
lipid bilayer (DPPC-water)... I think it has to do with the way that the 
normalization is done, 
because the ones that are calculated for a one component system (i.e. bulk 5CB) 
are normal (they do approach one). 

Thank you,
Antonia
  
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Re: [gmx-users] problems with non pbc simulations in parallel

[Maurício Menegatti Rigo]

Sorry Gavin,

I didnt resolve the problem yet. I just use your question as mine too. The
only thing I add was that my processor is an i7.
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Re: [gmx-users] problems with non pbc simulations in parallel

[Gavin Melaugh]

Maurício Menegatti Rigo wrote:
> I'm facing the same problem, just after I became to run the molecular
> dynamics at i7 processor.
>
Hi Mauricio

Was your response to my query. If so did you resolve the problem?

Gavin
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Re: [gmx-users] problems with non pbc simulations in parallel

[Maurício Menegatti Rigo]

I'm facing the same problem, just after I became to run the molecular
dynamics at i7 processor.
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[gmx-users] problems with non pbc simulations in parallel

[Gavin Melaugh]

Hi all

I have installed gromacs-4.0.7-parallel with open mpi. I have
successfully ran a few short simulations on 2,3 and 4 nodes using pbc. I
am now interested in simulating a cluster of 32 molecules with no pbc in
parallel and the simulation doe not proceed. I have set by box vectors
to 0 0 0 in the conf.gro file, pbc = no in the mdp file, and use
dparticle decomposition. The feedback I get from the following command

nohup mpirun -np 2 /local1/gromacs-4.0.7-parallel/bin/mdrun -pd -s &

is

Back Off! I just backed up md.log to ./#md.log.1#
Reading file topol.tpr, VERSION 4.0.7 (single precision)
starting mdrun 'test of 32 hexylcage molecules'
1000 steps,  0.0 ps.
[emerald:22662] *** Process received signal ***
[emerald:22662] Signal: Segmentation fault (11)
[emerald:22662] Signal code: Address not mapped (1)
[emerald:22662] Failing at address: (nil)
[emerald:22662] [ 0] /lib64/libpthread.so.0 [0x7fbc17eefa90]
[emerald:22662] [ 1]
/local1/gromacs-4.0.7-parallel/bin/mdrun(nosehoover_tcoupl+0x74) [0x436874]
[emerald:22662] [ 2]
/local1/gromacs-4.0.7-parallel/bin/mdrun(update+0x171) [0x4b2311]
[emerald:22662] [ 3]
/local1/gromacs-4.0.7-parallel/bin/mdrun(do_md+0x2608) [0x42dd38]
[emerald:22662] [ 4]
/local1/gromacs-4.0.7-parallel/bin/mdrun(mdrunner+0xe33) [0x430973]
[emerald:22662] [ 5]
/local1/gromacs-4.0.7-parallel/bin/mdrun(main+0x5b8) [0x431128]
[emerald:22662] [ 6] /lib64/libc.so.6(__libc_start_main+0xe6)
[0x7fbc17ba6586]
[emerald:22662] [ 7] /local1/gromacs-4.0.7-parallel/bin/mdrun [0x41e1e9]
[emerald:22662] *** End of error message ***
--
mpirun noticed that process rank 1 with PID 22662 on node emerald exited
on signal 11 (Segmentation fault).

p.s I have ran several of these non pbc simulations with the same system
in serial and have never experienced a problem. Has anyone ever come
across this sort of problem before? and if so could you please provide
some advice.

Many Thanks

Gavin

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RE: [gmx-users] diffusion coefficient of oxygen

[Berk Hess]

Hi,

I would think this is one of very few examples where most of the force field is 
quite
uncritical. Diffusion of a hydrophobic solute in water will mainly depend on 
the size
of the solute and the diffusion coefficient of the water model itself.
Of the common water models, SPC/E has the best diffusion coefficient and it
combines well with the Gromos force fields, so use that.

It is well known that the diffusion of SPC is twice what it should be.

Berk


> Date: Wed, 10 Mar 2010 07:35:41 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] diffusion coefficient of oxygen
> 
> 
> 
> Sunil Thapa wrote:
> > Respected Experts
> > 
> > I need your help
> > 
> > In my study of diffusion of a oxygen molecule in 255 molecules of water, 
> > I previously used SPC water model with ffgmx force field with cutoff L-J 
> > and Coulomb interaction. I wanted to reproduce the experimental value 
> > 2.4 unit for diffusion coefficient of oxygen in water at 298 K and 1 atm.
> > 
> > To equilibrate the system to the experimental water density of 997 I 
> > used Berendsen thermostat and the same barostat. The density of the 
> > system was 980(+-) 10 kg/m3 which is not the experimental value. After 
> > equilibration, I subjected the system to NVT ensemble md of 100 ns. I 
> > got the msd for oxygen molecule and analyzing first 4 ns (which was a st 
> > line part) of the plot, I got the diffusion coefficient of about 2.45 
> > unit which is close to the experimental value. The question is how can 
> > the diffusion coefficient be so close when density is not produced. Is 
> > this a mere coincidence?
> > 
> 
> More likely a consequence of the water model itself.  Keep in mind that SPC 
> water is not real water, it does not reproduce all properties of water 
> accurately.  No water model does.  Look into the literature for the expected 
> density of SPC, but 980 does sound close to what is expected.
> 
> > Thinking that I used TIP4P water model with the same number but 
> > different force field ffG3a
> > . I equilibrated the system to the same pressure and temperature with 
> > the same algorithms. After equilibration, the correspondng density was 
> > 991(+-) 15 kg/m3. Then I subjected it to the production run of 100ns. 
> > Now what I see is that the MSD curve is a hill, initially increasing, 
> > reaching maximum and again returning to the base. The diffusion 
> > coefficient is 0.7 unit for 100 ns of trajectory.
> > 
> > What would have happened? Is this due to the increased density? Your 
> > precious knowledge on the subject matter would give me a sigh of relief.
> > 
> 
> You must be careful interpreting your results.  If you only have one molecule 
> of 
> your solute, then statistics will likely be very poor.  You probably need 
> either 
> more solute molecules within a given system or many replicates of the same 
> single-solute system to gather any meaningful data.
> 
> The density of the system is a property dominated by the water model.  I am 
> also 
> unsure of the validity of G96 parameters (but you haven't said which 
> parameter 
> set, "ffG3a" is not real) when combined with TIP4P.  The Gromos force fields 
> were parameterized with SPC; TIP4P is more often used with OPLS.  I don't 
> know 
> exactly what effect that will have, but you should probably at least be using 
> a 
> robust combination, or demonstrate somehow that your application of the force 
> field/water model is correct.
> 
> -Justin
> 
> > Looking forward to hearing from you
> > neal
> > 
> > 
> > 
> 
> -- 
> 
> 
> 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] diffusion coefficient of oxygen

[Justin A. Lemkul]

Sunil Thapa wrote:

Respected Experts

I need your help

In my study of diffusion of a oxygen molecule in 255 molecules of water, 
I previously used SPC water model with ffgmx force field with cutoff L-J 
and Coulomb interaction. I wanted to reproduce the experimental value 
2.4 unit for diffusion coefficient of oxygen in water at 298 K and 1 atm.


To equilibrate the system to the experimental water density of 997 I 
used Berendsen thermostat and the same barostat. The density of the 
system was 980(+-) 10 kg/m3 which is not the experimental value. After 
equilibration, I subjected the system to NVT ensemble md of 100 ns. I 
got the msd for oxygen molecule and analyzing first 4 ns (which was a st 
line part) of the plot, I got the diffusion coefficient of about 2.45 
unit which is close to the experimental value. The question is how can 
the diffusion coefficient be so close when density is not produced. Is 
this a mere coincidence?




More likely a consequence of the water model itself.  Keep in mind that SPC 
water is not real water, it does not reproduce all properties of water 
accurately.  No water model does.  Look into the literature for the expected 
density of SPC, but 980 does sound close to what is expected.


Thinking that I used TIP4P water model with the same number but 
different force field ffG3a
. I equilibrated the system to the same pressure and temperature with 
the same algorithms. After equilibration, the correspondng density was 
991(+-) 15 kg/m3. Then I subjected it to the production run of 100ns. 
Now what I see is that the MSD curve is a hill, initially increasing, 
reaching maximum and again returning to the base. The diffusion 
coefficient is 0.7 unit for 100 ns of trajectory.


What would have happened? Is this due to the increased density? Your 
precious knowledge on the subject matter would give me a sigh of relief.




You must be careful interpreting your results.  If you only have one molecule of 
your solute, then statistics will likely be very poor.  You probably need either 
more solute molecules within a given system or many replicates of the same 
single-solute system to gather any meaningful data.


The density of the system is a property dominated by the water model.  I am also 
unsure of the validity of G96 parameters (but you haven't said which parameter 
set, "ffG3a" is not real) when combined with TIP4P.  The Gromos force fields 
were parameterized with SPC; TIP4P is more often used with OPLS.  I don't know 
exactly what effect that will have, but you should probably at least be using a 
robust combination, or demonstrate somehow that your application of the force 
field/water model is correct.


-Justin


Looking forward to hearing from you
neal





--


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] diffusion coefficient of oxygen

[Sunil Thapa]

Respected Experts

I need your help

In my study of diffusion of a oxygen molecule in 255 molecules of water, I 
previously used SPC water model with ffgmx force field with cutoff L-J and 
Coulomb interaction. I wanted to reproduce the experimental value 2.4 unit for 
diffusion coefficient of oxygen in water at 298 K and 1 atm.

To equilibrate the system to the experimental water density of 997 I used 
Berendsen thermostat and the same barostat. The density of the system was 
980(+-) 10 kg/m3 which is not the experimental value. After equilibration, I 
subjected the system to NVT ensemble md of 100 ns. I got the msd for oxygen 
molecule and analyzing first 4 ns (which was a st line part) of the plot, I got 
the diffusion coefficient of about 2.45 unit which is close to the experimental 
value. The question is how can the diffusion coefficient be so close when 
density is not produced. Is this a mere coincidence?

Thinking that I used TIP4P water model with the same number but different force 
field ffG3a
. I equilibrated the system to the same pressure and temperature with the same 
algorithms. After equilibration, the correspondng density was 991(+-) 15 kg/m3. 
Then I subjected it to the production run of 100ns. Now what I see is that the 
MSD curve is a hill, initially increasing, reaching maximum and again returning 
to the base. The diffusion coefficient is 0.7 unit for 100 ns of trajectory.

What would have happened? Is this due to the increased density? Your precious 
knowledge on the subject matter would give me a sigh of relief.

Looking forward to hearing from you
neal





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[gmx-users] Re: gmx-users Digest, Vol 71, Issue 37 (Calculating Binding Affinity between Protein and Ligand using FEP)

[Justin A. Lemkul]

sunita gupta wrote:

Thanks Justin

After going through the discussion on mailing list I got to know that 
"coulombic and LJ interections has to be decoupled separately and for 
better scaling Lambda should have closer values. But my query is that 
for what value of lambda LJ has to be decoupled and for values of lambda 
coulombic interactions has to be decoupled.


Like if I am having 11 lambda values ranging from 0 to 1...with 
successive increase of 0.1, what range of of lambda should have


couple-lambda0 = vdw-q

couple-lambda1 = vdw
(...to decouple only Coulombic interactions)

and what lambda values should have
couple-lambda0 = vdw
couple-lambda1 = none

(...to decouple van der Waals)

And what should be the value of couple-intramol:

Thanks in Advance



There are numerous papers that describe procedures suitable procedures for 
calculating ligand binding energy with free energy calculations.  I suggest you 
start there.


-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] editconf/genbox: molecular complex outside simulation box

[vedat durmaz]

thanks. things are getting clearer and life's going a little easier, now.


Justin A. Lemkul schrieb:
>
>
> dur...@zib.de wrote:
>> hi there,
>>
>> it's my first steps with gromacs and i can't get rid of the following
>> problem:
>>
>> i set up my box with
>>
>> editconf -bt dodecahedron -f complex.pdb -o complex.pdb -c -d 0.9
>>
>> and fill it up with water like
>>
>> genbox -cp complex.pdb -cs ffamber_tip3p.gro -o outfile.pdb -p
>> complex.top
>>
>> but when viewing the system of the resulting file (outfile.pdb),
>> parts of
>> the molecular complex turn out to be outside the box, although the
>> box is
>> obviously large enough. the complex is not centered, whether i use -c or
>> not. i've tried several water models (tip4p, ffamber_tip3p) and all box
>> shapes such as an octahedron, dodecah., cube, triclinic. the cubic
>> one is
>> the only one to result in a properly centered complex. but i prefer
>> to use
>> other box types.
>>
>> does anyone have an idea of the stage at which to search the cause for
>> that problem?
>>
>> thanks a lot and regards
>
> This is just a visualization artifact.  See, for instance:
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
>
> You can "correct" it by using trjconv (once you have assembled a .tpr
> file):
>
> trjconv -s *.tpr -f outfile.pdb -pbc mol -ur compact
>
> -Justin
>
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[gmx-users] Re: gmx-users Digest, Vol 71, Issue 37

[sunita gupta]

Thanks Justin

After going through the discussion on mailing list I got to know that
"coulombic and LJ interections has to be decoupled separately and for better
scaling Lambda should have closer values. But my query is that for what
value of lambda LJ has to be decoupled and for values of lambda coulombic
interactions has to be decoupled.

Like if I am having 11 lambda values ranging from 0 to 1...with successive
increase of 0.1, what range of of lambda should have

couple-lambda0 = vdw-q
couple-lambda1 = vdw
(...to decouple only Coulombic interactions)

and what lambda values should have
couple-lambda0 = vdw
couple-lambda1 = none
(...to decouple van der Waals)

And what should be the value of couple-intramol:

Thanks in Advance









On Sun, Mar 7, 2010 at 10:55 AM,  wrote:

> Send gmx-users mailing list submissions to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>   1. Calculating Binding Affinity between Protein and Ligand   using
>  FEP (sunita gupta)
>   2. Re: Calculating Binding Affinity between Protein and  Ligand
>  using FEP (Justin A. Lemkul)
>   3. SV: [gmx-users] Order parameter for unsaturated lipid chain
>  in UAmodel (Tim Sirk)
>   4. Force between groups (Michael McGovern)
>
>
> --
>
> Message: 1
> Date: Sat, 6 Mar 2010 19:30:33 +0530
> From: sunita gupta 
> Subject: [gmx-users] Calculating Binding Affinity between Protein and
>Ligand  using FEP
> To: gmx-users@gromacs.org
> Message-ID:
><2f68b8d51003060600l58cdb4ecoff09d97b6674...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello all
>
> Earlier also I posted a query regarding FEP for protein ligand complex, but
> I dint not help much.
> Again I would like to share detailed information regarding the protocol I
> am
> following for calculation the binding free energy between protein and
> ligand
> using FEP(free energy perturbation) method. Please correct me if I am wrong
> anywhereas the values of *dVpot/dlambda  dEkin/dlambda  dG/dl constr
> *are
> continuously coming zero(0).
>
> I followed the gromacs tutorial of protien-ligand complex (
> http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf)
> for
> preparing the coordinate and topology file for the whole system.
> For Free energy Calculation I followed the tutorial (
> http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial)
> for lambda value ranging from zero(0) to 1 and setup 11 independent job for
> each lambda value for 5 ns.
> But the* dVpot/dlambda  dEkin/dlambda  dG/dl constr* values in the *.log
> are
> continuously coming zero.
> Any help will be highly appreciated.
>
> For convenience I am also pasting my pro_constV.mdp (please let me know if
> any parameter is wrong of missing...which is leading to such problem)
>
> ; RUN CONTROL PARAMETERS =
> integrator   = md
> ; start time and timestep in ps =
> tinit= 0
> dt   = 0.002
> nsteps   = 500
> ; number of steps for center of mass motion removal =
> nstcomm  = 100
> ; OUTPUT CONTROL OPTIONS =
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout  = 5
> nstvout  = 5
> nstfout  = 0
> ; Output frequency for energies to log file and energy file =
> nstlog   = 500
> nstenergy= 500
> energygrps   = protein non-protein
> ; Output frequency and precision for xtc file =
> nstxtcout= 5000
> 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 =
> ; NEIGHBORSEARCHING PARAMETERS =
> ; nblist update frequency =
> nstlist  = 10
> ; 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 = 1.0
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon-r= 1
> ; Method for doing Van der Waals =
> vdw-type = cu

[gmx-users] Re:problem with interaction energy calculated by g_energy

[Qiong Zhang]

Hi gmx users,

Thanks Mark very much for all your suggestions, for your detailed explanation 
and your patience with me. :-)

Actually, I am going to study the desorption free energy of molecule 1 from the 
surface of molecule 2. So first I have to carry out the absorption of molecule 
1 onto surface of molecule 2. I have tried 8 different orientations of molecule 
1 with respect to the surface and have to choose ONE orientation with the most 
stability to proceed. I think the best criteria to choose ONE orientation is to 
compare the interaction energy between molecule 1 and 2. You mentioned relative 
free energy. But it seems to me difficult to compare the relative free energy 
between different orientations.  I read some papers on the simulation of 
Protein on some surface simulated by NAMD, [for example, Biomaterials 29 (2008) 
513–532] The approach they adopted is also to compare the interaction energy 
(E_inter = E_(1+2) - E_1 - E_2). They also used PME to deal with the long range 
electrostatic interaction. The force field they used is charmm.

Any advice or comment are welcome!

Thank you very much in advance.

Qiong

On 10/03/2010 7:56 AM, Qiong Zhang wrote:
Hi dear Mark,

Thank you very much for your reply!

Yes, you are right that I should have stated the gromacs version in my first
mail. I am sorry that I did not notice this issue. I will pay attention
to this next time.

As for the electrostatic interaction energy in the long range, I
am afraid that I have some different opinion which I am not sure
if it is correct or not. I think for some systems with strong
electrostatic interaction, for example, the interaction between a
Rutile (TiO2) surface and a protein, it seems that the electrostatic
interaction energy in the long range plays a very important role in
the total interaction energy as one of my colleagues shows. In such
cases, I think the electrostatic interaction energy in the long
range can not be neglected. What is your
  opinion please?
Important, yes - you need long-range electrostatics to sample the right 
ensemble. Numerically meaningful when extracted from the whole 
condensed-phase ensemble, no. If it's low, then the total energy has 
sloshed into other degrees of freedom - so what? This is not gas-phase 
ab initio quantum chemistry at 0K, where internal energy correlates with 
something useful, because there are no other energetic degrees of 
freedom. The frequency of occurrence of a region of structure space in a 
converged trajectory can tell you something, i.e. relative free energies.
And I think I understand now"the reciprocal-space
calculation cannot be decomposed group-wise."  Maybe a better way
to overcome this is using the formula:

E_interact=E_tot(1-2)-E_tot(1)-E_tot(2)

Do you agree with this?
No. The only term with long-range contributions is the reciprocal-space 
term and it cannot be decomposed. There is no way around this.
If you can find a published article explaining the usefulness of the 
analysis you're trying to do, they'll have used a forcefield and 
electrostatics model that are consistent with doing it. You should copy 
their method, in that case. I've given my advice three times, and am 
going to desist :-)
Mark





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