[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file

[leila karami]

Dear Chris

Happy new year
thanks for your reply.

please clarify these more:

cd src/tools
cp gmx_trjconv.c ../../exec/share/gromacs/template/my_tool.c

1) where is exact location of gmx_trjconv.c file?

when I enter cd /src, in src directory, there is not tools directory.

2) in my linux, gromacs path is as follows:

/usr/local/gromacs/share/gromacs/template

in template directory, there is only template.c file (containing 135 lines)
and not my_tool.c file.

which file should be copied? (gmx_trjconv.c or my_tool.c)
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[gmx-users] How to calculate rdf for some group respect to one reference axis

[英雄不再寂寞]

Dear gmxers,
   I am trying to calculate radial distribution function (RDF) between some 
particles
 and the radial axis of a SWNT. It is obvious tht the g_rdf can not calculate 
it. How
 to do this calculation? Are there such tools for doing it? Please kindly refer 
it to me?
 Thanks a lot for any reply.
 Best wishes
  
 Yours sincerely,
 Chaofu Wu, Dr.-- 
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[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file

[leila karami]

Dear Chris

I found gmx_trjconv.c file, It is in gromacs-4.0.7/src/tools.
since location of template directory is as follows:
gromacs-4.0.7/share/template,
I used cp gmx_trjconv.c ../../share/template/my_tool.c.
is it true?
I did those changes you said in my_tool.c file.
I created makefile without problem using sed "s/template/my_tool/g"
Makefile.x86_64-unknown-linux-gnu > Makefile.my_tool.
but when compile it, I encountered with following errors:

cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops   -I/usr/include/libxml2 -I/usr/local/gromacs/include
-I/usr/local/gromacs/include/gromacs -c -o my_tool.o my_tool.c
my_tool.c: In function ‘calc_pbc_cluster’:
my_tool.c:88: error: ‘bool’ undeclared (first use in this function)
my_tool.c:88: error: (Each undeclared identifier is reported only once
my_tool.c:88: error: for each function it appears in.)
my_tool.c:88: error: expected ‘;’ before ‘bChanged’
my_tool.c:94: error: ‘bMol’ undeclared (first use in this function)
my_tool.c:94: error: ‘bTmp’ undeclared (first use in this function)
my_tool.c:207: error: ‘bChanged’ undeclared (first use in this function)
my_tool.c: In function ‘put_residue_com_in_box’:
my_tool.c:316: error: ‘t_atom’ has no member named ‘resnr’
my_tool.c:339: error: ‘t_atom’ has no member named ‘resnr’
my_tool.c:357: error: ‘t_atom’ has no member named ‘resnr’
my_tool.c: In function ‘do_trunc’:
my_tool.c:418: error: ‘bool’ undeclared (first use in this function)
my_tool.c:418: error: expected ‘;’ before ‘bStop’
my_tool.c:431: warning: assignment makes integer from pointer without a cast
my_tool.c:432: warning: passing argument 1 of ‘gmx_fio_getfp’ makes pointer
from integer without a cast
my_tool.c:435: warning: passing argument 1 of ‘close_trn’ makes pointer from
integer without a cast
my_tool.c:438: warning: passing argument 1 of ‘gmx_fio_ftell’ makes pointer
from integer without a cast
my_tool.c:439: error: ‘bStop’ undeclared (first use in this function)
my_tool.c:440: error: ‘bOK’ undeclared (first use in this function)
my_tool.c:440: warning: passing argument 1 of ‘fread_trnheader’ makes
pointer from integer without a cast
my_tool.c:441: warning: passing argument 1 of ‘fread_htrn’ makes pointer
from integer without a cast
my_tool.c:463: warning: passing argument 1 of ‘close_trn’ makes pointer from
integer without a cast
my_tool.c:475: warning: passing argument 1 of ‘close_trn’ makes pointer from
integer without a cast
my_tool.c: In function ‘gmx_trjconv’:
my_tool.c:622: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘bAppend’
my_tool.c:622: error: ‘bAppend’ undeclared (first use in this function)
my_tool.c:622: error: ‘bSeparate’ undeclared (first use in this function)
my_tool.c:622: error: ‘bVels’ undeclared (first use in this function)
my_tool.c:622: error: ‘bForce’ undeclared (first use in this function)
my_tool.c:623: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘bCenter’
my_tool.c:623: error: ‘bCenter’ undeclared (first use in this function)
my_tool.c:623: error: ‘bTer’ undeclared (first use in this function)
my_tool.c:715: error: ‘bool’ undeclared (first use in this function)
my_tool.c:715: error: expected ‘;’ before ‘bFit’
my_tool.c:717: error: expected ‘;’ before ‘bRmPBC’
my_tool.c:718: error: expected ‘;’ before ‘bCopy’
my_tool.c:719: error: expected ‘;’ before ‘bExec’
my_tool.c:720: error: expected ‘;’ before ‘bHaveFirstFrame’
my_tool.c:721: error: expected ‘;’ before ‘bSubTraj’
my_tool.c:722: error: expected ‘;’ before ‘bWriteFrame’
my_tool.c:727: error: expected ‘;’ before ‘bWarnCompact’
my_tool.c:745: warning: passing argument 9 of ‘parse_common_args’ from
incompatible pointer type
my_tool.c:745: error: too few arguments to function ‘parse_common_args’
my_tool.c:747: warning: assignment discards qualifiers from pointer target
type
my_tool.c:751: warning: assignment discards qualifiers from pointer target
type
my_tool.c:760: error: ‘bSetBox’ undeclared (first use in this function)
my_tool.c:761: error: ‘bSetTime’ undeclared (first use in this function)
my_tool.c:762: error: ‘bSetPrec’ undeclared (first use in this function)
my_tool.c:763: error: ‘bSetUR’ undeclared (first use in this function)
my_tool.c:764: error: ‘bExec’ undeclared (first use in this function)
my_tool.c:765: error: ‘bTimeStep’ undeclared (first use in this function)
my_tool.c:766: error: ‘bTDump’ undeclared (first use in this function)
my_tool.c:767: error: ‘bDropUnder’ undeclared (first use in this function)
my_tool.c:768: error: ‘bDropOver’ undeclared (first use in this function)
my_tool.c:769: error: ‘bTrans’ undeclared (first use in this function)
my_tool.c:770: error: ‘bSplit’ undeclared (first use in this function)
my_tool.c:773: warning: passing argument 1 of ‘nenum’ from incompatible
pointer type
my_tool.c:774: error: ‘bFit’ undeclared (first use in this function)
my_tool.c:775: error: ‘bFitXY’ undeclared (first use in this function)
my_tool.c:776: error: ‘bReset’ undeclared (firs

Re: [gmx-users] g_tune_pme big standard deviation in perf.out output

[Carsten Kutzner]

Dear Yanbin,

On Dec 30, 2010, at 9:20 PM, WU Yanbin wrote:
> I'm simulating a SPC/E water box with the size of 4nm by 4nm by 4nm. The 
> command "g_tune_pme" was used to find the optimal PME node numbers, Coulomb 
> cutoff radius and grid spacing size. 
> 
> The following command is used:
> g_tune_pme -np 24 -steps 5000 -resetstep 500 ...
> rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12
> 
> The simulation is done with no error. Below is the output:
> ---
> Line tpr PME nodes  Gcycles Av. Std.dev.   ns/dayPME/fDD 
> grid
>0   0   12  2813.762  187.1159.6040.3614   
> 3   1
>1   0   11  2969.826  251.2109.1120.510   13   
> 1   1
>2   0   10  2373.469  154.005   11.3850.4452   
> 7   1
>3   09  2129.519   58.132   12.6650.6015   
> 3   1
>4   08  2411.653  265.233   11.2480.5704   
> 4   1
>5   07  2062.770  514.023   13.4900.616   17   
> 1   1
>6   06  1539.237   89.189   17.5470.7486   
> 3   1
>7   00  1633.318  113.037   16.548  -  6   
> 4   1
>8   0   -1(  4) 1330.146   32.362   20.2761.0504   
> 5   1
> ---
> 
> The optimal -npme is 4.
> 
> It seems to me that the "Std. dev" is too huge.
This is the standard deviation resulting from multiple runs with the
same settings. If you do not specify "-r" for the number of repeats 
explicitly to g_tune_pme, it will do two tests for each setting. For
the optimum of 4 PME nodes the standard deviation is 2.4 percent of the 
mean, thus not large at all.

> Can anyone tell me the meaning of "Gcycles Av." and "Std. dev" and their 
> relations to the accuracy of "ns/day"?
Both the number of CPU cycles as the ns/day values are determined from
the md.log output file of the respective runs. g_tune_pme does the averaging
for you, but you can also look at the individual results, these log files
are still there after the tuning run. The standard deviation is printed
only for the Gcycles - maybe it is a good idea to also print the standard
deviation for the ns/day values. If the standard dev is X percent of the
mean for the cycles, then it is also X percent of the mean ns/day.

> 
> Another question:
> I tried 
> g_tune_pme -np 24 -steps 1000 -resetstep 100 ... (the default value of 
> g_tune_pme)
> rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12
> 
> The optimal -npme is 6, different from "-npme=4" as obtained with big 
> "-nsteps".
> Should I increase "-nsteps" even more to get better estimate, or what else 
> parameters should I try?
> 
In principle the results will become more exact, the longer the test runs
are. For your system it seems that the load between the processes is not yet
optimally balanced after the default 100 steps so that -resetstep 500 gives
you a more accurate value. I think the -steps 5000 value is large enough, 
but another test with a higher resetstep value would answer your question.
Since you already know that 7-12 PME nodes will not perform well, I would
try

g_tune_pme -np 24 -steps 5000 -resetstep 5000 -min 0.16 -max 0.25 ...

Regards,
  Carsten

> Do let me know if the questions are not made clear.
> Thank you.
> 
> Best,
> Yanbin
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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Re: [gmx-users] Major code reorganization in git coming up

[Tsjerk Wassenaar]

Hi Erik,

Happy New Year!

Last year (:p) I rewrote the routine from Andrea Amadei for
application of rotational constraints in a statistical mechanical
consistent manner. It's completely parallellelellized and consistent
with pd/dd as well as application every so many steps. The tests seem
good, although some small changes in handling the reference structure
may be required. Bottom line is, it was a pain getting it working with
the >4.1 releases due to all the changes and I'm a bit afraid of
what's to come :) So maybe a good idea to add it soon for beta? I can
provide the patch against the release-4.5-patches. I've implemented it
as an additional COMM removal mode.

Cheers,

Tsjerk

On Thu, Dec 30, 2010 at 7:09 PM, Erik Lindahl  wrote:
> Hi!
>
> We figured we'd celebrate the upcoming new year with some major changes in 
> the git development branch, consisting primarily of C++ support and a more 
> modular organization of files.
> This is a gradual process, so this mail is a bit of a warning-message that 
> the master/development branch might have some issues with compilers/build 
> environments the next couple of weeks.
>
> If you occasionally use a git build to run production simulation, just use 
> the release-4-5-patches branch instead, and everything should be fine.
>
> However, If you are working on your own code based on the git master branch, 
> it might be a good idea to either switch to the release-4-5-patches branch, 
> or create your own branch that you no longer sync with master as frequently. 
> In the latter case you might have to go through some pain to port your code 
> back to the new file organization later (sorry about that).
>
> The upside of all this is that the file organization will gradually get 
> easier to understand, and the code itself should also get much more modular 
> and readable (which we hope will lead to a faster release schedule and more 
> features :-)
>
>
>
> Happy new year!
>
>
> Erik
> --
> Erik Lindahl 
> Professor of Theoretical & Computational Biophysics
> Department of Theoretical Physics & Swedish e-Science Research Center
> Royal Institute of Technology, Stockholm, Sweden
> Tel: +46855378029 Cell: +46703844534
>
> --
> 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/Support/Mailing_Lists/Search before posting!
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] Umbrella sampling

[Nilesh Dhumal]

Hello
I am trying to run umbrella sampling for my system. I have system with
four ion pair (cation and anion) of ionic liquids and 2048 water
molecules. I am trying to PMF calculation with cation-anion distance as a
reaction coordinate.  I choose cation as group1 and anion group2.
Box dimensions are 39.222 39.222 39.222 90 90 90

Durinh equilibratation cation and anion gets dissociate and move far from
each other (around 7-8 A). Both cation and anion are close to edges of the
box. I am more interested in structure where cation and anion close
(around 2-4A).How can I do the PMF simulation to get this structure. Can I
define pull_rate1 = -0.01 to get cation and anion to get close.
How can I keep cation and anion at center or if they close to the box
edges then  does the periodic images of the system will interact?

Down I pasted the part of pull code used in my.mdp file.


Nilesh


; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= Y Y Y
pull_start  = YES ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = EMI
pull_group1 = ETS
pull_init1  = 0.0
pull_rate1  = -0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2



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Re: [gmx-users] electron density

[Jianhui Tian]

Date: Fri, 31 Dec 2010 19:08:50 -0500
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] electron density
To: Discussion list for GROMACS users 
Message-ID: <4d1e7092.7060...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Jianhui Tian wrote:
> Hi gmx users,
>
> I tried to calculate both the mass density and electron density for the
> water layer of a membrane simulation. The mass density is 1000 kg/m^3,
> however the electron density I got is smaller than about 0.33 e/A^3. I

> How much smaller?
I got about 0.27 e/A^3.

> am using a CHARMM force field and the CHARMM version of TIP3P water. Am
> I doing anything wrong when calculating the electron density? Thanks a
lot.
>

> Possibly, but without seeing what you used for input, information about
your
> simulation, etc it's impossible to say.
In the electrons.dat file, I had
2
OW = 8.834
HW1 = 0.583
HW2 = 0.583
And then used g_density ... -ei electrons.dat -dens electron ...


-Justin
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[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc message

[chris . neale]

Dear Leila:

I looked at the source file that you sent me by personal email looks correct.

Did you use the correct version of the template directory? My makefile  
looks like this (see below). If you used I am not sure where you gt  
the makefile since you mentioned many different places in your online  
posts and by email, but be sure that you are using the one produced by  
the 4.0.7 compilation.


Chris.

# Generated automatically from Makefile.in by configure.
#
# This is a Gromacs 3.0 my_tool makefile for your own utility programs.
#
# Copy this file to whatever directory you are using for your own
# software and add more targets like the my_tool one below.
#
# If you are using gmake it is relatively straightforward to add
# an include based on environment variables (like previous Gromacs versions)
# to select compiler flags and stuff automatically, but below it is static:
#

# Variables set by the configuration script:
LIBS = -lmd -lgmx -lnsl -lfftw3f -lm
LDFLAGS  =  
-L/project/pomes/cneale/GPC/exe/intel/gromacs-4.0.7/exec/lib  
-L/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2/exec/lib
CFLAGS   = -O3 -fomit-frame-pointer -finline-functions -Wall  
-Wno-unused -funroll-all-loops   
-I/project/pomes/cneale/GPC/exe/intel/gromacs-4.0.7/exec/include  
-I/project/pomes/cneale/GPC/exe/intel/gromacs-4.0.7/exec/include/gromacs

CC   = cc
LD   = $(CC)

# The real make targets - note that most make programs support
# the shortcut $^ instead of listing all object files a second
# time, but we cannot count on it...

my_tool:my_tool.o
$(LD) $(LDFLAGS) -o $@ my_tool.o $(LIBS)


I found gmx_trjconv.c file, It is in gromacs-4.0.7/src/tools.
since location of template directory is as follows:
gromacs-4.0.7/share/template,
I used cp gmx_trjconv.c ../../share/template/my_tool.c.
is it true?
I did those changes you said in my_tool.c file.
I created makefile without problem using sed "s/template/my_tool/g"
Makefile.x86_64-unknown-linux-gnu > Makefile.my_tool.
but when compile it, I encountered with following errors:

cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops   -I/usr/include/libxml2 -I/usr/local/gromacs/include
-I/usr/local/gromacs/include/gromacs -c -o my_tool.o my_tool.c
my_tool.c: In function ?calc_pbc_cluster?:
my_tool.c:88: error: ?bool? undeclared (first use in this function)

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Re: [gmx-users] electron density

[Justin A. Lemkul]

Jianhui Tian wrote:

Date: Fri, 31 Dec 2010 19:08:50 -0500
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] electron density
To: Discussion list for GROMACS users >

Message-ID: <4d1e7092.7060...@vt.edu >
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Jianhui Tian wrote:

 Hi gmx users,

 I tried to calculate both the mass density and electron density for the
 water layer of a membrane simulation. The mass density is 1000 kg/m^3,
 however the electron density I got is smaller than about 0.33 e/A^3. I



 How much smaller?

I got about 0.27 e/A^3.


 am using a CHARMM force field and the CHARMM version of TIP3P water. Am
 I doing anything wrong when calculating the electron density? Thanks a 

lot.




 Possibly, but without seeing what you used for input, information 

about your

 simulation, etc it's impossible to say.
In the electrons.dat file, I had 
2 
OW = 8.834

HW1 = 0.583
HW2 = 0.583
And then used g_density ... -ei electrons.dat -dens electron ...



There are several problems.  The first line of electrons.dat indicates there are 
only two unique atom names, but clearly you're supplying three.  Second, this 
file is read in such that at integral number of electrons is detected on each 
line.  So, in your case, two lines are being read, one that detects 8 electrons, 
and another that detects zero.


-Justin



-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] Umbrella sampling

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello
I am trying to run umbrella sampling for my system. I have system with
four ion pair (cation and anion) of ionic liquids and 2048 water
molecules. I am trying to PMF calculation with cation-anion distance as a
reaction coordinate.  I choose cation as group1 and anion group2.
Box dimensions are 39.222 39.222 39.222 90 90 90

Durinh equilibratation cation and anion gets dissociate and move far from
each other (around 7-8 A). Both cation and anion are close to edges of the
box. I am more interested in structure where cation and anion close
(around 2-4A).How can I do the PMF simulation to get this structure. Can I
define pull_rate1 = -0.01 to get cation and anion to get close.
How can I keep cation and anion at center or if they close to the box
edges then  does the periodic images of the system will interact?



You need to define a series of configurations along a pre-defined reaction 
coordinate to properly do umbrella sampling.  Whether or not you can converge 
four independent pairs is questionable, but I've never tried it.  I think I've 
said this before: simplify your system.  Start with one pair in water and see if 
you get a sensible answer and understand the workflow, then build your system up.


If your umbrella restraint distance is larger than half the smallest box vector 
in the pull dimension, the periodic distance is used instead of the distance 
directly across the unit cell.  Knowing whether or not the periodic distance 
will be used comes from proper planning - define the range of distances that 
will make up your reaction coordinate, then make your box at least twice as 
large (allowing some extra space for oscillation about your longest restraint 
distance and pressure coupling, if applicable).


All of the conceptual details are described in a tutorial I wrote.  It sounds to 
me like you're trying to generate a PMF from a single umbrella sampling window, 
which cannot be done.


http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

-Justin


Down I pasted the part of pull code used in my.mdp file.


Nilesh


; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= Y Y Y
pull_start  = YES ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = EMI
pull_group1 = ETS
pull_init1  = 0.0
pull_rate1  = -0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2





--


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] Umbrella sampling

[Nilesh Dhumal]

 Justin,
I considered single ion- pair.
sorry for typing mistake (I wrote 4 ion-pairs).

How can I define distance range.
ONe more my cation and anion are close in box edges in my equilibrated
strucutre.

By defining pull_rate1  = -0.01 can cation and anion will come close
to each other?

Nilesh


Does will it affect on results?

On Sat, January 1, 2011 2:01 pm, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Hello
>> I am trying to run umbrella sampling for my system. I have system with
>> four ion pair (cation and anion) of ionic liquids and 2048 water
>> molecules. I am trying to PMF calculation with cation-anion distance as
>> a reaction coordinate.  I choose cation as group1 and anion group2. Box
>> dimensions are 39.222 39.222 39.222 90 90 90
>>
>> Durinh equilibratation cation and anion gets dissociate and move far
>> from each other (around 7-8 A). Both cation and anion are close to edges
>> of the box. I am more interested in structure where cation and anion
>> close (around 2-4A).How can I do the PMF simulation to get this
>> structure. Can I define pull_rate1 = -0.01 to get cation and anion to
>> get close. How can I keep cation and anion at center or if they close to
>> the box edges then  does the periodic images of the system will
>> interact?
>>
>
> You need to define a series of configurations along a pre-defined
> reaction coordinate to properly do umbrella sampling.  Whether or not you
> can converge four independent pairs is questionable, but I've never tried
> it.  I think I've said this before: simplify your system.  Start with one
> pair in water and see if you get a sensible answer and understand the
> workflow, then build your system up.
>
> If your umbrella restraint distance is larger than half the smallest box
> vector in the pull dimension, the periodic distance is used instead of the
> distance directly across the unit cell.  Knowing whether or not the
> periodic distance will be used comes from proper planning - define the
> range of distances that will make up your reaction coordinate, then make
> your box at least twice as large (allowing some extra space for
> oscillation about your longest restraint distance and pressure coupling,
> if applicable).
>
> All of the conceptual details are described in a tutorial I wrote.  It
> sounds to me like you're trying to generate a PMF from a single umbrella
> sampling window, which cannot be done.
>
> http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sam
> pling
>
> -Justin
>
>
>> Down I pasted the part of pull code used in my.mdp file.
>>
>>
>>
>> Nilesh
>>
>>
>>
>> ; Pull code
>> pull= umbrella pull_geometry   = distance pull_dim= Y
>> Y Y
>> pull_start  = YES ; define initial COM distance > 0
>> pull_ngroups= 1 pull_group0 = EMI pull_group1 = ETS pull_init1
>> = 0.0
>> pull_rate1  = -0.01  ; 0.01 nm per ps = 10 nm per ns pull_k1
>> = 1000  ; kJ mol^-1 nm^-2
>>
>>
>>
>>
>
> --
> 
>
>
> 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
>
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
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>
>
>


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[gmx-users] Umbrella sampling

[chris . neale]

Nilesh,

In the time it take Justin to answer, you can already have tested some  
of this out for yourself. Pick a single window and run the pull-code  
dynamics and then look at the trajectory with VMD and plot the  
coord.xvg file and check the distance by g_dist. You'll learn a lot  
more like this.


Chris.

-- original message --

 Justin,
I considered single ion- pair.
sorry for typing mistake (I wrote 4 ion-pairs).

How can I define distance range.
ONe more my cation and anion are close in box edges in my equilibrated
strucutre.

By defining pull_rate1  = -0.01 can cation and anion will come close
to each other?

Nilesh


Does will it affect on results?

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Re: [gmx-users] electron density

[Jianhui Tian]

Problem solved.
The "2" in the text is just a typo when I sent the email.
So actually there is no partial charge in the electrons.dat file.
Thanks, Justin.

Jianhui

Date: Sat, 01 Jan 2011 13:56:45 -0500
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] electron density
To: Discussion list for GROMACS users 
Message-ID: <4d1f78ed.5070...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Jianhui Tian wrote:
> Date: Fri, 31 Dec 2010 19:08:50 -0500
> From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
> Subject: Re: [gmx-users] electron density
> To: Discussion list for GROMACS users  
>
> Message-ID: <4d1e7092.7060...@vt.edu >
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Jianhui Tian wrote:
>>  Hi gmx users,
>>
>>  I tried to calculate both the mass density and electron density for the
>>  water layer of a membrane simulation. The mass density is 1000 kg/m^3,
>>  however the electron density I got is smaller than about 0.33 e/A^3. I
>
>>  How much smaller?
> I got about 0.27 e/A^3.
>
>>  am using a CHARMM force field and the CHARMM version of TIP3P water. Am
>>  I doing anything wrong when calculating the electron density? Thanks a
> lot.
>>
>
>>  Possibly, but without seeing what you used for input, information
> about your
>>  simulation, etc it's impossible to say.
> In the electrons.dat file, I had
> 2
> OW = 8.834
> HW1 = 0.583
> HW2 = 0.583
> And then used g_density ... -ei electrons.dat -dens electron ...
>

There are several problems.  The first line of electrons.dat indicates there
are
only two unique atom names, but clearly you're supplying three.  Second,
this
file is read in such that at integral number of electrons is detected on
each
line.  So, in your case, two lines are being read, one that detects 8
electrons,
and another that detects zero.

-Justin
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[gmx-users] how to simulate linear rigid rod

[Sanku M]

Hi,
  I am planning to do a simulation with a pair of rigid linear rods in SPC/E 
water . More specifically, I want to calculate the free energy of association 
of 
a pair of rigid rod in water, using umbrella sampling.  But, I was wondering 
how 
to keep a chain molecule, around 10-mer, rigid . I am not sure whether just 
constraining the bond lengths using LINCS will be good idea for stable 
simulation . But, not sure whether, the molecule will still be linear or not ?
Any suggestion will be appreciated.
Sanku


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[gmx-users] The sum of the O-H distancesof the backbone hydrogen bonds ROH

[sreelakshmi ramesh]

Dear all,
 I have a protein in water and i have simulated it for few
nanoseconds and i now i wanted to monitor the  The sum of the O-H distances
(in Å) of the backbone
hydrogen bonds ROH:i dono how to extract the value from the trajectory
file.Any siuggestion please.Thanks in advance

regards,
sree.
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[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc message

[leila karami]

Dear Chris

I did all of steps again. this tims when compile Makefile.my_tool by both of
make and gmake:

make: *** No rule to make target `my_tool.o', needed by `my_tool'.  Stop.

my Makefile.my_tool is as follows:

# Generated automatically from Makefile.in by configure.
#
# This is a Gromacs 3.0 my_tool makefile for your own utility programs.
#
# Copy this file to whatever directory you are using for your own
# software and add more targets like the my_tool one below.
#
# If you are using gmake it is relatively straightforward to add
# an include based on environment variables (like previous Gromacs versions)
# to select compiler flags and stuff automatically, but below it is static:
#

# Variables set by the configuration script:
LIBS = -lmd -lgmx -lxml2  -L/usr/lib64 -lnsl -lfftw3f -lm   -lSM
-lICE -lX11
LDFLAGS  = -L/usr/local/gromacs/lib
CFLAGS = -O3 -fomit-frame-pointer -finline-functions -Wall
-Wno-unused -funroll-all-loops   -I/usr/include/libxml2
-I/usr/local/gromacs/include -I/usr/local/gromacs/include/gromacs
CC   = cc
LD   = $(CC)

# The real make targets - note that most make programs support
# the shortcut $^ instead of listing all object files a second
# time, but we cannot count on it...

my_tool:my_tool.o
$(LD) $(LDFLAGS) -o $@ my_tool.o $(LIBS)
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