[gmx-users] Problem in pullx file

[Aswathy]

Dear Gromacs users,

I am doing SMD of a ligand pathway, and then want ot do the PMF analysis.
Initially I pulled the ligand from extra to intracellular side of the
protein. The pull code used are given below.

pull = umbrella
pull_geometry= distance
pull_dim =  N N Y
pull_start   = yes
pull_nstxout =  10
pull_nstfout =  10
pull_ngroups =  1
pull_group0  =  r_57
pull_group1  =  r_C1
pull_rate1   =  0.005
pull_k1  =  1000

here group0 is one residue at the extracellular region and r_C1 is the side
chain Carbon atom of the ligand.

My question is , the total length of the channel is almost 40 Angstrom and
as per my knowledge, when we did the pulling the pullx file will give the
coordinate of the ligand through the channel.
Even though ligand reaches the opposite end of the channel, in pullx file I
am getting around 19 Angstrom in total.

Again I calculate the g_dist of the ligand and the center of the channel, it
shows around 40 Ang in total . Please find the links provided

Am I misunderstanding anything about the pullx file.

Could you please suggest me where thing get wrong?

http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en

http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en


Thank you,
-- 
-Aswathy
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Re: [gmx-users] gmx 4.5 configure options confusing

[Rossen Apostolov]

 Hi,

This was a typo in configure.ac, the second line should say 
--without-qmmm-orca.


Fixed it for the next release. Thanks for reporting.

Rossen

On 7/31/10 12:11 PM, Alan wrote:

For gmx 4.5 beta, I see with ./configure --help:

  --without-qmmm-mopacUse modified Mopac 7 for QM-MM (see website)
  --without-qmmm-mopacUse ORCA for QM-MM

What that really means?

Thanks,

Alan

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


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Re: [gmx-users] tests for gmx 4.5

[Rossen Apostolov]

 Hi,

The tests haven't been ported to 4.5 yet but I hope to fix that before 
the final release.


Rossen

On 7/31/10 7:08 PM, Alan wrote:
Is there a proper set of tests for gmx 4.5 because neither 
ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz or "git clone 
git://git.gromacs.org/regressiontests.git 
" is working due to the 
several modifications done in gmx 4.5 including automatic thread for 
mdrun (I am using a Mac with dual core) and more warnings.


Thanks,

Alan

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


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RE: [gmx-users] Precision in trajectory file

[Berk Hess]

From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Date: Wed, 4 Aug 2010 12:56:54 +1000
Subject: Re: [gmx-users] Precision in trajectory file



- Original Message -
From: Inon Sharony 
Date: Tuesday, August 3, 2010 20:55
Subject: [gmx-users] Precision in trajectory file
To: "gmx-users@gromacs.org" , gmx-developers 


> Good afternoon!
> 
> It seems to me that although I'm running a double-precision 
> installation of GROMACS, the printout to file (of the positions 
> and velocities) is of much less precision. i.e. the computation 
> is done on numbers with something like 16 significant digits, 
> but the last 10 of those are simply truncated and lost (e.g. 
> positions are given in single-precision as 0.000 nm, and in 
> double-precision as 0.0 nm). Since I've already spent 
> computation time at getting double-precision, I'd like to make 
> use of all of it -- for my own reasons. I already searched the 
> manuals, mailing lists and source code for instruction but 
> didn't find any.
> Could you please tell me how I can change the number of digits 
> printed out (e.g. to the .trr file)? I'm looking for a more 
> elegant solution than adding a printf line to the source code. 
> Something along the lines of changing the format of numbers in 
> the function that prints to .trr .

You seem confused about something. The .trr file contains a binary 
representation of the value, in the appropriate precision. There's no nonsense 
about the number of digits *it* has - it has full single/double-precision 
binary floating-point numbers, and its precision is not measured in digits.

Some program that reads those numbers and writes human-readable forms might 
choose to lose precision, but the underlying precision was always there...

There's no straightforward way to get large amounts of precision output with 
GROMACS tools, because only a few of the digits are actually significant. You 
could hack the code to g_traj or gmxdump to get all the precision if you really 
want it.

Mark

For the next 4.5 beta I added a -fp option to g_traj that will print output in 
full precision,
i.e. exponential format will all relevant decimals for both single and double 
precision compilation.

Berk

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Re: [gmx-users] Can I make make_ndx interactive?

[Jochen Hub]

Jennifer Williams wrote:


Hi,


Is there some way of making the make_ndx file interactive so that I 
can include it in a script?


I would usually type in  "a C_O and O_C" to select my atoms

I've tried altering the example on the webpage for making commands 
interactive:


make_ndx -flags <
try:

cat << EOF | make_ndx -f prot.pdb
a C_O
q
EOF

Jochen


but -flags doesn't seem to be recognized. Does anyone know a work around?

Thanks

Jenny








--
---
Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
---

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Re: [gmx-users] Problem in pullx file

[Justin A. Lemkul]

Aswathy wrote:

Dear Gromacs users,

I am doing SMD of a ligand pathway, and then want ot do the PMF 
analysis. Initially I pulled the ligand from extra to intracellular side 
of the protein. The pull code used are given below.


pull = umbrella
pull_geometry= distance
pull_dim =  N N Y
pull_start   = yes
pull_nstxout =  10
pull_nstfout =  10
pull_ngroups =  1
pull_group0  =  r_57
pull_group1  =  r_C1
pull_rate1   =  0.005
pull_k1  =  1000

here group0 is one residue at the extracellular region and r_C1 is the 
side chain Carbon atom of the ligand.


My question is , the total length of the channel is almost 40 Angstrom 
and as per my knowledge, when we did the pulling the pullx file will 
give the coordinate of the ligand through the channel.


Not quite.  Look at the data labels in the .xvg file.  The pullx file contains 
the coordinates (in all of the pull directions) for the reference group, and 
then the distance between the reference and the pull group along all pull axes.


Even though ligand reaches the opposite end of the channel, in pullx 
file I am getting around 19 Angstrom in total.


Again I calculate the g_dist of the ligand and the center of the 
channel, it shows around 40 Ang in total . Please find the links provided




You're measuring two different things.  The pullx distance is given relative to 
your pull_group0, which you said is a residue on one side of the channel.  Then 
you're using g_dist to measure to the center of the channel.



Am I misunderstanding anything about the pullx file.

Could you please suggest me where thing get wrong?

http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en 



http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en 





For some reason these documents are inaccessible.  It is probably better to use 
a site like photobucket and post actual images.  Google is great, but not 
everyone has an account and I've also been told that their usage agreement is 
troubling, in that anything you upload to Google Docs becomes property of 
Google.  Not something I've looked into, but I don't ever post my research data 
there.


-Justin



Thank you,
--
-Aswathy



--


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] What version of cmake is required to compile v4.5b2 for GPUs?

[Szilárd Páll]

Hi Chris,


First of all, as Rossen said, the <=2.6.4 is a typo, it was meant to
be >=2.6.4, it _should_ work with 2.8.0 (I took the FindCUDA.cmake
script from the 2.8 cmake sources :), but...

icc is _not_ supported by CUDA, AFAIR some people reported getting it
work but only in some very limited special cases.

Could you try with gcc and see if it works? Please get back to us if it doesn't!

Cheers,
--
Szilárd


On Tue, Aug 3, 2010 at 1:06 AM,   wrote:
> Ah, I see that I need version <=2.6.4
>
> This info is on the web, but not in the INSTALL_GPU file... perhaps that
> file could include all of the information found here:
>
> http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/Gromacs_on_GPUs
>
> Thanks,
> Chris.
>
> -- original message --
>
> It seems that cmake 2.8.0 is not recent enough?
>
> I attempted to compile like this:
>
> cd /project/pomes/cneale/GPC/exe/intel/gromacs-4.5-beta2
> module purge
> module load intel
> module load cuda     #cuda 3.0
> module load cmake    #cmake 2.8.0
> export CC=icc
> export CXX=icpc
> cmake /project/pomes/cneale/GPC/exe/intel/gromacs-4.5-beta2/src
> -DGMX_OPENMM=ON -DGMX_THREADS=OFF
> make mdrun
> make install-mdrun
>
> #
>
> Here is the output that I get:
>
> -- The C compiler identification is Intel
> -- The CXX compiler identification is Intel
> -- Check for working C compiler:
> /project/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icc
> -- Check for working C compiler:
> /project/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Check for working CXX compiler:
> /project/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icpc
> -- Check for working CXX compiler:
> /project/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icpc -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> CMake Error at gmxlib/CMakeLists.txt:110 (install):
>   install TARGETS given no ARCHIVE DESTINATION for static library target
>   "gmx".
>
>
> CMake Error at mdlib/CMakeLists.txt:12 (install):
>   install TARGETS given no ARCHIVE DESTINATION for static library target
>   "md".
>
>
> CMake Error at kernel/gmx_gpu_utils/CMakeLists.txt:18
> (CUDA_INCLUDE_DIRECTORIES):
>   Unknown CMake command "CUDA_INCLUDE_DIRECTORIES".
>
>
> CMake Warning (dev) in CMakeLists.txt:
>   No cmake_minimum_required command is present.  A line of code such as
>
>     cmake_minimum_required(VERSION 2.8)
>
>   should be added at the top of the file.  The version specified may be
> lower
>   if you wish to support older CMake versions for this project.  For more
>   information run "cmake --help-policy CMP".
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
> -- Configuring incomplete, errors occurred!
> make: *** No rule to make target `mdrun'.  Stop.
> make: *** No rule to make target `install-mdrun'.  Stop.
>
>
> 
>
> thank you,
> Chris.
>
>
>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] What version of cmake is required to compile v4.5b2 for GPUs?

[Szilárd Páll]

Hi Chris,

Though I'm repeating myself, for the sake of not leaving this post
unanaswered (btw reposts should be avoided as much as possible!):

First of all, as Rossen said, the <=2.6.4 is a typo, it was meant to
be >=2.6.4, it _should_ work with 2.8.0 (I took the FindCUDA.cmake
script from the 2.8 cmake sources :), but...

icc is _not_ supported by CUDA, AFAIR some people reported getting it
work but only in some very limited special cases.

Could you try with gcc and see if it works? Please get back to us if it doesn't!

Cheers,
--
Szilárd



On Wed, Aug 4, 2010 at 12:38 AM,   wrote:
> Thanks Rossen, I did not yet get it working. I just posted under a more
> relevant title, please see the post:
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-August/052939.html
>
> (there were 2 errors, one that I fixed and one that I am still struggling
> with).
>
> Chris.
>
> -- original message --
>
>
> Actually this was a mistake on the website, it must be CMake >= 2.6.4,
> so 2.8.0 is fine. Although the build system requires CUDA 3.1, that
> doesn't seem to be the problem from your log.
>
> Did you get it to work?
>
> Rossen
>
>
>
> --
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[gmx-users] compiling GPU 4.5b2, CUDA_INCLUDE_DIRECTORIES function is undefined

[chris . neale]

Dear Szilárd and Rossen:

I have attempted with gcc4.4.0 and I got the same result. I can verify  
that cmale/FindCUDA.cmake exists and contains the MARCO for  
CUDA_INCLUDE_DIRECTORIES but it seems that this library is not, for  
some reason, getting loaded in by at least  
kernel/gmx_gpu_utils/CMakeLists.txt because if I add that macro to  
that file then the error disappears.


Thank you,
Chris.

## what I did:

module purge
module load gcc/gcc-4.4.0
module load cmake/2.8.0  #need version >=2.6.4
module load cuda/cuda-3.1
mkdir gpuexec
export  
OPENMM_ROOT_DIR=/project/pomes/cneale/GPC/exe/OpenMM2.0-Source/exec/openmm
cmake /project/pomes/cneale/GPC/exe/intel/gromacs-4.5-beta2/src  
-DGMX_OPENMM=ON -DGMX_THREADS=OFF  
-DCMAKE_INSTALL_PREFIX=$(pwd)/gpuexec -DLIB_INSTALL_DIR=$(pwd)/gpuexec


## output

CMake Error at kernel/gmx_gpu_utils/CMakeLists.txt:18  
(CUDA_INCLUDE_DIRECTORIES):

  Unknown CMake command "CUDA_INCLUDE_DIRECTORIES".


CMake Warning (dev) in CMakeLists.txt:
  No cmake_minimum_required command is present.  A line of code such as

cmake_minimum_required(VERSION 2.8)

  should be added at the top of the file.  The version specified may be lower
  if you wish to support older CMake versions for this project.  For more
  information run "cmake --help-policy CMP".
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Configuring incomplete, errors occurred!


PS I also tried without -DCMAKE_INSTALL_PREFIX=$(pwd)/gpuexec  
-DLIB_INSTALL_DIR=$(pwd)/gpuexec and got the same thing.


Also, sorry for the repost, I was trying to change the subject line to  
something more representative.


Thanks,
Chris.

-- original message --

Hi Chris,

Though I'm repeating myself, for the sake of not leaving this post
unanaswered (btw reposts should be avoided as much as possible!):

First of all, as Rossen said, the <=2.6.4 is a typo, it was meant to
be >=2.6.4, it _should_ work with 2.8.0 (I took the FindCUDA.cmake
script from the 2.8 cmake sources :), but...

icc is _not_ supported by CUDA, AFAIR some people reported getting it
work but only in some very limited special cases.

Could you try with gcc and see if it works? Please get back to us if  
it doesn't!


Cheers,
--
Szilárd



On Wed, Aug 4, 2010 at 12:38 AM,   wrote:

Thanks Rossen, I did not yet get it working. I just posted under a more
relevant title, please see the post:

http://lists.gromacs.org/pipermail/gmx-users/2010-August/052939.html

(there were 2 errors, one that I fixed and one that I am still struggling
with).

Chris.

-- original message --


Actually this was a mistake on the website, it must be CMake >= 2.6.4,
so 2.8.0 is fine. Although the build system requires CUDA 3.1, that
doesn't seem to be the problem from your log.

Did you get it to work?

Rossen




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Re: [gmx-users] tests for gmx 4.5

[Mark Abraham]

I'm glad there's some interest in the test set. I'm happy to update what I did 
for 4.0.7 for 4.5 also, but there are a number of issues that need attention 
from someone other than me. I listed those that occurred to me here 
http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.html, 
linked also from the Test Set page on the website.

Among those issues is that we need a single GROMACS version that produces 
reliable reference data for all cases we wish to test! Various of the 3.3.x 
series have known issues that make test set maintenance awkward.

If I do the necessary updates to release-3-3-patches branch to make a 
hypothetical GROMACS 3.3.4 that is useful for making test set reference 
calculations, should we make such a release? Alternatively, we can just 
announce that the reference data was generated by the 3-3-version with a given 
git hash and not release. Thoughts?

Mark

- Original Message -
From: Rossen Apostolov 
Date: Wednesday, August 4, 2010 17:56
Subject: Re: [gmx-users] tests for gmx 4.5
To: gmx-users@gromacs.org

 
   ---
| 

>  Hi,
 > 
>  The tests haven't been ported to 4.5 yet but I hope to fix that 
> before the final release.
 > 
>  Rossen
 > 
>  On 7/31/10 7:08 PM, Alan wrote: 
Is there a proper set of tests for gmx 4.5 because   neither 
ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz   or "git clone 
git://git.gromacs.org/regressiontests.git"   is working due to the several 
modifications done in gmx 4.5   including automatic thread for mdrun (I am 
using a Mac with dual   core) and more warnings.
  > Thanks,   > 
  > Alan > 
>  -- 
>  Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
>  Department of Biochemistry, University of Cambridge. 
>  80 Tennis Court Road, Cambridge CB2 1GA, UK.
>  >>http://www.bio.cam.ac.uk/~awd28<<
 > 
|
---
  > -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Tabulated potentials and performance

[João M . Damas]

Hi guys,

>From what I've tested, it seems that performances decreases linearly with
the amount of tables used, exactly the opposite of what Lanyuan has said.
I've tested this for GROMACS 4.0.4 and from 1 to 190 tables. Near 190
tables, it seems that a threshold in performance starts to form, but nothing
very clear.

Hence, is there really this cache size problem?

João M. Damas

On Mon, Jul 19, 2010 at 11:18 PM, Lanyuan Lu  wrote:

> >From our group's experience, there is a critical point for dramatic
> performance drop when one uses two many tables. The possible reason is that
> the size of tables exceeds the cache size. However, this only happens when
> the number of tables is beyond something like 50. The total table size for
> the critical point can depend on the hardware condition.
>  Lanyuan
>
> On Mon, Jul 19, 2010 at 1:49 PM, ms  wrote:
>
>> On 19/07/10 18:32, Da-Wei Li wrote:
>>
>>> I remember the manu states that it won't cost too much compared with
>>> standard potential function form.
>>>
>>
>> Well, I find in the manual exactly the opposite:
>> "Note that table lookup is significantly slower than computation of the
>> most simple Lennard-Jones and Coulomb interaction." (p.133)
>>
>> But I am already using tables for most nonbonded interactions and the
>> performance is OK. What I would like to know is, if I increase the *number
>> of tables* (keeping the number of particles/interactions the same, but, say,
>> using two tables where I used only one before), is it going to be
>> significantly worse or not?
>>
>> thanks!
>>
>> m.
>>
>>
>>  dawei
>>>
>>> On Mon, Jul 19, 2010 at 1:22 PM, ms  wrote:
>>>
 On 19/07/10 17:32, Da-Wei Li wrote:

>
> It will be very little from my experience. Remember that the dominate
> part is the non-bonded force calculation.
>

 Well, that's exactly what I tabulate.


> dawei
>
> On Mon, Jul 19, 2010 at 12:22 PM, mswrote:
>
>>
>> Hi,
>>
>> Do you know where can I find some information on how using tabulated
>> potential affects gmx performance, and how? I have to decide how to
>> project
>> a custom model but I don't want to calculate dozens of tables only to
>> find
>> that gmx grinds to a halt.
>>
>> thanks!
>> M.
>> --
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Protein Modelling Group
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[gmx-users] Intermolecular RDF in DPPC

[prithvi raj pandey]

Dear gmx users,

I want to calculate intermolecular RDF between N and carbonyl oxygen atoms
in a DPPC bilayer. As suggested in some mails in the mailing list i wanted
to generate one tpr file for the purpose containing exclusion 49 (as united
atom model of DPPC contains 50 atoms). But while generating the tpr file
using the following command

grompp -f grompp.mdp -p topol.top -c dppc08.pdb -o rdf.tpr

the grompp program hangs saying

checking input for internal consistency...
processing topology...
Opening library file
/export/softexport/gromacs/share/gromacs/top/ffG53a6.itp
Opening library file
/export/softexport/gromacs/share/gromacs/top/ffG53a6nb.itp
Opening library file
/export/softexport/gromacs/share/gromacs/top/ffG53a6bon.itp
Opening library file /export/softexport/gromacs/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations
Opening library file /export/softexport/gromacs/share/gromacs/top/spc.itp

Excluding 49 bonded neighbours molecule type 'DPPC'

and does not proceed further. What is wrong? Can anyone please help?

-- 
Prithvi Raj Pandey
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Re: [gmx-users] Intermolecular RDF in DPPC

[Justin A. Lemkul]

prithvi raj pandey wrote:

Dear gmx users,

I want to calculate intermolecular RDF between N and carbonyl oxygen 
atoms in a DPPC bilayer. As suggested in some mails in the mailing list 
i wanted to generate one tpr file for the purpose containing exclusion 
49 (as united atom model of DPPC contains 50 atoms). But while 
generating the tpr file using the following command


grompp -f grompp.mdp -p topol.top -c dppc08.pdb -o rdf.tpr

the grompp program hangs saying

checking input for internal consistency...
processing topology...
Opening library file 
/export/softexport/gromacs/share/gromacs/top/ffG53a6.itp
Opening library file 
/export/softexport/gromacs/share/gromacs/top/ffG53a6nb.itp
Opening library file 
/export/softexport/gromacs/share/gromacs/top/ffG53a6bon.itp

Opening library file /export/softexport/gromacs/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations
Opening library file /export/softexport/gromacs/share/gromacs/top/spc.itp

Excluding 49 bonded neighbours molecule type 'DPPC'

and does not proceed further. What is wrong? Can anyone please help?



You're probably running out of memory.  Generating that many exclusions will 
take up a lot of resources.  Beyond that, you don't need 49 exclusions for DPPC. 
 50 atoms does not imply the longest distance between two atoms is 49 bonds.  I 
believe, for DPPC, the maximum you need should be 25.  If you only need to 
exclude interactions through the carbonyl, that number drops to 9 or so.


-Justin


--
Prithvi Raj Pandey



--


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] Force field parameters for the heme in ff53a6

[Arthur Roberts]

Hi, All,

Does anyone know where the force field parameters for the heme in the  
ff53a6 force field were obtained?


Much appreciated,
Art

Art Roberts
7254 Shoreline Dr. #130
San Diego, CA 92122
cell: 206-850-7468
email: aroberts99...@yahoo.com
skype=aroberts92122





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Re: [gmx-users] Force field parameters for the heme in ff53a6

[Justin A. Lemkul]

It appears that the parameters in 53a6 are unchanged relative to 43a1, the 
reference for which is the GROMOS manual.  Unfortunately, you have to pay the 
licensing fee to obtain the manual.  There are certainly several literature 
references for various aspects of the GROMOS functional form and parameters, but 
none that I am aware of that specifically details the derivation of heme.


-Justin

Arthur Roberts wrote:

Hi, All,

Does anyone know where the force field parameters for the heme in the 
ff53a6 force field were obtained?


Much appreciated,
Art

Art Roberts
7254 Shoreline Dr. #130
San Diego, CA 92122
cell: 206-850-7468
email: aroberts99...@yahoo.com
skype=aroberts92122







--


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] Re: Resilin Project

[Justin A. Lemkul]

You've basically got the idea.  As a subtle point, the "strength" of a method is 
completely user-defined (by the tau_p parameter, how frequently the temperature 
is coupled).  No one method is "stronger" than another, but it is correct to say 
that the Nose-Hoover thermostat produces a rigorous NVT ensemble.  When used 
with Parrinello-Rahman for pressure control, a rigorous NPT ensemble is produced.


If I remember our discussion correctly, you want to fix one end of the molecule 
and pull on the other, correct?  If so, your pull_group0 will be the residue at 
one end of the protein (N- or C-terminus, depending on how you set it up), and 
pull_group1 will be the other terminus.


-Justin

Ravi Kappiyoor wrote:
Thank you, Justin. To make sure I understood correctly, you use weak 
coupling methods during equilibration (such as V-rescale and Berendsen) 
in order to try and avoid large fluctuations. However, during actual MD 
simulations, you would recommend using stronger coupling methods such as 
Nose-Hoover, correct? Also, one question I forgot to ask in the last 
e-mail, in the umbrella sampling, I believe you used the pull command to 
pull chain A of the amyloid fibril with respect to chain B. In my case, 
I will be testing a single chain of resilin, so how would I adapt this 
segment?


On Wed, Aug 4, 2010 at 6:45 PM, Justin A. Lemkul > wrote:



Hi Ravi,

Your questions raise a number of interesting points, most of which
take a few years of experience to fully appreciate :)  I will try to
give you a short take on the whole idea of equilibration, as best as
email will allow.  I will note, though, that to fully address the
subtleties of what you're asking, it takes quite a lot of textbook
reading.  I can recommend a few to you, if you like.  We devoted
several weeks to this type of discussion in the class we taught.

The initial equilibration of any system should be approached gently.
 Solvent that is added has a very regular, almost crystalline,
configuration.  It is very unnatural.  NVT equilibration is
typically done before NPT, although I happen to know that the
amyloid fibrils are incredibly resilient and do not require NVT
equilibration.  This is only something I happen to have figured out
after a few years of working on my project.  Generally speaking
(about 99% of the time), you should do NVT first.  Weak temperature
coupling methods like Berendsen or V-rescale are used because the
system is far from equilibrium and any initial clashes will induce
huge temperature fluctuations if you apply the Nose-Hoover method.
 The only explanation for these observations lies in the primary
literature for the thermostat algorithms.  I'll warn you, the math
is heavy. Sorry to say there is no quick link to provide.  I've
never seen anyone be able to give a concise description of these
algorithms, let alone the difference between them :)

I used Parrinello-Rahman for the lysozyme NPT since, during NPT, the
system is less sensitive to pressure oscillations once NVT has been
done.  In the umbrella sampling tutorial, since I did not do NVT, I
maintained a weak coupling method.  This is because the first
equilibration you do should always use some form of weak coupling.

Certainly during actual data collection you should use Nose-Hoover
or V-rescale for your thermostat and Parrinello-Rahman for your
barostat.  The Berendsen method is quick and convenient, but does
not generate a proper statistical mechanical ensemble.  Because of
this, the temperature and pressure distributions it generates are
non-physical and the free energy surface of the simulation
trajectory is not correct.

Let us know if you have any further questions.

-Justin


Ravi Kappiyoor wrote:

Sorry to bother you again, but I have some questions regarding
the MD simulation after getting the protein structure. As Joe
had suggested previously, I've used Modeler to create a
structure based on multiple templates (attached). I used 1KAP
and 1GO8 as they had better sequence identities (28 and 26%
respectively, as opposed to 21% and 19% for the other two
templates). I've been going through Justin's lysozyme and
umbrella sampling tutorials (except using the attached resilin
pdb instead of the pdb files that the tutorial files mention).
However, after going through both of them, I have a few
questions. In the lysozyme tutorial, after running an energy
minimization, an NVT minimization was done before an NPT
minimization, while the umbrella tutorial simply went straight
from energy minimization to NPT. I was wondering why NVT was
skipped in the umbrella tutorial. Also, in the coupling,
different coupling parameters were used between the two
simulat

[gmx-users] frezzing a bond : NPT and NVT simulations

[Nilesh Dhumal]

Hello
I am trying to constraints of a bond. I checked the distance using g_dist,
distance changes from 3.5 A to ~ 8.0A.
Can anyone tell why it changes.
Here I have pasted mdp file and itp file.
Nilesh
Solvent.itp
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
;  name  bond_typemasscharge   ptype  sigma  epsilon
  opls_997   PA 0   100.1.000   A0.4e-01  0.82890e-01
  opls_998   NE 0   100.   -1.000   A0.4e-01  0.82890e-01

[ bondtypes ]
; ij  func   b0  kb
  PANE  10.35   00

[ moleculetype ]
 ; name  nrexcl
 ABC 3

[ atoms ]
 ;   nr  typeresnr   residu  atomcgnrcharge mass
 1  opls_9971   ABCPA  11.  100.
 2  opls_9981   ABCNE  1   -1.  100.000

[ constraints ]
  1   2   10.35000


pr.mdp
title   =  cpeptid position restraining
cpp =  /usr/bin/cpp
constraints =  none
integrator  =  md
dt  =  0.001; ps !
nsteps  =  25  ; total 1.0 ps.
nstcomm =  1
nstxout =  10
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1.0
coulombtype = PME
vdwtype = cut-off
rcoulomb=  1.0
rvdw=  1.4
fourierspacing  = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
constraint-algorithm = SHAKE
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1
tc-grps  =system
ref_t =   400
; Pressure coupling is not  on
Pcoupl  = no
pcoupltype  = isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  400.0
gen_seed=  173529


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Re: [gmx-users] frezzing a bond : NPT and NVT simulations

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello
I am trying to constraints of a bond. I checked the distance using g_dist,
distance changes from 3.5 A to ~ 8.0A.
Can anyone tell why it changes.
Here I have pasted mdp file and itp file.


Maybe there's a bug in the interpretation of the constraints?  The combination 
of "constraints = none" + [constraints] directive should constrain the bond. 
Have you tried simply defining a [bonds] directive and using "constraints = 
all-bonds"?


-Justin


Nilesh
Solvent.itp
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
;  name  bond_typemasscharge   ptype  sigma  epsilon
  opls_997   PA 0   100.1.000   A0.4e-01  0.82890e-01
  opls_998   NE 0   100.   -1.000   A0.4e-01  0.82890e-01

[ bondtypes ]
; ij  func   b0  kb
  PANE  10.35   00

[ moleculetype ]
 ; name  nrexcl
 ABC 3

[ atoms ]
 ;   nr  typeresnr   residu  atomcgnrcharge mass
 1  opls_9971   ABCPA  11.  100.
 2  opls_9981   ABCNE  1   -1.  100.000

[ constraints ]
  1   2   10.35000


pr.mdp
title   =  cpeptid position restraining
cpp =  /usr/bin/cpp
constraints =  none
integrator  =  md
dt  =  0.001; ps !
nsteps  =  25  ; total 1.0 ps.
nstcomm =  1
nstxout =  10
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1.0
coulombtype = PME
vdwtype = cut-off
rcoulomb=  1.0
rvdw=  1.4
fourierspacing  = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
constraint-algorithm = SHAKE
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1
tc-grps  =system
ref_t =   400
; Pressure coupling is not  on
Pcoupl  = no
pcoupltype  = isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  400.0
gen_seed=  173529




--


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] frezzing a bond : NPT and NVT simulations

[Nilesh Dhumal]

constraints = all-bonds is working. I have solvent molecule for which I
don't want constraints on them. I can't use constraints = all-bonds for
simulation.
Nilesh

On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Hello
>> I am trying to constraints of a bond. I checked the distance using
>> g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone tell why it
>> changes. Here I have pasted mdp file and itp file.
>>
>
> Maybe there's a bug in the interpretation of the constraints?  The
> combination of "constraints = none" + [constraints] directive should
> constrain the bond. Have you tried simply defining a [bonds] directive and
> using "constraints = all-bonds"?
>
> -Justin
>
>
>> Nilesh
>> Solvent.itp
>> ; Derived from parsing of runfiles/alat.top.orig
>> [ defaults ]
>> ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
>> ;1   3   yes 0.5 0.5
>> ; comb-rule 3 is square-root sigma, the OPLSAA version
>>
>>
>> [ atomtypes ]
>> ; full atom descriptions are available in ffoplsaa.atp
>> ;  name  bond_typemasscharge   ptype  sigma  epsilon
>>  opls_997   PA 0   100.1.000   A0.4e-01
>> 0.82890e-01
>> opls_998   NE 0   100.   -1.000   A0.4e-01  0.82890e-01
>>
>> [ bondtypes ]
>> ; ij  func   b0  kb
>> PANE  10.35   00
>>
>>
>> [ moleculetype ]
>> ; name  nrexcl
>> ABC 3
>>
>>
>> [ atoms ]
>> ;   nr  typeresnr   residu  atomcgnrcharge mass
>> 1  opls_9971   ABCPA  11.  100.
>> 2  opls_9981   ABCNE  1   -1.  100.000
>>
>>
>> [ constraints ]
>> 1   2   10.35000
>>
>>
>>
>> pr.mdp title   =  cpeptid position restraining cpp
>> =  /usr/bin/cpp
>> constraints =  none integrator  =  md dt
>> =  0.001; ps !
>> nsteps  =  25  ; total 1.0 ps. nstcomm =
>> 1
>> nstxout =  10 nstvout =  1000 nstfout
>> =  0
>> nstlog  =  10 nstenergy   =  10 nstlist =
>> 10
>> ns_type =  grid rlist   =  1.0 coulombtype
>> = PME
>> vdwtype = cut-off rcoulomb=  1.0 rvdw
>> =  1.4
>> fourierspacing  = 0.12 fourier_nx   = 0 fourier_ny
>> = 0
>> fourier_nz   = 0 pme_order   = 4 ewald_rtol  =
>> 1e-5
>> optimize_fft= yes constraint-algorithm = SHAKE ; Berendsen
>> temperature coupling is on Tcoupl = v-rescale
>> tau_t = 0.1 tc-grps  =system ref_t =   400 ; Pressure coupling is not  on
>> Pcoupl  = no
>> pcoupltype  = isotropic tau_p   =  0.5 compressibility
>> =  4.5e-5
>> ref_p   =  1.0 ; Generate velocites is on at 300 K.
>> gen_vel =  yes gen_temp=  400.0 gen_seed
>> =  173529
>>
>>
>>
>
> --
> 
>
>
> 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
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>
>
>


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Re: [gmx-users] frezzing a bond : NPT and NVT simulations

[Justin A. Lemkul]

Nilesh Dhumal wrote:

constraints = all-bonds is working. I have solvent molecule for which I
don't want constraints on them. I can't use constraints = all-bonds for
simulation.


So you used g_dist to determine the distances with the setup shown below, but 
did you correct for PBC effects?  Is there a systematic increase in the distance 
between the two particles, or does it oscillate?


-Justin


Nilesh

On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote:


Nilesh Dhumal wrote:


Hello
I am trying to constraints of a bond. I checked the distance using
g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone tell why it
changes. Here I have pasted mdp file and itp file.


Maybe there's a bug in the interpretation of the constraints?  The
combination of "constraints = none" + [constraints] directive should
constrain the bond. Have you tried simply defining a [bonds] directive and
using "constraints = all-bonds"?

-Justin



Nilesh
Solvent.itp
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version


[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
;  name  bond_typemasscharge   ptype  sigma  epsilon
 opls_997   PA 0   100.1.000   A0.4e-01
0.82890e-01
opls_998   NE 0   100.   -1.000   A0.4e-01  0.82890e-01

[ bondtypes ]
; ij  func   b0  kb
PANE  10.35   00


[ moleculetype ]
; name  nrexcl
ABC 3


[ atoms ]
;   nr  typeresnr   residu  atomcgnrcharge mass
1  opls_9971   ABCPA  11.  100.
2  opls_9981   ABCNE  1   -1.  100.000


[ constraints ]
1   2   10.35000



pr.mdp title   =  cpeptid position restraining cpp
=  /usr/bin/cpp
constraints =  none integrator  =  md dt
=  0.001; ps !
nsteps  =  25  ; total 1.0 ps. nstcomm =
1
nstxout =  10 nstvout =  1000 nstfout
=  0
nstlog  =  10 nstenergy   =  10 nstlist =
10
ns_type =  grid rlist   =  1.0 coulombtype
= PME
vdwtype = cut-off rcoulomb=  1.0 rvdw
=  1.4
fourierspacing  = 0.12 fourier_nx   = 0 fourier_ny
= 0
fourier_nz   = 0 pme_order   = 4 ewald_rtol  =
1e-5
optimize_fft= yes constraint-algorithm = SHAKE ; Berendsen
temperature coupling is on Tcoupl = v-rescale
tau_t = 0.1 tc-grps  =system ref_t =   400 ; Pressure coupling is not  on
Pcoupl  = no
pcoupltype  = isotropic tau_p   =  0.5 compressibility
=  4.5e-5
ref_p   =  1.0 ; Generate velocites is on at 300 K.
gen_vel =  yes gen_temp=  400.0 gen_seed
=  173529




--



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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 Please don't post (un)subscribe requests to the list. Use the
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--


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


--
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Re: [gmx-users] frezzing a bond : NPT and NVT simulations

[Nilesh Dhumal]

Its oscillate between +/- 3-4 A.
If I freeze the distance by using freeze groups and dim in mdp file. It
works perfectly for NVT simulations. It oscillate for NPT simulation.
Nilesh

On Wed, August 4, 2010 9:56 pm, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> constraints = all-bonds is working. I have solvent molecule for which I
>>  don't want constraints on them. I can't use constraints = all-bonds
>> for simulation.
>
> So you used g_dist to determine the distances with the setup shown below,
> but did you correct for PBC effects?  Is there a systematic increase in
> the distance between the two particles, or does it oscillate?
>
> -Justin
>
>
>> Nilesh
>>
>>
>> On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote:
>>
>>
>>> Nilesh Dhumal wrote:
>>>
>>>
 Hello
 I am trying to constraints of a bond. I checked the distance using
 g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone tell why
 it changes. Here I have pasted mdp file and itp file.

>>> Maybe there's a bug in the interpretation of the constraints?  The
>>> combination of "constraints = none" + [constraints] directive should
>>> constrain the bond. Have you tried simply defining a [bonds]
>>> directive and using "constraints = all-bonds"?
>>>
>>> -Justin
>>>
>>>
>>>
 Nilesh
 Solvent.itp
 ; Derived from parsing of runfiles/alat.top.orig
 [ defaults ]
 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
 ;1   3   yes 0.5 0.5
 ; comb-rule 3 is square-root sigma, the OPLSAA version



 [ atomtypes ]
 ; full atom descriptions are available in ffoplsaa.atp
 ;  name  bond_typemasscharge   ptype  sigma
 epsilon opls_997   PA 0   100.1.000   A0.4e-01
 0.82890e-01
 opls_998   NE 0   100.   -1.000   A0.4e-01
 0.82890e-01


 [ bondtypes ]
 ; ij  func   b0  kb
 PANE  10.35   00



 [ moleculetype ]
 ; name  nrexcl
 ABC 3



 [ atoms ]
 ;   nr  typeresnr   residu  atomcgnrcharge mass
 1  opls_9971   ABCPA  11.  100.
 2  opls_9981   ABCNE  1   -1.  100.000



 [ constraints ]
 1   2   10.35000




 pr.mdp title   =  cpeptid position restraining cpp =
 /usr/bin/cpp
 constraints =  none integrator  =  md dt =  0.001
 ; ps !
 nsteps  =  25  ; total 1.0 ps. nstcomm
 =
 1
 nstxout =  10 nstvout =  1000 nstfout =  0
 nstlog  =  10 nstenergy   =  10 nstlist
 =
 10
 ns_type =  grid rlist   =  1.0 coulombtype =
 PME
 vdwtype = cut-off rcoulomb=  1.0 rvdw =  1.4
 fourierspacing  = 0.12 fourier_nx   = 0 fourier_ny =
 0
 fourier_nz   = 0 pme_order   = 4 ewald_rtol
 =
 1e-5
 optimize_fft= yes constraint-algorithm = SHAKE ;
 Berendsen
 temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps
 =system ref_t =   400 ; Pressure coupling is not  on
 Pcoupl  = no
 pcoupltype  = isotropic tau_p   =  0.5
 compressibility =  4.5e-5
 ref_p   =  1.0 ; Generate velocites is on at 300 K.
 gen_vel =  yes gen_temp=  400.0 gen_seed =
 173529




>>> --
>>> 
>>>
>>>
>>>
>>> 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
>>> 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
>>>
>>>
>>>
>>>
>>
>>
>>
>
> --
> 
>
>
> 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
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>  Please don'

Re: [gmx-users] frezzing a bond : NPT and NVT simulations

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Its oscillate between +/- 3-4 A.
If I freeze the distance by using freeze groups and dim in mdp file. It
works perfectly for NVT simulations. It oscillate for NPT simulation.


I don't know if there have been any changes (I don't see anything in the 
revision history), but as far as I know, freezing is incompatible with NPT 
ensembles due to the inability to scale the frozen coordinates.


-Justin


Nilesh

On Wed, August 4, 2010 9:56 pm, Justin A. Lemkul wrote:


Nilesh Dhumal wrote:


constraints = all-bonds is working. I have solvent molecule for which I
 don't want constraints on them. I can't use constraints = all-bonds
for simulation.

So you used g_dist to determine the distances with the setup shown below,
but did you correct for PBC effects?  Is there a systematic increase in
the distance between the two particles, or does it oscillate?

-Justin



Nilesh


On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote:



Nilesh Dhumal wrote:



Hello
I am trying to constraints of a bond. I checked the distance using
g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone tell why
it changes. Here I have pasted mdp file and itp file.


Maybe there's a bug in the interpretation of the constraints?  The
combination of "constraints = none" + [constraints] directive should
constrain the bond. Have you tried simply defining a [bonds]
directive and using "constraints = all-bonds"?

-Justin




Nilesh
Solvent.itp
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version



[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
;  name  bond_typemasscharge   ptype  sigma
epsilon opls_997   PA 0   100.1.000   A0.4e-01
0.82890e-01
opls_998   NE 0   100.   -1.000   A0.4e-01
0.82890e-01


[ bondtypes ]
; ij  func   b0  kb
PANE  10.35   00



[ moleculetype ]
; name  nrexcl
ABC 3



[ atoms ]
;   nr  typeresnr   residu  atomcgnrcharge mass
1  opls_9971   ABCPA  11.  100.
2  opls_9981   ABCNE  1   -1.  100.000



[ constraints ]
1   2   10.35000




pr.mdp title   =  cpeptid position restraining cpp =
/usr/bin/cpp
constraints =  none integrator  =  md dt =  0.001
; ps !
nsteps  =  25  ; total 1.0 ps. nstcomm
=
1
nstxout =  10 nstvout =  1000 nstfout =  0
nstlog  =  10 nstenergy   =  10 nstlist
=
10
ns_type =  grid rlist   =  1.0 coulombtype =
PME
vdwtype = cut-off rcoulomb=  1.0 rvdw =  1.4
fourierspacing  = 0.12 fourier_nx   = 0 fourier_ny =
0
fourier_nz   = 0 pme_order   = 4 ewald_rtol
=
1e-5
optimize_fft= yes constraint-algorithm = SHAKE ;
Berendsen
temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps
=system ref_t =   400 ; Pressure coupling is not  on
Pcoupl  = no
pcoupltype  = isotropic tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0 ; Generate velocites is on at 300 K.
gen_vel =  yes gen_temp=  400.0 gen_seed =
173529





--




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
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








--



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
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









--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
j

Re: [gmx-users] frezzing a bond : NPT and NVT simulations

[Nilesh Dhumal]

Then it looks there is bug ater define the constraints in itp file, bond
distance changes.


On Wed, August 4, 2010 10:22 pm, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Its oscillate between +/- 3-4 A.
>> If I freeze the distance by using freeze groups and dim in mdp file. It
>> works perfectly for NVT simulations. It oscillate for NPT simulation.
>
> I don't know if there have been any changes (I don't see anything in the
> revision history), but as far as I know, freezing is incompatible with NPT
>  ensembles due to the inability to scale the frozen coordinates.
>
> -Justin
>
>
>> Nilesh
>>
>>
>> On Wed, August 4, 2010 9:56 pm, Justin A. Lemkul wrote:
>>
>>
>>> Nilesh Dhumal wrote:
>>>
>>>
 constraints = all-bonds is working. I have solvent molecule for
 which I don't want constraints on them. I can't use constraints =
 all-bonds for simulation.
>>> So you used g_dist to determine the distances with the setup shown
>>> below, but did you correct for PBC effects?  Is there a systematic
>>> increase in the distance between the two particles, or does it
>>> oscillate?
>>>
>>> -Justin
>>>
>>>
>>>
 Nilesh



 On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote:



> Nilesh Dhumal wrote:
>
>
>
>> Hello
>> I am trying to constraints of a bond. I checked the distance
>> using g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone
>> tell why it changes. Here I have pasted mdp file and itp file.
>>
> Maybe there's a bug in the interpretation of the constraints?
> The
> combination of "constraints = none" + [constraints] directive
> should constrain the bond. Have you tried simply defining a
> [bonds]
> directive and using "constraints = all-bonds"?
>
> -Justin
>
>
>
>
>> Nilesh
>> Solvent.itp
>> ; Derived from parsing of runfiles/alat.top.orig
>> [ defaults ]
>> ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
>> ;1   3   yes 0.5 0.5
>> ; comb-rule 3 is square-root sigma, the OPLSAA version
>>
>>
>>
>>
>> [ atomtypes ]
>> ; full atom descriptions are available in ffoplsaa.atp
>> ;  name  bond_typemasscharge   ptype  sigma
>> epsilon opls_997   PA 0   100.1.000   A
>> 0.4e-01
>> 0.82890e-01
>> opls_998   NE 0   100.   -1.000   A0.4e-01
>> 0.82890e-01
>>
>>
>>
>> [ bondtypes ]
>> ; ij  func   b0  kb
>> PANE  10.35   00
>>
>>
>>
>>
>> [ moleculetype ]
>> ; name  nrexcl
>> ABC 3
>>
>>
>>
>>
>> [ atoms ]
>> ;   nr  typeresnr   residu  atomcgnrcharge mass
>> 1  opls_9971   ABCPA  11.
>> 100.
>> 2  opls_9981   ABCNE  1   -1.
>> 100.000
>>
>>
>>
>>
>> [ constraints ]
>> 1   2   10.35000
>>
>>
>>
>>
>>
>> pr.mdp title   =  cpeptid position restraining cpp
>> =
>> /usr/bin/cpp
>> constraints =  none integrator  =  md dt =
>> 0.001
>> ; ps !
>> nsteps  =  25  ; total 1.0 ps. nstcomm =
>> 1
>> nstxout =  10 nstvout =  1000 nstfout =
>> 0
>> nstlog  =  10 nstenergy   =  10 nstlist =
>> 10
>> ns_type =  grid rlist   =  1.0
>> coulombtype = PME
>> vdwtype = cut-off rcoulomb=  1.0 rvdw =
>> 1.4
>> fourierspacing  = 0.12 fourier_nx   = 0
>> fourier_ny = 0
>> fourier_nz   = 0 pme_order   = 4 ewald_rtol =
>>  1e-5
>> optimize_fft= yes constraint-algorithm = SHAKE ;
>> Berendsen
>> temperature coupling is on Tcoupl = v-rescale tau_t = 0.1
>> tc-grps =system ref_t =   400 ; Pressure coupling is not  on
>> Pcoupl  = no
>> pcoupltype  = isotropic tau_p   =  0.5
>> compressibility =  4.5e-5 ref_p   =  1.0 ; Generate
>> velocites is on at 300 K. gen_vel =  yes gen_temp
>> =  400.0 gen_seed =
>> 173529
>>
>>
>>
>>
>>
> --
> 
>
>
>
>
> 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
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archi

Re: [gmx-users] frezzing a bond : NPT and NVT simulations

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Then it looks there is bug ater define the constraints in itp file, bond
distance changes.




Then file a bugzilla so the developers can either confirm the bug and fix it, or 
provide an explanation as to what is going on.


-Justin


On Wed, August 4, 2010 10:22 pm, Justin A. Lemkul wrote:


Nilesh Dhumal wrote:


Its oscillate between +/- 3-4 A.
If I freeze the distance by using freeze groups and dim in mdp file. It
works perfectly for NVT simulations. It oscillate for NPT simulation.

I don't know if there have been any changes (I don't see anything in the
revision history), but as far as I know, freezing is incompatible with NPT
 ensembles due to the inability to scale the frozen coordinates.

-Justin



Nilesh


On Wed, August 4, 2010 9:56 pm, Justin A. Lemkul wrote:



Nilesh Dhumal wrote:



constraints = all-bonds is working. I have solvent molecule for
which I don't want constraints on them. I can't use constraints =
all-bonds for simulation.

So you used g_dist to determine the distances with the setup shown
below, but did you correct for PBC effects?  Is there a systematic
increase in the distance between the two particles, or does it
oscillate?

-Justin




Nilesh



On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote:




Nilesh Dhumal wrote:




Hello
I am trying to constraints of a bond. I checked the distance
using g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone
tell why it changes. Here I have pasted mdp file and itp file.


Maybe there's a bug in the interpretation of the constraints?
The
combination of "constraints = none" + [constraints] directive
should constrain the bond. Have you tried simply defining a
[bonds]
directive and using "constraints = all-bonds"?

-Justin





Nilesh
Solvent.itp
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version




[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
;  name  bond_typemasscharge   ptype  sigma
epsilon opls_997   PA 0   100.1.000   A
0.4e-01
0.82890e-01
opls_998   NE 0   100.   -1.000   A0.4e-01
0.82890e-01



[ bondtypes ]
; ij  func   b0  kb
PANE  10.35   00




[ moleculetype ]
; name  nrexcl
ABC 3




[ atoms ]
;   nr  typeresnr   residu  atomcgnrcharge mass
1  opls_9971   ABCPA  11.
100.
2  opls_9981   ABCNE  1   -1.
100.000




[ constraints ]
1   2   10.35000





pr.mdp title   =  cpeptid position restraining cpp
=
/usr/bin/cpp
constraints =  none integrator  =  md dt =
0.001
; ps !
nsteps  =  25  ; total 1.0 ps. nstcomm =
1
nstxout =  10 nstvout =  1000 nstfout =
0
nstlog  =  10 nstenergy   =  10 nstlist =
10
ns_type =  grid rlist   =  1.0
coulombtype = PME
vdwtype = cut-off rcoulomb=  1.0 rvdw =
1.4
fourierspacing  = 0.12 fourier_nx   = 0
fourier_ny = 0
fourier_nz   = 0 pme_order   = 4 ewald_rtol =
 1e-5
optimize_fft= yes constraint-algorithm = SHAKE ;
Berendsen
temperature coupling is on Tcoupl = v-rescale tau_t = 0.1
tc-grps =system ref_t =   400 ; Pressure coupling is not  on
Pcoupl  = no
pcoupltype  = isotropic tau_p   =  0.5
compressibility =  4.5e-5 ref_p   =  1.0 ; Generate
velocites is on at 300 K. gen_vel =  yes gen_temp
=  400.0 gen_seed =
173529






--





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
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







--




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
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 th

Re: [gmx-users] Problem in pullx file

[Aswathy]

On Wed, Aug 4, 2010 at 4:31 PM, Justin A. Lemkul  wrote:

>
>
> Aswathy wrote:
>
>> Dear Gromacs users,
>>
>> I am doing SMD of a ligand pathway, and then want ot do the PMF analysis.
>> Initially I pulled the ligand from extra to intracellular side of the
>> protein. The pull code used are given below.
>>
>> pull = umbrella
>> pull_geometry= distance
>> pull_dim =  N N Y
>> pull_start   = yes
>> pull_nstxout =  10
>> pull_nstfout =  10
>> pull_ngroups =  1
>> pull_group0  =  r_57
>> pull_group1  =  r_C1
>> pull_rate1   =  0.005
>> pull_k1  =  1000
>>
>> here group0 is one residue at the extracellular region and r_C1 is the
>> side chain Carbon atom of the ligand.
>>
>> My question is , the total length of the channel is almost 40 Angstrom and
>> as per my knowledge, when we did the pulling the pullx file will give the
>> coordinate of the ligand through the channel.
>>
>
> Not quite.  Look at the data labels in the .xvg file.  The pullx file
> contains the coordinates (in all of the pull directions) for the reference
> group, and then the distance between the reference and the pull group along
> all pull axes.

I am still confused.   I have measured the distance between the reference
group(residue outside) to the other end of the channel. that is around
40Angstrom. if so, 1dz should give around 40 Angstrom? Because  once the
pulling completed,  the distance between group0 and group1 , should be equal
to the length of the channel.

Sorry that i am repeating the same query, i think I am still preconceived
about this. Otherwise could you please suggest some good tutorial for the
same . I will read that.



>
>  Even though ligand reaches the opposite end of the channel, in pullx file
>> I am getting around 19 Angstrom in total.
>>
>> Again I calculate the g_dist of the ligand and the center of the channel,
>> it shows around 40 Ang in total . Please find the links provided
>>
>>
> You're measuring two different things.  The pullx distance is given
> relative to your pull_group0, which you said is a residue on one side of the
> channel.  Then you're using g_dist to measure to the center of the channel.
>
>  Am I misunderstanding anything about the pullx file.
>>
>> Could you please suggest me where thing get wrong?
>>
>>
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en<
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en
>> >
>>
>>
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en<
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en
>> >
>>
>>
> For some reason these documents are inaccessible.  It is probably better to
> use a site like photobucket and post actual images.  Google is great, but
> not everyone has an account and I've also been told that their usage
> agreement is troubling, in that anything you upload to Google Docs becomes
> property of Google.  Not something I've looked into, but I don't ever post
> my research data there.
>
>

> -Justin
>
>
>> Thank you,
>> --
>> -Aswathy
>>
>>
> --
> 
>
> 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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-- 
Aswathy
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