[gmx-users] R: gmx-users Digest, Vol 82, Issue 113

2011-02-15 Thread Anna Marabotti
Tsjerk, 
sure, I meant exactly what you are saying, by my english is not as good as
yours...
Thank you again
Anna

--

Message: 1
Date: Mon, 14 Feb 2011 17:36:27 +0100
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [gmx-users] R: visualizing more than  residues...
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
AANLkTi=PB=SJMJVKNxB75zAzZMYM7CPmiuH=fravp...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1

Hi Anna,

I didn't say the PDB format does not allow more than  residues. It
does. But it does not allow numbers higher than . Thus, with more
residues, it will start counting over.

Cheers,

Tsjerk

On Mon, Feb 14, 2011 at 4:52 PM, Anna Marabotti
anna.marabo...@isa.cnr.it wrote:
 Dear Tsjerk,
 thank you very much. I really didn't know that the PDB format does not
allow
 more than  residues (in fact, it is the first time I have such a big
 system to manage). I will follow your suggestions trying to solve the
 problem with chain identifiers.
 Many thanks and best regards
 Anna

 --

 Message: 6
 Date: Mon, 14 Feb 2011 16:43:29 +0100
 From: Tsjerk Wassenaar tsje...@gmail.com
 Subject: Re: [gmx-users] visualizing more than  residues
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID:
AANLkTikVM8kt1F5p3=4o9s9kjdgvvk-pxkznro6an...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 Hi Anna,

 The 'problem' is the PDB file format. It is a fixed-width format that
 does not allow for residue numbers with more than 4 digits. Both VMD
 and PyMOL do not have problems reading structures with more residues,
 but they will choke if you renumber the residues, giving numbers with
 five or more digits. It breaks the file format. It may be a bit
 troublesome making selections if you have ambiguous residue
 identifiers, but that's the way it is with PDB files. You can try to
 be creative with chain identifiers and segment identifiers to give all
 residues unique markers.

 Cheers,

 Tsjerk

 On Mon, Feb 14, 2011 at 4:29 PM, Anna Marabotti
 anna.marabo...@isa.cnr.it wrote:
 Dear gmx-users,
 I have a system formed by protein+ligand+lipid bilayer that accounts for
 about 10500 residues (56000 atoms). It seems to me that it is not
possible
 to visualize correctly such a large system with Pymol or VMD, because it
 seems that the max number of residues that I can manage with both
programs
 is exactly . Moreover, it's not only a visualization problem, since I
 also had several problems trying to use Pymol or VMD to create the system
 in
 which the protein+ligand is correctly oriented with respect to the lipid
 bilayer, to proceed further with g_membed. I had several problems in
 saving
 the .pdb file (after the th residue, the numbering restarted from 0;
 when I manually corrected this prroblem and re-numbered the file, I
opened
 it with VMD and Python and found some aberrant visualization of the water
 molecules exceeding the number of . At last, I decided to remove the
 exceeding waters).
 I know that this is a Gromacs user list, not a Pymol or VMD user list,
but
 since it seems to me that these two programs are generally considered as
a
 graphical interface with respect to Gromacs, I'd like to know how you
 folks manage this problem without removing residues. I searched for some
 hints in the gmx-user list and in Google but I didn't find anything.
 Thank you very much and sorry for this off-topic question.
 Anna Marabotti

 __
 Anna Marabotti, Ph.D.
 Laboratory of Bioinformatics and Computational Biology
 Institute of Food Science - CNR
 Via Roma, 64
 83100 Avellino
 Phone: +39 0825 299651
 Fax: +39 0825 781585
 E-mail: amarabo...@isa.cnr.it
 Skype account: annam1972
 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm

 When a man with a gun meets a man with a pen, the man with the gun is a
 dead man

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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] number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology

2011-02-15 Thread Parul tew
Hi all,
first I would like to thank Justin A. Lemkul for the tutorials
provided which are very helpful for new users like me.
I am doing a membrane protein simulation and now doing packing of the
lipids around the protein. I had run the inflategro.pl script and
and now I am facing a problem doing energy minimization of my inflated
system (contatining protein and the lipid membrane) using grompp.
I have updated my topology file accordingly ie removed the spc.itp,
ions.itp it now only contains protein and dppc
the protein is of 3881 atoms but after updating my topolgy it still
gives the following error:
Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 9331)
 does not match topology (topol.top, 10281)
As i understand it could be because of the deleted lipids of the
system, if so how can I know the deleted number of lipids.

My topology file looks like
-
;
;   This is your topology file
;   protein
;
; Include forcefield parameters
#include ffG53a6_lipid.itp

[ moleculetype ]
; Namenrexcl
Protein_A   3

[ atoms ]
.
.
.
.
; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include strong_posre.itp
#endif

; Include DPPC chain topology
#include dppc.itp


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


[ system ]
; Name
protein
128-Lipid DPPC Bilayer

[ molecules ]
; Compound#mols
Protein_A   1
DPPC128


thank you,
Parul Tewatia
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[gmx-users] ffamber03 top file problem

2011-02-15 Thread gromacs564
Dear All:
 I want to obtain a top file for protein with ffamber03 force field,and correct 
some bonds and angles parameter.
 I added a new atom type HD(D2O) in ffamber03  [ atomtypes ], so I added some 
HD parameters in ffbond.itp、atomtypes.atp and ffnonbond.itp files,the output of 
the program indicate:


---
Program grompp_m, VERSION 4.5.1
Source code file: toppush.c, line: 1631

Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Bond.
For more information and tips for troubleshooting, please check the GROM···




I added some bonds and angles parameters like this:
··
; residue  44 ASN rtp ASN  q  0.0
   664  N 44ASN  N664  -0.430106  14.01   ; qtot 
4.57
   665 HD44ASN HD665   0.250466  2.016   ; qtot 
4.824
   666 CT 44ASN CA666   0.044609  12.01   ; qtot 
4.869
···
[ bonds ]
;  aiaj functc0c1c2c3
···
  676   678 1 
  678   679 1 0.10115 
  678   680 1 
  680   681 1 
···
[ angles ]
;  aiajak functc0c1c2c3

  648   650   652 1 
  651   650   652 1 115.149 
  650   652   653 1 
  650   652   654 1 


Any help will highly appreciated!-- 
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Re: [gmx-users] number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology

2011-02-15 Thread Terry
On Tue, Feb 15, 2011 at 5:25 PM, Parul tew parul...@gmail.com wrote:

 Hi all,
 first I would like to thank Justin A. Lemkul for the tutorials provided which 
 are very helpful for new users like me.
 I am doing a membrane protein simulation and now doing packing of the lipids 
 around the protein. I had run the inflategro.pl script and

 and now I am facing a problem doing energy minimization of my inflated system 
 (contatining protein and the lipid membrane) using grompp.
 I have updated my topology file accordingly ie removed the spc.itp, ions.itp 
 it now only contains protein and dppc

 the protein is of 3881 atoms but after updating my topolgy it still gives the 
 following error:
 Fatal error:
 number of coordinates in coordinate file (system_inflated.gro, 9331)
  does not match topology (topol.top, 10281)

 As i understand it could be because of the deleted lipids of the system, if 
 so how can I know the deleted number of lipids.

 My topology file looks like
 -

 ;
 ; This is your topology file
 ; protein
 ;
 ; Include forcefield parameters
 #include ffG53a6_lipid.itp

 [ moleculetype ]
 ; Namenrexcl
 Protein_A   3

 [ atoms ]
 .
 .
 .
 .
 ; Strong position restraints for InflateGRO
 #ifdef STRONG_POSRES
 #include strong_posre.itp
 #endif

 ; Include DPPC chain topology
 #include dppc.itp


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


 [ system ]
 ; Name
 protein
 128-Lipid DPPC Bilayer

 [ molecules ]
 ; Compound#mols
 Protein_A   1
 DPPC128


After insertion, there are probably several DPPC molecules removed. Check
outputs from inflategro.pl, then update accordingly.

Terry



 thank you,
 Parul Tewatia



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Re: [gmx-users] g_hbond and 4.5.2 version

2011-02-15 Thread Erik Marklund

Justin A. Lemkul skrev 2011-02-09 23.03:



Zuzana Benkova wrote:

Dear GROMACS users,

I have used g_hbond of version 4.5.2 to analyze number of hydrogen 
bonds in water. I got the average  number per time frame and number 
of water oxygen atoms equal to 0.839. When I used g_hbond of version 
4.0.7 I got 1.677, which is twice the former value. TIP3P model 
predicts over 3 hydrogen bonds per one water molecule. I am a bit 
puzzled. If I multiply the digit from version 4.0.7. by 2 I get the 
expected number. That is why I supposed that the number of 1.677 
means per one water oxygen and  per one water molecule means 2x1.677 
since two water molecules participate at one hydrogen bond.
However, I do not know yet if my interpretation is correct and how to 
interpret the number obtained by version 4.5.2.

I would appreciate any help. Thank you in advance.



Try pulling the latest stable development version.  This issue was 
reported in 4.5.1:


http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html

but not fixed until after 4.5.3 was released:

http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html

-Justin


Greetings
Zuzana



Are people who are reporting this error using a triclinic boxes or 
cuboid boxes. That information may help my bugfixing.


--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] ffamber03 top file problem

2011-02-15 Thread X.Periole
Check the topology section in the gromacs manual. You'll find the format you should use for bonds, angles etc.On 15-02-11, gromacs564  gromacs...@126.com wrote:Dear All: I want to obtain a top file for protein with ffamber03 force field,and correct some bonds and angles parameter. I added a new atom type HD(D2O) in ffamber03  [ atomtypes ], so I added some HD parameters in ffbond.itp、atomtypes.atp and ffnonbond.itp files,the output of the program indicate:---Program grompp_m, VERSION 4.5.1Source code file: toppush.c, line: 1631Fatal error:Incorrect number of parameters - found 1, expected 2 or 4 for Bond.For more information and tips for troubleshooting, please check the GROM···I added some bonds and angles parameters like this:··; residue  44 ASN rtp ASN  q  0.0   664          N     44    ASN      N    664  -0.430106      14.01   ; qtot 4.57   665         HD    44    ASN     HD    665   0.250466      2.016   ; qtot 4.824   666         CT     44    ASN     CA    666   0.044609      12.01   ; qtot 4.869···[ bonds ];  ai    aj funct            c0            c1            c2            c3···  676   678     1   678   679     1     0.10115   678   680     1   680   681     1 ···[ angles ];  ai    aj    ak funct            c0            c1            c2            c3  648   650   652     1   651   650   652     1     115.149   650   652   653     1   650   652   654     1 Any help will highly appreciated!
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[gmx-users] Whereabouts of NDLP???

2011-02-15 Thread ifat shub
Hi,
Was this server ever reestablished?
Is there a link which I can use to calculate the optimal box?
Thanks,
Ifat* *




Hi Alan,

Unfortunately there have been server problems (severe hacking) in
Groningen some while ago, and the NDLP server was terminated. But,
we're right about to reestablish an improved server here in Utrecht.
This server will be much faster, seconds rather than hours - the
optimal packing for the GroEL/GroES complex (60k atoms) took somewhere
around a minute maybe, and will also provide an optimal simulation
cell for a given ensemble (NMR, ENM, MD). In addition, the principal
author at the time was not in favour of adding the program to the
Gromacs suite, and there were some depency issues as well. I don't see
why the new program should not also become incorporated in Gromacs.

That being said, we still need a bit of time here to wrap things up.
In the mean time, as long as I'm not run over by requests, you can
send me a (few) structure(s) off the list, and I'll be happy to
calculate the packing.

Best,

Tsjerk

On Sat, Mar 15, 2008 at 5:15 AM, Alan Chen achen at
artsci.wustl.eduhttp://www.gromacs.org/mailman/listinfo/gmx-users
wrote:
* Hi All:
**
**  I recently came across  Tsjerk Wassenaar's JCC papers about  a
**  Near-Densest Lattice Packing
**  algorithm for choosing the optimal triclinic box for a non-spherical
**  macromolecule.
**
http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Wassenaar:Tsjerk_A=.html
**
**  I have a rather cylindrical  RNA I am studying right now, and I wanted
**  to try out NDLP only the website referred to by the paper
**  no longer exists, and I can't find any reference to NDLP on the new
**  rug.nl homepage nor does google give me any clues. Does
**  anyone know as to this package's current whereabouts?
**
**  Thanks,
**  Alan Chen
**
**
**  ___
**  gmx-users mailing listgmx-users at
gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-users
**  http://www.gromacs.org/mailman/listinfo/gmx-users
**  Please search the archive at http://www.gromacs.org/search before
posting!
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**
*


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Whereabouts of NDLP???

2011-02-15 Thread Tsjerk Wassenaar
Hi Ifat,

It has: http://haddock.chem.uu.nl/Squeeze/

Cheers,

Tsjerk

On Tue, Feb 15, 2011 at 12:46 PM, ifat shub shubi...@gmail.com wrote:
 Hi,
 Was this server ever reestablished?
 Is there a link which I can use to calculate the optimal box?
 Thanks,
 Ifat




 Hi Alan,

 Unfortunately there have been server problems (severe hacking) in
 Groningen some while ago, and the NDLP server was terminated. But,
 we're right about to reestablish an improved server here in Utrecht.
 This server will be much faster, seconds rather than hours - the
 optimal packing for the GroEL/GroES complex (60k atoms) took somewhere
 around a minute maybe, and will also provide an optimal simulation
 cell for a given ensemble (NMR, ENM, MD). In addition, the principal
 author at the time was not in favour of adding the program to the
 Gromacs suite, and there were some depency issues as well. I don't see
 why the new program should not also become incorporated in Gromacs.

 That being said, we still need a bit of time here to wrap things up.
 In the mean time, as long as I'm not run over by requests, you can
 send me a (few) structure(s) off the list, and I'll be happy to
 calculate the packing.

 Best,

 Tsjerk

 On Sat, Mar 15, 2008 at 5:15 AM, Alan Chen achen at artsci.wustl.edu
 wrote:
 Hi All:

  I recently came across  Tsjerk Wassenaar's JCC papers about  a
  Near-Densest Lattice Packing
  algorithm for choosing the optimal triclinic box for a non-spherical
  macromolecule.

 http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Wassenaar:Tsjerk_A=.html

  I have a rather cylindrical  RNA I am studying right now, and I wanted
  to try out NDLP only the website referred to by the paper
  no longer exists, and I can't find any reference to NDLP on the new
  rug.nl homepage nor does google give me any clues. Does
  anyone know as to this package's current whereabouts?

  Thanks,
  Alan Chen


  ___
  gmx-users mailing list    gmx-users at gromacs.org
  http://www.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-request at gromacs.org.
  Can't post? Read http://www.gromacs.org/mailing_lists/users.php




 --
 Tsjerk A. Wassenaar, Ph.D.
 Junior UD (post-doc)
 Biomolecular NMR, Bijvoet Center
 Utrecht University
 Padualaan 8
 3584 CH Utrecht
 The Netherlands
 P: +31-30-2539931
 F: +31-30-2537623



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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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Re: [gmx-users] g_hbond and 4.5.2 version

2011-02-15 Thread Zuzana Benkova
Hello Justin, I was using cubic boxes. GreetingsZuzanaOn 02/15/11, Erik Marklund  er...@xray.bmc.uu.se wrote:Justin A. Lemkul skrev 2011-02-09 23.03:Zuzana Benkova wrote:Dear GROMACS users,I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average  number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and  per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond.However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2.I would appreciate any help. Thank you in advance.Try pulling the latest stable development version.  This issue was reported in 4.5.1:http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.htmlbut not fixed until after 4.5.3 was released:http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html-JustinGreetingsZuzanaAre people who are reporting this error using a triclinic boxes or cuboid boxes. That information may help my bugfixing.-- ---Erik Marklund, PhD studentDept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596,    75124 Uppsala, Swedenphone:    +46 18 471 4537    fax: +46 18 511 755er...@xray.bmc.uu.se    http://folding.bmc.uu.se/-- gmx-users mailing list    gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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[gmx-users] g_dipole

2011-02-15 Thread Nilesh Dhumal
Hello,

I want to calculate dipole autocorrelation function without normalization.
How can I calculate dipole autocorrelation function without normalization.
I am using gromacs 4.0.7 version.

Thanks
Nilesh

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Re: [gmx-users] g_dipole

2011-02-15 Thread David van der Spoel

On 2011-02-15 13.51, Nilesh Dhumal wrote:

Hello,

I want to calculate dipole autocorrelation function without normalization.
How can I calculate dipole autocorrelation function without normalization.
I am using gromacs 4.0.7 version.

Thanks
Nilesh


g_dipoles -h


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Re: [gmx-users] g_dipole

2011-02-15 Thread Nilesh Dhumal
I used following command.

g_dipoles -f 6.trr -s 6.tpr -corr total -normalize NO -c

Its not working.

Its giving following error
Invalid command line argument:
NO

Nilesh


On Tue, February 15, 2011 7:57 am, David van der Spoel wrote:
 On 2011-02-15 13.51, Nilesh Dhumal wrote:

 Hello,


 I want to calculate dipole autocorrelation function without
 normalization. How can I calculate dipole autocorrelation function
 without normalization. I am using gromacs 4.0.7 version.


 Thanks
 Nilesh


 g_dipoles -h


 --
 David van der Spoel, Ph.D., Professor of Biology
 Dept. of Cell  Molec. Biol., Uppsala University.
 Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
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Re: [gmx-users] g_dipole

2011-02-15 Thread Justin A. Lemkul



Nilesh Dhumal wrote:

I used following command.

g_dipoles -f 6.trr -s 6.tpr -corr total -normalize NO -c

Its not working.

Its giving following error
Invalid command line argument:
NO



With arguments listed as -[no]option, the proper argument is -nooption so in 
your case, -nonormalize.


-Justin


Nilesh


On Tue, February 15, 2011 7:57 am, David van der Spoel wrote:

On 2011-02-15 13.51, Nilesh Dhumal wrote:


Hello,


I want to calculate dipole autocorrelation function without
normalization. How can I calculate dipole autocorrelation function
without normalization. I am using gromacs 4.0.7 version.


Thanks
Nilesh



g_dipoles -h


--
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Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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Virginia Tech
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[gmx-users] NVE simulation

2011-02-15 Thread Thomas Koller
Hello!

Is it possible to run NVE simulations insteed of NVT or NPT in Gromacs?

Thomas
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Re: [gmx-users] NVE simulation

2011-02-15 Thread Justin A. Lemkul



Thomas Koller wrote:

Hello!

Is it possible to run NVE simulations insteed of NVT or NPT in Gromacs?


Yes.

http://www.gromacs.org/Documentation/Terminology/NVE

-Justin



Thomas


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[gmx-users] Umbrella sampling windows

2011-02-15 Thread Susana Tomasio
Hi all,

I'm running umbrella sampling of an ion through a lipid bilayer with gromacs
4.5.1.
I used g_wham to create the histograms of the configurations within the
umbrella sampling windows (1 Angstrom interval).
I did not get a sufficient overlap between the windows, so I was wodering
which is the better way of increasing the sampling:  to
 include additional windows in the regions where there is no overlap or to
increase the force constant ?
If I increase the force constant can I continue the simulation with the new
constant or do I have to start again?
I used a force contant of 3000 kJ mol^-1 nm^-2.

Thank you in advance,

Susana
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Re: [gmx-users] Umbrella sampling windows

2011-02-15 Thread Justin A. Lemkul



Susana Tomasio wrote:

Hi all,

I'm running umbrella sampling of an ion through a lipid bilayer with 
gromacs 4.5.1.
I used g_wham to create the histograms of the configurations within the 
umbrella sampling windows (1 Angstrom interval).
I did not get a sufficient overlap between the windows, so I was 
wodering which is the better way of increasing the sampling:  to
 include additional windows in the regions where there is no overlap or 
to increase the force constant ?


If you increase the force constant, you will make the distributions narrower, 
and thus I would expect the overlap would be worse.  Insufficient simulation 
length could be an issue, too, but you haven't said how long your simulations are.


If I increase the force constant can I continue the simulation with the 
new constant or do I have to start again?


You'd have to start over again, I'd think, otherwise if you pass one .tpr file 
to g_wham per window, it will contain incorrect information that will mess up 
the calculations.



I used a force contant of 3000 kJ mol^-1 nm^-2.



That seems somewhat high, but there are no hard and fast rules about these 
things, I don't think.  You probably want either (1) a lower force constant or 
(2) more windows along your reaction coordinate.  Option (2) seems to be more 
efficient, since you don't have to re-do your simulations, you can just run some 
more.


-Justin


Thank you in advance,

Susana



--


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 windows

2011-02-15 Thread Laura Kingsley

Hello Susana,

I agree with Justin, 3000 kj/molnm2 seems pretty high. I've been using 
about a 1000kj/molnm2 force constant with window separation of about 
0.8, that seems to work well for my system.


-Laura

On 02/15/2011 09:51 AM, Susana Tomasio wrote:

Hi all,

I'm running umbrella sampling of an ion through a lipid bilayer with 
gromacs 4.5.1.
I used g_wham to create the histograms of the configurations within 
the umbrella sampling windows (1 Angstrom interval).
I did not get a sufficient overlap between the windows, so I was 
wodering which is the better way of increasing the sampling:  to
 include additional windows in the regions where there is no overlap 
or to increase the force constant ?
If I increase the force constant can I continue the simulation with 
the new constant or do I have to start again?

I used a force contant of 3000 kJ mol^-1 nm^-2.

Thank you in advance,

Susana


--
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Purdue University
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Re: [gmx-users] Umbrella sampling windows

2011-02-15 Thread Susana Tomasio
Thank you very much for your help.
I've run my simulations for 80 ns.
I will add more windows along the reaction coordinate.

Thank you,

Susana


On Tue, Feb 15, 2011 at 2:56 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Susana Tomasio wrote:

 Hi all,

 I'm running umbrella sampling of an ion through a lipid bilayer with
 gromacs 4.5.1.
 I used g_wham to create the histograms of the configurations within the
 umbrella sampling windows (1 Angstrom interval).
 I did not get a sufficient overlap between the windows, so I was wodering
 which is the better way of increasing the sampling:  to
  include additional windows in the regions where there is no overlap or to
 increase the force constant ?


 If you increase the force constant, you will make the distributions
 narrower, and thus I would expect the overlap would be worse.  Insufficient
 simulation length could be an issue, too, but you haven't said how long your
 simulations are.


  If I increase the force constant can I continue the simulation with the
 new constant or do I have to start again?


 You'd have to start over again, I'd think, otherwise if you pass one .tpr
 file to g_wham per window, it will contain incorrect information that will
 mess up the calculations.


  I used a force contant of 3000 kJ mol^-1 nm^-2.


 That seems somewhat high, but there are no hard and fast rules about these
 things, I don't think.  You probably want either (1) a lower force constant
 or (2) more windows along your reaction coordinate.  Option (2) seems to be
 more efficient, since you don't have to re-do your simulations, you can just
 run some more.

 -Justin


  Thank you in advance,

 Susana


 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | +15402319080(540) 231-9080 +15402319080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
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Re: [gmx-users] Umbrella sampling windows

2011-02-15 Thread Susana Tomasio
Thank you very much for your help.
I've run my simulations for 80 ns.
I will add more windows along the reaction coordinate.

Thank you,

Susana


On Tue, Feb 15, 2011 at 2:56 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Susana Tomasio wrote:

 Hi all,

 I'm running umbrella sampling of an ion through a lipid bilayer with
 gromacs 4.5.1.
 I used g_wham to create the histograms of the configurations within the
 umbrella sampling windows (1 Angstrom interval).
 I did not get a sufficient overlap between the windows, so I was wodering
 which is the better way of increasing the sampling:  to
  include additional windows in the regions where there is no overlap or to
 increase the force constant ?


 If you increase the force constant, you will make the distributions
 narrower, and thus I would expect the overlap would be worse.  Insufficient
 simulation length could be an issue, too, but you haven't said how long your
 simulations are.


  If I increase the force constant can I continue the simulation with the
 new constant or do I have to start again?


 You'd have to start over again, I'd think, otherwise if you pass one .tpr
 file to g_wham per window, it will contain incorrect information that will
 mess up the calculations.


  I used a force contant of 3000 kJ mol^-1 nm^-2.


 That seems somewhat high, but there are no hard and fast rules about these
 things, I don't think.  You probably want either (1) a lower force constant
 or (2) more windows along your reaction coordinate.  Option (2) seems to be
 more efficient, since you don't have to re-do your simulations, you can just
 run some more.

 -Justin


  Thank you in advance,

 Susana


 --
 

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | +15402319080(540) 231-9080 +15402319080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
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[gmx-users] top2psf.pl issue: trying to use vmd w/ MARTINI protein

2011-02-15 Thread John
Hello,

While trying to visualize a MARTINI protein/trajectory in VMD, I came across
the script top2psf.pl. i attempted to use it as:

 ./top2psf.pl -i martini.top -o martini.psf
this generates the error:
 Cannot open atoms for reading: No such file or directory

Anyone encounter this or have any suggestions for visualizing MARTINI
proteins in VMD? Thank you for any help.

-j
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Re: [gmx-users] top2psf.pl issue: trying to use vmd w/ MARTINI protein

2011-02-15 Thread Justin A. Lemkul



John wrote:

Hello,

While trying to visualize a MARTINI protein/trajectory in VMD, I came 
across the script top2psf.pl http://top2psf.pl. i attempted to use it as:


  ./top2psf.pl http://top2psf.pl -i martini.top -o martini.psf
this generates the error:
  Cannot open atoms for reading: No such file or directory

Anyone encounter this or have any suggestions for visualizing MARTINI 
proteins in VMD? Thank you for any help.


The required input is the actual protein topology (usually an #included .itp 
file within the .top).


-Justin

 
-j




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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] Simulation using Martini force field

2011-02-15 Thread politr

regarding parameterization of phosphorylated serine 
I checked the Martini papers and I couldn't find how it is done. Can  
somebody please instruct me.
In addition in JCTC paper from 2008 I saw that they simulated  
pentapeptides without imposing secondary structure. How can I do it?  
The problem is that there is no good tutorial how to use Martini  
(something general). If I still want to use Martini without imposing  
secondary structure how should I do it?
What tutorial is better to use the one for lipids or the one for  
proteins in water. I think I should explain what exactly I want to do.  
I want to simulate casein protein that is natively unstructured. The  
only thing that is known about this protein that it creates micelles.  
I just want to see if it possible to create micelles with Martini and  
I'm trying to understand what is the better way to run Martini taking  
into consideration the limitations of the force field and my system.  
As I'm not an expert in Gromacs neither in Martini force field I will  
appreciate very much any help for setting this simulation.

Thank you very much in advance.
Regina

n Feb 14, 2011, at 11:43 PM, pol...@fh.huji.ac.il wrote:

Thank you very much for you reply. Can you please explain me why do  
i need secondary structure file at all and why secondary structure  
is pre-defined and thus static throughout a simulation? I didn't  
see that something like this defined for lipids.
Have look at the Martini paper for protein (JCTC-2009) you might find  
some stuff quite instructive in there :))


FYI lipids do not have secondary structure or something that would  
succgest they could have different interacting behavior in function of  
their conformation.
How do I use do_dssp to build the needed file? I saw that I need a  
topology file in rder to use do_dssp. Where can I find this topology  
file? I hope this is ok that I'm asking so many questions. Thank you  
very much for your help.

No problem it just shows how it was a good idea to make a tutorial :))
have look there cgmartini.nl

Regina
Quoting XAvier Periole x.peri...@rug.nl:



Dear Regina,

You have two problems:
1- the parameterization of phosphorylated serine should be done
following the same philosophy of Martini. Check the Martini papers
to see how this is done. In short partitioning is of primary importance.
2- you want to simulate unfolded protein ... indeed there is evidently
no persistent structure in such system and therefore the choice for
secondary structure would be coil in the Martini force field.
However the definition of coil for Martini has not been parameterize
to reproduce anything even close to what an unfolded protein, assuming
that we know what it looks like :)) The Martini coil is simply something
flexible.

I am afraid Martini is just not ready for simulating unfolded proteins.
Any outcome of a simulation would have to be interpreted with CARE!

XAvier.

On Feb 14, 2011, at 2:09 PM, pol...@fh.huji.ac.il wrote:


Dear Gromacs users and developers,
I'm interested to run simulation of natively unstructured protein  
(casein), that can self assembly and create micelles, using  
Martini force field. The initial structure of the monomer was  
created and minimized using Sybyl. This protein includes also 4  
phosporylated serines. I'm trying to understand how should I set  
my system. I started from the tutorial  
(http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water)  
but I found that have no idea how to create a phosphorylated  
serine inCG structure (I have it in my initial pdb). In addition,  
I found that I need a secondary structure of the protein and I  
don't have something like this. Moreover, this protein doesn't  
have one. I will appreciated very much if somebody can help me and  
guide me a little.

Thank you very much in advance.
Regina


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[gmx-users] Advanced Simulation Analysis

2011-02-15 Thread simon sham
Hi,
I have been trying to follow the tutorial posted by David van der Spoel to 
generate the order parameters at:
https://extras.csc.fi/chem/courses/gmx2007/analysis/index.html

When I ran g_rotacf, I got the following message:

Fatal error:
Number of index elements not multiple of 2, these can not be atom doublet.

Has anyone tried that tutorial?

Best,

Simon Sham 



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Re: [gmx-users] Advanced Simulation Analysis

2011-02-15 Thread David van der Spoel

On 2011-02-15 18.01, simon sham wrote:

Hi,
I have been trying to follow the tutorial posted by David van der Spoel
to generate the order parameters at:
https://extras.csc.fi/chem/courses/gmx2007/analysis/index.html

When I ran g_rotacf, I got the following message:

Fatal error:
Number of index elements not multiple of 2, these can not be atom doublet.

Has anyone tried that tutorial?

Best,

Simon Sham



You need to specify a list of atom pairs, I guess N H N H etc.

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[gmx-users] Re: free energy

2011-02-15 Thread TJ Mustard



  

  
Moeed,




Sorry for the late response, and yes I did need to include more information in my answer.




1) If your polymers are physically close together in reality you might want to have multiple polymers in a single FEP job.



I run single ligands in proteins, so this has never been an issue. You may want to run both and see what the differences in energy are. If there are none you may be able to do longer md/sd runs with a smaller one polymer system than you could with multiple polymers in the same time.



In other words I have no idea what your system will need. Sorry.




2) How many windows and how long are the md/sd runs for each window?



I personally found that 21 windows works well for my systems. This however will vary by the dV/dlambda graph. If and when your dV/dlambda is changing more (ddV/dlambda) you will need more windows to get a more accurate energy. Most systems change the most at the beginning and end of lambda values. I run a lambda every 0.05, but my systems are huge! (100,000 atoms)




3) Bennett acceptance ratio is an extra step in setup but makes getting your data much easier to interpret. Once you are done with all your windows you run g_bar and it will print out on your screen the energy from each window and the total energy in kJ/mol with a standard deviation.




This can be found in the manual and also in the gmx_user archives. This entailes making a .mdp file for every step (but you probably do this already) and setting the foreign lambdas correctly.



ie for lambda values: 0.00, 0.25, 0.50, 0.75 and 1.00

Your foreign lambda values for the 0.00 mdp file would be: 0.25

Your foreign lambda values for the 0.25 mdp file would be: 0.00 0.50

Your foreign lambda values for the 0.50 mdp file would be: 0.25 0.75

Your foreign lambda values for the 0.75 mdp file would be: 0.50 1.00

Your foreign lambda values for the 0.50 mdp file would be: 0.75



This of course is a small number of lambda values you will want to use more.



Please email me with questions if you need more.



Thank you,

TJ Mustard

Email: musta...@onid.orst.edu





PS more below





  
   On February 14, 2011 at 8:54 PM Moeed lecie...@googlemail.com wrote:
  

  

  Hello,



  



  Sorry but it seems you wanted to answer my question on gmx list but I dont see anything!...



  



  
  
   --
   Moeed Shahamat
   Graduate Student (Materials Modeling Research Group)
   McGill University- Department of Chemical Engineering
   Montreal, Quebec H3A 2B2, Canada
   Web:http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php
   Web:http://mmrg.chemeng.mcgill.ca/

  




TJ Mustard
Email: musta...@onid.orst.edu






  Dear experts,
  
   I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon solvent. I have prepared a system consisting of 4 polymer chains and 480 hexane molecules with the actual density of polymer solution (~ 0.5 g/cm3).
  
   1- For such a study I dont know how many polymers I need to have in my system. If FE can be done with only one chain, am I making system bigger in vain? Does this matter affect the accuracy of results?



  
2- I have switched off electrostatics so I am using

 free_energy = yes
 init_lambda = 0
 delta_lambda = 0
 sc_alpha = 0.5
 sc-power = 1
 sc_sigma = 0.3
 couple-lambda0 = vdw
 couple-lambda1 = none
 couple-intramol = no

 In David Mobleys turorial the last three lines are not included. I wanted to know if I am to run say 10 simulations for different lambda, what purpose does the last three lines serve in 4.0.7 ? I got very close values in that tutorial without these settings. ( I know what these lines mean, just curious how these three lines affect the results in 4 X +).


  


This old tutorial is for an old gromacs which needs you to set the state a and state b. In the newer gromacs releases you set the state a, and gromacs will go to state b without you setting each atom. This considerably saves time making .itp files. All you need is a methane .itp file (got mine from antechamber) and then you set couple-lambda0 and couple-lambda1 to what you are looking for.



I personally go from couple-lambda0 = vdw-q to couple-lambda1 = none.


  
Please let me know your comments/point of view about the system and setting I am using.

 Thanks
 Moeed
  




TJ Mustard
 Email: musta...@onid.orst.edu

Re: [gmx-users] free energy

2011-02-15 Thread Michael Shirts
One other thing I would point out is that the solvation free energy is
dependent on concentration.  you will get a different result with 4
polymer chains vs 3 vs 3, etc.  Make sure you understand the
dependence.  Also, the free energy will depend on the polymer chain
length.

Polymer and finite concentration calculations are harder to interpret
than monomer and infinite dilution calculations.  Make sure you
understand the differences.   I'm not sure understand all of them,
though, so you'll have to think about it yourself!  Basically, you
need to make sure the physical picture of the molecules in gromacs is
the physical picture of the realistic molecular system itself.


On Mon, Feb 14, 2011 at 6:28 PM, Moeed lecie...@googlemail.com wrote:

 Dear experts,

 I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon
 solvent. I have prepared a system consisting of 4 polymer chains and 480
 hexane molecules with the actual density of polymer solution (~ 0.5 g/cm3).

 1- For such a study I dont know how many polymers I need to have in my
 system. If FE can be done with only one chain, am I making system bigger in
 vain? Does this matter affect the accuracy of results?

 2- I have switched off electrostatics so I am using

 free_energy  =   yes
 init_lambda  =   0
 delta_lambda =   0
 sc_alpha =   0.5
 sc-power =   1
 sc_sigma =   0.3
 couple-lambda0   =   vdw
 couple-lambda1   =   none
 couple-intramol  =   no

 In David Mobley's turorial the last three lines are not included. I wanted
 to know if I am to run say 10 simulations for different lambda, what purpose
 does the last three lines serve in 4.0.7  ? I got very close values in that
 tutorial without these settings. ( I know what these lines mean, just
 curious how these three lines affect the results in 4 X +).

 Please let me know your comments/point of view about the system and setting
 I am using.

 Thanks
 Moeed

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Re: [gmx-users] Gromacs Installation

2011-02-15 Thread majid hasan
So, I installed the development package for x-window-system, and reinstalled 
both fftw, and gromacs, and now everything seems fine. I do see the animation 
after running demo.

Thanks,
Majid




From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Mon, February 14, 2011 9:39:12 PM
Subject: Re: [gmx-users] Gromacs Installation

 On 15/02/2011 4:35 PM, majid hasan wrote: 
Okay, I'll do this. I have also realized after browsing   through 
config.log, that Xlib.h is absent. Where do I get it,   I want it to 
run 
ngmx.

You will need the X windowing system installed, and probably the associated 
devel packages. Use your distribution's package manager.

Mark



Thanks,
Majid





From: ZHAO Lina lnzha...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Mon,   February 14, 2011 9:07:15 PM
Subject: Re: [gmx-users] Gromacs Installation

clean reinstallation.

make uninstall
make distclean
rm -r the untar one 

from source re-install it again.

lina


On Tue, Feb 15, 2011 at 12:39 PM,   majid hasan 
pu_majidha...@yahoo.com wrote:

Okay. Actually, second time, I over-worte the   first 
installation. I mean I didn't uninstall the   first one, I 
just ran the whole process again   starting from 
fftw$./configure. I am not sure if   that is all right, I 
just did it to find out the   problem. In the third 
attempt 
(without issuing   --enable-shared anywher), I again 
over-wrote the   gromacs installation files, and this went 
well. It   worked, but I don't know why?


Best,
Majid




 From: ZHAO Lina lnzha...@gmail.com 

To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Mon, February 14, 2011 8:04:38 PM 

Subject: Re: [gmx-users] Gromacs Installation
 

You are right, it's relevant to the shared   libs.
but I don't know why you failed in the second   
attempt 
if you did a clean reinstallation.

lina






Food fight? Enjoy some healthy debate
in the Yahoo! Answers Food  Drink QA.



 

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[gmx-users] Repulsion instead of adsorption

2011-02-15 Thread mina Madah






























 Dear all 
I'm working on simulation of adsorption on the sheet .
I use periodic boundary conditions in two dimension (X,Y) .
in my work the initial configurations were minimized at first then system 
equilibrated for 100 ps and followed by 500 ps production run.
when I look at the .xtc  and .gro file by  vmd  in the end of my work (after 
final mdrun), the  particles are so much far from the sheet and realy no 
adsorption occur.sheet repulsed particles I also understood that after 
equilibration step the particle start to geting distance from sheet.
I made the parameters of force field for the sheet by own ( bonding and 
nonbonding ) , because a proper force field for my compound didn't exist in 
defualt gromacs.
 
why adsorption don't occur ?

any help will highly appreciated.





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Re: [gmx-users] Repulsion instead of adsorption

2011-02-15 Thread Justin A. Lemkul



mina Madah wrote:
 Dear all 
I'm working on simulation of adsorption on the sheet .

I use periodic boundary conditions in two dimension (X,Y) .
in my work the initial configurations were minimized at first then 
system equilibrated for 100 ps and followed by 500 ps production run.
when I look at the .xtc  and .gro file by  vmd  in the end of my work 
(after final mdrun), the  particles are so much far from the sheet and 
realy no adsorption occur.sheet repulsed particles I also understood 
that after equilibration step the particle start to geting distance from 
sheet.
I made the parameters of force field for the sheet by own ( bonding and 
nonbonding ) , because a proper force field for my compound didn't 
exist in defualt gromacs.
 
why adsorption don't occur ?




Either your model (parameters, initial configuration, etc) is wrong or you 
didn't simulate long enough.  500 ps is an extremely short timeframe.


-Justin


any help will highly appreciated.





--


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] Simulation using Martini force field

2011-02-15 Thread devicerandom

On 15/02/11 06:34, XAvier Periole wrote:

You have two problems:
1- the parameterization of phosphorylated serine should be done
following the same philosophy of Martini. Check the Martini papers
to see how this is done. In short partitioning is of primary importance.
2- you want to simulate unfolded protein ... indeed there is evidently
no persistent structure in such system and therefore the choice for
secondary structure would be coil in the Martini force field.
However the definition of coil for Martini has not been parameterize
to reproduce anything even close to what an unfolded protein, assuming
that we know what it looks like :)) The Martini coil is simply
something
flexible.

I am afraid Martini is just not ready for simulating unfolded proteins.
Any outcome of a simulation would have to be interpreted with CARE!


Agree with Xavier. I am working exactly on a coarse grained generic FF
that could allow this kind of simulations, but it's far from being
production ready -not an easy task at all. :)

thanks for your support devicerandom!


Uh... was it sarcastic or are you serious? (in any case: welcome!)



XAvier.

On Feb 14, 2011, at 2:09 PM, pol...@fh.huji.ac.il wrote:


Dear Gromacs users and developers,
I'm interested to run simulation of natively unstructured protein
(casein), that can self assembly and create micelles, using Martini
force field. The initial structure of the monomer was created and
minimized using Sybyl. This protein includes also 4 phosporylated
serines. I'm trying to understand how should I set my system. I
started from the tutorial
(http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water)
but
I found that have no idea how to create a phosphorylated serine inCG
structure (I have it in my initial pdb). In addition, I found that I
need a secondary structure of the protein and I don't have something
like this. Moreover, this protein doesn't have one. I will appreciated
very much if somebody can help me and guide me a little.
Thank you very much in advance.
Regina


This message was sent using IMP, the Internet Messaging Program.

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[gmx-users] on force fields

2011-02-15 Thread Mr Bernard Ramos
Hi everyone!
 
I need to update the gromos force field 53A6 with the new force field 53ACARBO 
(JCC 10 NOV 2010). 
 
1. I will have to change the parameter values in the file ff_bonded.itp and 
ff_nonbonded.itp in the gromos53a6.ff. Are these the only files that I need to 
update if I need to switch to a new force field?
 
2. The new force field 53ACARBO has a new gromos functional form for select 
torsional potentials. How to I go over implementing this in gromos?
 
Thanks. Your help is greatly appreciated. 
 


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[gmx-users] g_rmsf reference structure?

2011-02-15 Thread kulleperuma . kulleperuma

Dear all,

I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the  
C-atoms with reference to the average structure between 5-10 ns of a  
total of 10 ns simulation as below;

g_rmsf  ?f md.xtc  ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg

My understanding of the RMSF is as follows;

 RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2)

where T is the time over which one wants to average, and Xi is the  
reference position of particle i, which is the time-averaged position  
of the same particle i.
What I am confused is whether g_rmsf takes the reference structure  
from the structure file (-s), which in my case, the md.tpr and NOT the  
time averaged position over the specified time?


Thanking in advance for clarification.


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Re: [gmx-users] on force fields

2011-02-15 Thread Mark Abraham

On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote:

Hi everyone!
I need to update the gromos force field 53A6 with the new force field 
53ACARBO (JCC 10 NOV 2010).
1. I will have to change the parameter values in the file 
ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these the 
only files that I need to update if I need to switch to a new force field?




You should make a copy of the whole force field directory into your 
working directory, rename the new directory suitably, make a suitable 
change to forcefield.doc, and then edit .itp files suitably. This means 
you're leaving your reference version untouched and can edit locally to 
your heart's content, and can be sure you're selecting the right force 
field with pdb2gmx and/or in your .top file.


2. The new force field 53ACARBO has a new gromos functional form 
for select torsional potentials. How to I go over implementing this in 
gromos?




Preferably as a sum of existing functional forms. Or use tabulated 
bonded interactions (see manual and wiki).


Mark
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Re: [gmx-users] g_rmsf reference structure?

2011-02-15 Thread Mark Abraham

On 16/02/2011 3:44 PM, kulleperuma.kulleper...@utoronto.ca wrote:

Dear all,

I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the 
C-atoms with reference to the average structure between 5-10 ns of a 
total of 10 ns simulation as below;

g_rmsf  ?f md.xtc  ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg

My understanding of the RMSF is as follows;

 RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2)

where T is the time over which one wants to average, and Xi is the 
reference position of particle i, which is the time-averaged position 
of the same particle i.
What I am confused is whether g_rmsf takes the reference structure 
from the structure file (-s), which in my case, the md.tpr and NOT the 
time averaged position over the specified time?


It does take the reference structure from -s. Whether you actually want 
the RMSF from the non-physical time-averaged structure is up to you. 
IIRC you might be able to get such an average from g_cluster.


Mark
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[gmx-users] Conatant pH simulation in GROMACS

2011-02-15 Thread bipin singh
Hi all,

I want to know that, whether we I can do constant pH simulation in gromacs.
Please provide some details regarding this.
-- 
*
-
Thanks and regards
Bipin Singh
*
*
*
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Re: [gmx-users] Conatant pH simulation in GROMACS

2011-02-15 Thread Mark Abraham

On 16/02/2011 6:04 PM, bipin singh wrote:

Hi all,

I want to know that, whether we I can do constant pH simulation in 
gromacs.

Please provide some details regarding this.


Please search first ;-)

http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

Mark
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