Re: [gmx-users] RMSIP

[Mark Abraham]

- Original Message -
From: pawan raghav 
Date: Wednesday, May 19, 2010 16:28
Subject: [gmx-users] RMSIP
To: gmx-users@gromacs.org

> Thanks mark, but I think that g_anaeig calculates the degree of overlap then 
> what method would you use to calculate this?> 

I don't know what you are asking, and I certainly don't know the answer :-).

Mark
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[gmx-users] Re: OPLS-AA/L force field

[you zou]

Hi Justin,
Thank you for your help, But when I run x2top command there is one error that 
is:"Can not find forcefield for atom C1-1 with 2 bondsCan not find forcefield 
for atom C4-4 with 2 bonds...Program x2top, VERSION 4.0.5Source code file: 
x2top.c, line: 207Fatal error:Could only find a forcefield type for 6 out of 24 
atoms"I don't know how can I adjust this error.I have one more question again, 
this command give me a top file, if I want gro file of this pdb (drug that has 
removed from drug-enzyme complex) how can I do that?
you zou wrote:
> Dear Users,
> 
> I have one question about Drug-Enzyme Complex,Similar to tutorial If I 
> want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug 
> but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg 
> Beta version" server too, or not?

No. You can't use two different force fields in one simulation system.

> If I can't use this server, how can I make .gro file and .itp file for 
> drug that remove from initial .pdb file?
> 

There are several programs in the User Contributions from the website, x2top 
(which is distributed with Gromacs), or you can build the topology by hand. No 
matter what you choose, you need a thorough understanding of the mechanics of 
your chosen force field, methods of validation, and of course Chapter 5 in the 
Gromacs manual.

Thanks

  
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Re: [gmx-users] water medium

[tahereh tekieh]

but genion only accepts one type of ion, how can we insert different types?

On Tue, May 18, 2010 at 3:38 PM, Justin A. Lemkul  wrote:

>
>
> tahereh tekieh wrote:
>
>> dear friends
>> i want to simulate a water medium in which 5 types of different ions flow
>> in it. how can i do that with gromacs?
>> thanks
>>
>>
> Assuming they are monoatomic, you can use genion after you have added
> water.  If they are polyatomic, use genbox -ci -nmol (before filling the box
> with water).
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] water medium

[Mark Abraham]

- Original Message -
From: tahereh tekieh 
Date: Wednesday, May 19, 2010 17:09
Subject: Re: [gmx-users] water medium
To: jalem...@vt.edu, Discussion list for GROMACS users 

> but genion only accepts one type of ion, how can we insert different types?

I suggested some approaches to this problem on this list in the last week. 
Please search the archives.

Mark
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Re: [gmx-users] DSSP

[Carsten Kutzner]

Hi,

there was a problem in do_dssp when used on proteins with more
than 10 chains. Is this the case? I just saw that I
only fixed that in the head, but not in 4.0.x.  

Carsten



On May 18, 2010, at 3:49 PM, shahid nayeem wrote:

> Hi
> When I run  dssp alone with a .pdb file it works well. But when I run with 
> Gromacs as do_dssp it gives segmentation fault and does not do any 
> calculation except giving some intermediate files as follows.
> 
> Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
> Reading frame   0 time0.000
> Warning: if there are broken molecules in the trajectory file,
>  they can not be made whole without a run input file
>  
>  
> Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1#
> Segmentation fault
> 
> shahid 
> 
> 
>  
> On 5/18/10, Justin A. Lemkul  wrote:
> 
> 
> shahid nayeem wrote:
> Hi
> After posting this mail I did some google search and after changing the 
> executible name to dssp I moved it in /usr/local/bin/ After this when I did 
> do_dssp it starts running asks to select a group I choose main chain 5, then 
> it generates some intermediate file and gives error as segmentation fault. I 
> though this problem was because of the executible in /usr/local/bin/ and rest 
> of file in another directory say /home/shahid/software/dssp/. For this first 
> I set the path in ~/.bascrc 
> 
> Other files should be irrelevant.  The only file you need is the dssp binary.
> 
> as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the 
> same intermediate file generated backing up the previous one. 
> 
> Intermediate files are not an issue.  When the executable is in this 
> directory, does the calculation otherwise work?
> 
> Then I moved all the files of dssp directory to /usr/local/bin/ and then 
> tried to run do_dssp I am in the same situation.
> 
> If the executable in your home directory structure works, but in 
> /usr/local/bin it fails, then it could be some sort of permission error.  It 
> ultimately doesn't matter where your executable is, /usr/local/bin is 
> default, but you can set any other location you like with the DSSP 
> environment variable.
> 
> -Justin
> 
> waiting for your help
> shahid nayeem
> 
>  On 5/18/10, *Justin A. Lemkul* mailto:jalem...@vt.edu>> 
> wrote:
> 
> 
> 
>shahid nayeem wrote:
> 
>Dear All
>I downloaded dsspcmbi.tar.gz, and compiled  using command
>./DsspCompileGCC as given in Readme.txt file. when I try to run
>do_dssp command in gromacs I get error
> 
> 
>Well, what happened?
> 
> 
>Fatal error:
>DSSP executable (/usr/local/bin/dssp) does not exist (use setenv
>DSSP)
> 
>I checked for DSSP executible in /usr/local/bin/ and I couldnt
>find. I
> 
> 
>It won't be there unless you put it there and you have re-named it.
> I believe the default name of the dssp program is "dsspcmbi," which
>you need to change when you move the executable.
> 
>http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
> 
>-Justin
> 
>even tried dsspcmbi.zip file but again I got the same error. I
>compiled dssp as root. Now what shoul I do in order to run do_dssp
>comand of gromacs.
>Shahid nayeem
> 
> 
>-- 
> 
>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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>.
>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
> 
> 
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Re: [gmx-users] RMSIP

[Tsjerk Wassenaar]

Hi,

The answer is given by g_anaeig (-h):

When -v, -eig, -v2 and -eig2 are given, a single number for the overlap
between the covariance matrices is generated. The formulas are:
difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2))
normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))
 shape overlap = 1 - sqrt(tr((sqrt(M1/tr(M1)) - sqrt(M2/tr(M2)))^2))
where M1 and M2 are the two covariance matrices and tr is the trace of a
matrix. The numbers are proportional to the overlap of the square root of the
fluctuations. The normalized overlap is the most useful number, it is 1 for
identical matrices and 0 when the sampled subspaces are orthogonal.

A more elaborate explanation is given in chapter 8.10 of the manual.
The definition for the RMSIP is a different one, but can readily be
found in literature.

Cheers,

Tsjerk


On Wed, May 19, 2010 at 9:02 AM, Mark Abraham  wrote:
>
>
> - Original Message -
> From: pawan raghav 
> Date: Wednesday, May 19, 2010 16:28
> Subject: [gmx-users] RMSIP
> To: gmx-users@gromacs.org
>
>> Thanks mark, but I think that g_anaeig calculates the degree of overlap then 
>> what method would you use to calculate this?>
>
> I don't know what you are asking, and I certainly don't know the answer :-).
>
> Mark
> --
> gmx-users mailing list    gmx-us...@gromacs.org
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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[gmx-users] Re: water medium

[Thomas Schlesier]

Use genion multiple times.
If you want to insert Na+ and K+, then first use genion with one and 
then with the other ion.


Greetings
Thomas



Message: 5
Date: Wed, 19 May 2010 11:37:09 +0430
From: tahereh tekieh 
Subject: Re: [gmx-users] water medium
To: jalem...@vt.edu, Discussion list for GROMACS users

Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

but genion only accepts one type of ion, how can we insert different types?

On Tue, May 18, 2010 at 3:38 PM, Justin A. Lemkul  wrote:

> >
> >
> > tahereh tekieh wrote:
> >
>> >> dear friends
>> >> i want to simulate a water medium in which 5 types of different 
ions flow

>> >> in it. how can i do that with gromacs?
>> >> thanks
>> >>
>> >>
> > Assuming they are monoatomic, you can use genion after you have added
> > water.  If they are polyatomic, use genbox -ci -nmol (before 
filling the box

> > with water).
> >
> > -Justin
> >
> > --
> > 
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before 
posting!
> > Please don't post (un)subscribe requests to the list. Use the www 
interface

> > or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
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Re: [gmx-users] Re: water medium

[tahereh tekieh]

but it over writes on the previous status.

On Wed, May 19, 2010 at 2:12 PM, Thomas Schlesier wrote:

> Use genion multiple times.
> If you want to insert Na+ and K+, then first use genion with one and then
> with the other ion.
>
> Greetings
> Thomas
>
>
>
> Message: 5
> Date: Wed, 19 May 2010 11:37:09 +0430
>
> From: tahereh tekieh 
> Subject: Re: [gmx-users] water medium
> To: jalem...@vt.edu, Discussion list for GROMACS users
>
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> but genion only accepts one type of ion, how can we insert different types?
>
> On Tue, May 18, 2010 at 3:38 PM, Justin A. Lemkul  wrote:
>
> > >
> > >
> > > tahereh tekieh wrote:
> > >
> >> >> dear friends
> >> >> i want to simulate a water medium in which 5 types of different ions
> flow
> >> >> in it. how can i do that with gromacs?
> >> >> thanks
> >> >>
> >> >>
> > > Assuming they are monoatomic, you can use genion after you have added
> > > water.  If they are polyatomic, use genbox -ci -nmol (before filling
> the box
> > > with water).
> > >
> > > -Justin
> > >
> > > --
> > > 
> > >
> > > Justin A. Lemkul
> > > Ph.D. Candidate
> > > ICTAS Doctoral Scholar
> > > MILES-IGERT Trainee
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > 
> > > --
> > > 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
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> > >
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[gmx-users] Solvation free energy

[afsaneh maleki]

Hi,

I want to calculate the solvation free energy of Wild-type human IAPP
(hIAPP) with 37 residues in length that residu26 isoleucine is mutated to
proline (ile26pro). I used dual topology in Thermodynamic integration (TI)
for calculating salvation free energy.  For the solvation free energy
calculations I need some parameter as *Sc_alpha*, *Sc_power* and *Sc_power *
in* *mdp file.

I also read manual of Dr David van der spoel about salvation free energy and
manual of Gromacs. Nevertheless, I couldn’t decide best value for these
parameters and my protein.

I used the following values in mdp file:

free_energy = yes

init_lambda = 0.00

sc_alpha= 0.5

sc_power= 1.0

sc_sigma= 0.3



What values do you suggest for these parameters?

Thanks very much,
Afsaneh Maleki
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Re: [gmx-users] Re: water medium

[Justin A. Lemkul]

tahereh tekieh wrote:

but it over writes on the previous status.



Not if you use the right input.  Insert your first ion type with genion, update 
the topology, generate a new .tpr file and insert your second ion type, etc.  If 
you use the same .tpr file (containing only solvent) for each addition, you 
essentially re-set the system of interest back to solvent-only.  If you make 
changes to the system, those have to be accounted for.


-Justin

On Wed, May 19, 2010 at 2:12 PM, Thomas Schlesier <mailto:schl...@uni-mainz.de>> wrote:


Use genion multiple times.
If you want to insert Na+ and K+, then first use genion with one and
then with the other ion.

Greetings
Thomas



Message: 5
Date: Wed, 19 May 2010 11:37:09 +0430

From: tahereh tekieh mailto:golesan...@gmail.com>>
Subject: Re: [gmx-users] water medium
To: jalem...@vt.edu <mailto:jalem...@vt.edu>, Discussion list for
GROMACS users
   mailto:gmx-users@gromacs.org>>
Message-ID:
   mailto:aanlktikvksqelk-hu04toj6a_fg2iqwrlcx0xj_jn...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"


but genion only accepts one type of ion, how can we insert different
types?

On Tue, May 18, 2010 at 3:38 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:

 > >
 > >
 > > tahereh tekieh wrote:
 > >
 >> >> dear friends
 >> >> i want to simulate a water medium in which 5 types of
different ions flow
 >> >> in it. how can i do that with gromacs?
 >> >> thanks
 >> >>
 >> >>
 > > Assuming they are monoatomic, you can use genion after you have
added
 > > water.  If they are polyatomic, use genbox -ci -nmol (before
filling the box
 > > with water).
 > >
 > > -Justin
 > >
 > > --
 > > 
 > >
 > > Justin A. Lemkul
 > > Ph.D. Candidate
 > > ICTAS Doctoral Scholar
 > > MILES-IGERT Trainee
 > > Department of Biochemistry
 > > Virginia Tech
 > > Blacksburg, VA
 > > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 > >
 > > 
 > > --
 > > gmx-users mailing listgmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
 > > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > > Please search the archive at http://www.gromacs.org/search
before posting!
 > > Please don't post (un)subscribe requests to the list. Use the
www interface
 > > or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
 > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 > >
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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] Re: OPLS-AA/L force field

[Justin A. Lemkul]

you zou wrote:

Hi Justin,

Thank you for your help, But when I run x2top command there is one error 
that is:

"
Can not find forcefield for atom C1-1 with 2 bonds
Can not find forcefield for atom C4-4 with 2 bonds
...
Program x2top, VERSION 4.0.5
Source code file: x2top.c, line: 207

Fatal error:
Could only find a forcefield type for 6 out of 24 atoms"



Not all of your atom types are described by ffoplsaa.n2t so you will have to add 
them.  There are only a limited number of types that are covered by default.


http://www.gromacs.org/Documentation/File_Formats/.n2t_File


I don't know how can I adjust this error.
I have one more question again, this command give me a top file, if I 
want gro file of this pdb (drug that has removed from drug-enzyme 
complex) how can I do that?




Do you just need a .gro file, and not a .top?  My understanding from your first 
message was that you needed a topology.  If you just need a .gro, then simply 
pass your .pdb file to editconf.


-Justin


you zou wrote:

Dear Users,

I have one question about Drug-Enzyme Complex,Similar to tutorial If I 

  want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug 
but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg 
Beta version" server too, or not?


No. You can't use two different force fields in one simulation system.

If I can't use this server, how can I make .gro file and .itp file for 
drug that remove from initial .pdb file?




There are several programs in the User Contributions from the website, x2top 
(which is distributed with Gromacs), or you can build the topology by hand. No 
matter what you choose, you need a thorough understanding of the mechanics of 
your chosen force field, methods of validation, and of course Chapter 5 in the 


Gromacs manual.


Thanks



Hotmail: Free, trusted and rich email service. Get it now. 





--


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] enegry minimisation

[sonali dhindwal]

Hello All
This question may sound trivial to many, but as i am new to this field, please 
help.
I want to ask a question regarding my previous query of distortion of protein 
strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using steepest decent algorithm, 
using emtol of 1000 kJ mol-1 nm-1 .
So is it necessary to do enegry minimisation step before MD, because this is my 
modeled protein, and i have  already done energy minimisation using different 
program and after that I have done refinement also.
Thanks and regards


--
Sonali Dhindwal

-- 
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Re: [gmx-users] Re: OPLS-AA/L force field

[Oliver Grant]

Can you not run pdb2gmx for each of your molecules that you want separate
force fields for? Then cat the gro files, renumber and include the molecule
types as .itp files in the .top file as below. If I'm doing anything wrong
please let me know! :)

 ;
;This is your topology file
;"What If None Of Your Dreams Come True ?" (E. Costello)
;
; Include forcefield parameters
#include "ffamber99sb.itp"

[ atomtypes ]
from
the top file of the non amber force field
;name  bond_typemasscharge   ptype  sigma  epsilon
CYCY  0.  0.  A   3.39967e-01  4.57730e-01
O  O  0.  0.  A   2.95992e-01  8.78640e-01
HOHO  0.  0.  A   0.0e+00  0.0e+00
H1H1  0.  0.  A   2.47135e-01  6.56888e-02
O2O2  0.  0.  A   2.95992e-01  8.78640e-01
N  N  0.  0.  A   3.25000e-01  7.11280e-01
H2H2  0.  0.  A   2.29317e-01  6.56888e-02
OYOY  0.  0.  A   3.1e-01  7.11280e-01
HCHC  0.  0.  A   2.64953e-01  6.56888e-02
H  H  0.  0.  A   1.06908e-01  6.56888e-02
C  C  0.  0.  A   3.39967e-01  3.59824e-01
OSOS  0.  0.  A   3.1e-01  7.11280e-01
CGCG  0.  0.  A   3.39967e-01  4.57730e-01
OHOH  0.  0.  A   3.06647e-01  8.80314e-01

#include
"protein.itp"from
the top file of the amber force field, contains everything usually specified
here under [molecule types].

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

#ifdef POSRES_CA
#include "CA_posre.itp"
#endif

#include
"trisacc.itp"from
the top file of the non amber force field, contains charges etc.

; Include Position restraint file
#ifdef POSRES_trisacc
#include "trisacc_posre.itp"
#endif

; Include water topology
#include "ffamber_tip3p.itp"

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

; Include generic topology for ions
#include "Na_amber99sb.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_A   1
trisacc1
SOL 10697
Na  4



2010/5/19 you zou 

>  Hi Justin,
>
> Thank you for your help, But when I run x2top command there is one error
> that is:
> "
> Can not find forcefield for atom C1-1 with 2 bonds
> Can not find forcefield for atom C4-4 with 2 bonds
> ...
> Program x2top, VERSION 4.0.5
> Source code file: x2top.c, line: 207
>
> Fatal error:
> Could only find a forcefield type for 6 out of 24 atoms"
>
> I don't know how can I adjust this error.
> I have one more question again, this command give me a top file, if I want
> gro file of this pdb (drug that has removed from drug-enzyme complex) how
> can I do that?
>
> you zou wrote:
> > Dear Users,
> >
> > I have one question about Drug-Enzyme Complex,Similar to tutorial If I
>
> >
>   want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
> > but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg
> > Beta version" server too, or not?
>
> No. You can't use two different force fields in one simulation system.
>
> > If I can't use this server, how can I make .gro file and .itp file for
> > drug that remove from initial .pdb file?
> >
>
> There are several programs in the User Contributions from the website, x2top
>
> (which is distributed with Gromacs), or you can build the topology by hand. No
> matter what you choose, you need a thorough understanding of the mechanics of
> your chosen force field, methods of validation, and of course Chapter 5 in the
>
> Gromacs manual.
>
>
> Thanks
>
>
> --
> Hotmail: Free, trusted and rich email service. Get it 
> now.
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
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Re: [gmx-users] enegry minimisation

[Justin A. Lemkul]

sonali dhindwal wrote:

Hello All
This question may sound trivial to many, but as i am new to this field, 
please help.
I want to ask a question regarding my previous query of distortion of 
protein strucutre after molecular dynamcs simulation.


Can you provide a link to your previous post, for reference?

I have noticed that after enegry minimisation using steepest decent 
algorithm, using emtol of 1000 kJ mol^-1 nm^-1 .
So is it necessary to do enegry minimisation step before MD, because 
this is my modeled protein, and i have  already done energy minimisation 
using different program and after that I have done refinement also.


Have you added solvent or anything else to the protein model?  If so, then the 
answer is yes.  Solvation with a regularly-ordered lattice of solvent molecules 
can (and often does) lead to bad clashes with your protein structure, thus 
necessitating further minimization.


There are plenty of reasons why a protein structure might be unstable, most of 
them related to .mdp file settings, but you haven't posted those so there's no 
way to know if you're doing things correctly.


-Justin


Thanks and regards
^

--
Sonali Dhindwal




--


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] enegry minimisation

[Erik Marklund]

sonali dhindwal skrev:

Hello All
This question may sound trivial to many, but as i am new to this 
field, please help.
I want to ask a question regarding my previous query of distortion of 
protein strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using steepest decent 
algorithm, using emtol of 1000 kJ mol^-1 nm^-1 .
So is it necessary to do enegry minimisation step before MD, because 
this is my modeled protein, and i have  already done energy 
minimisation using different program and after that I have done 
refinement also.

Thanks and regards
^

--
Sonali Dhindwal


That depends how that minimization was carried out. Did it use the same 
forcefield parameters and the same boxsize etc., then in principle no. 
If not, then I strongly suggest doing EM before MD to prevent problems 
later on.


I don't understand what it is that you noticed after energy minimization.

Cheers,

--
---
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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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Re: OPLS-AA/L force field

[Justin A. Lemkul]

Oliver Grant wrote:
Can you not run pdb2gmx for each of your molecules that you want 
separate force fields for? Then cat the gro files, renumber and include 
the molecule types as .itp files in the .top file as below. If I'm doing 
anything wrong please let me know! :)


Combining different force fields into a single system completely invalidates it, 
so yes, I'd say you're doing something wrong :)


-Justin



 ;
;This is your topology file
;"What If None Of Your Dreams Come True ?" (E. Costello)
;
; Include forcefield parameters
#include "ffamber99sb.itp"

[ atomtypes ] 
from 
the top file of the non amber force field

;name  bond_typemasscharge   ptype  sigma  epsilon
CYCY  0.  0.  A   3.39967e-01  4.57730e-01
O  O  0.  0.  A   2.95992e-01  8.78640e-01
HOHO  0.  0.  A   0.0e+00  0.0e+00
H1H1  0.  0.  A   2.47135e-01  6.56888e-02
O2O2  0.  0.  A   2.95992e-01  8.78640e-01
N  N  0.  0.  A   3.25000e-01  7.11280e-01
H2H2  0.  0.  A   2.29317e-01  6.56888e-02
OYOY  0.  0.  A   3.1e-01  7.11280e-01
HCHC  0.  0.  A   2.64953e-01  6.56888e-02
H  H  0.  0.  A   1.06908e-01  6.56888e-02
C  C  0.  0.  A   3.39967e-01  3.59824e-01
OSOS  0.  0.  A   3.1e-01  7.11280e-01
CGCG  0.  0.  A   3.39967e-01  4.57730e-01
OHOH  0.  0.  A   3.06647e-01  8.80314e-01

#include 
"protein.itp"from 
the top file of the amber force field, contains everything usually 
specified here under [molecule types].


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

#ifdef POSRES_CA
#include "CA_posre.itp"
#endif

#include 
"trisacc.itp"from 
the top file of the non amber force field, contains charges etc.


; Include Position restraint file
#ifdef POSRES_trisacc
#include "trisacc_posre.itp"
#endif

; Include water topology
#include "ffamber_tip3p.itp"

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

; Include generic topology for ions
#include "Na_amber99sb.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_A   1
trisacc1
SOL 10697
Na  4



2010/5/19 you zou mailto:zou@live.com>>

Hi Justin,

Thank you for your help, But when I run x2top command there is one
error that is:
"
Can not find forcefield for atom C1-1 with 2 bonds
Can not find forcefield for atom C4-4 with 2 bonds
...
Program x2top, VERSION 4.0.5
Source code file: x2top.c, line: 207

Fatal error:
Could only find a forcefield type for 6 out of 24 atoms"

I don't know how can I adjust this error.
I have one more question again, this command give me a top file, if
I want gro file of this pdb (drug that has removed from drug-enzyme
complex) how can I do that?

you zou wrote:
> Dear Users,
> 
> I have one question about Drug-Enzyme Complex,Similar to tutorial If I 



>
  want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug 
> but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg 
> Beta version" server too, or not?


No. You can't use two different force fields in one simulation system.



> If I can't use this server, how can I make .gro file and .itp file for 
> drug that remove from initial .pdb file?
> 

There are several programs in the User Contributions from the website, x2top 



(which is distributed with Gromacs), or you can build the topology by hand. No 
matter what you choose, you need a thorough understanding of the mechanics of 
your chosen force field, methods of validation, and of course Chapter 5 in the 



Gromacs manual.


Thanks



Hotmail: Free, trusted and rich email service. Get it now.


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Please search the archive at http://www.gromacs.org/search before
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.
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[gmx-users] enegry minimisation

[sonali dhindwal]

Hello All
This question may sound trivial to many, but as i am new to this field, please 
help.
I want to ask a question regarding my previous query of distortion of protein 
strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using steepest decent algorithm, 
using emtol of 1000 kJ mol-1 nm-1 , large amount of distortion occurs.
So
is it necessary to do enegry minimisation step before MD, because this
is my modeled protein, and i have  already done energy minimisation
using different program and after that I have done refinement also.
Thanks and regards



--
Sonali Dhindwal

-- 
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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www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] enegry minimisation

[Erik Marklund]

sonali dhindwal skrev:

Hello All
This question may sound trivial to many, but as i am new to this 
field, please help.
I want to ask a question regarding my previous query of distortion of 
protein strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using steepest decent 
algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large amount of 
distortion occurs.
So is it necessary to do enegry minimisation step before MD, because 
this is my modeled protein, and i have  already done energy 
minimisation using different program and after that I have done 
refinement also.

Thanks and regards
^


--
Sonali Dhindwal


So how has your system setup changed since your previous EM? Addition of 
water? Cutoffs? PME?


--
---
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] enegry minimisation

[sonali dhindwal]

Thanks Justin for your reply.
Yes I have included solvent in the protein using genbox.
I am pasting .mdp file which I used for MD simulation :

title   = trp_drg MD
cpp = /lib/cpp ; location of cpp on SGI
constraints = all-bonds
integrator  = md
dt  = 0.002 ; ps !
nsteps  = 50 ; total 1 ns.
nstcomm =1
nstxout = 500 ; output coordinates every 1.0 ps
nstvout =0
nstfout =0
nstlist = 5
ns_type = grid
rlist   = 0.9
coulombtype = PME
rcoulomb    = 0.9
rvdw    = 1.4
fourierspacing  = 0.12
fourier_nx    =0
fourier_ny    =0
fourier_nz    =0
pme_order =6
ewald_rtol    = 1e-5
optimize_fft  = yes
; Berendsen temperature coupling is on in four groups
Tcoupl    = berendsen
tau_t   = 0.1    0.1   0.1   0.1   0.1   0.1
tc_grps = Protein    SOL    MG   PEP   E4P   NA+
ref_t   = 300    300   300   300   300   300
; Pressure coupling is on
Pcoupl  = berendsen
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 = 300.0
gen_seed = 173529

I hope it will help you to guide me futher.
Thanks

--
Sonali Dhindwal

--- On Wed, 19/5/10, Justin A. Lemkul  wrote:

From: Justin A. Lemkul 
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" 
Date: Wednesday, 19 May, 2010, 5:17 PM



sonali dhindwal wrote:
> Hello All
> This question may sound trivial to many, but as i am new to this field, 
> please help.
> I want to ask a question regarding my previous query of distortion of protein 
> strucutre after molecular dynamcs simulation.

Can you provide a link to your previous post, for reference?

> I have noticed that after enegry minimisation using steepest decent 
> algorithm, using emtol of 1000 kJ mol^-1 nm^-1 .
> So is it necessary to do enegry minimisation step before MD, because this is 
> my modeled protein, and i have  already done energy minimisation using 
> different program and after that I have done refinement also.

Have you added solvent or anything else to the protein model?  If so, then the 
answer is yes.  Solvation with a regularly-ordered lattice of solvent molecules 
can (and often does) lead to bad clashes with your protein structure, thus 
necessitating further minimization.

There are plenty of reasons why a protein structure might be unstable, most of 
them related to .mdp file settings, but you haven't posted those so there's no 
way to know if you're doing things correctly.

-Justin

> Thanks and regards
> ^
> 
> --
> Sonali Dhindwal
> 
> 

-- 

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 list    gmx-users@gromacs.org
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Re: [gmx-users] enegry minimisation

[Justin A. Lemkul]

sonali dhindwal wrote:

Thanks Justin for your reply.
Yes I have included solvent in the protein using genbox.


Then you should do energy minimization after constructing the system.


I am pasting .mdp file which I used for MD simulation :

title   = trp_drg MD
cpp = /lib/cpp ; location of cpp on SGI
constraints = all-bonds
integrator  = md
dt  = 0.002 ; ps !
nsteps  = 50 ; total 1 ns.
nstcomm =1


I don't know if this matters or not, but I think your parameters and values 
should be separated from the '=' by whitespace.  I also don't know if that will 
have any effect on your unstable system (see below), but do check to make sure 
that all of your settings have been interpreted correctly.  Confirm your input 
settings with the mdout.mdp file produced by grompp.



nstxout = 500 ; output coordinates every 1.0 ps
nstvout =0
nstfout =0
nstlist = 5
ns_type = grid
rlist   = 0.9
coulombtype = PME
rcoulomb= 0.9
rvdw= 1.4
fourierspacing  = 0.12
fourier_nx=0
fourier_ny=0
fourier_nz=0
pme_order =6
ewald_rtol= 1e-5
optimize_fft  = yes
; Berendsen temperature coupling is on in four groups
Tcoupl= berendsen
tau_t   = 0.10.1   0.1   0.1   0.1   0.1
tc_grps = ProteinSOLMG   PEP   E4P   NA+
ref_t   = 300300   300   300   300   300


This thermostat setup is certainly incorrect.  You should not couple all the 
components of your system to separate thermostats.  See here:


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

You have a fairly complicated system.  Are some of these species small 
molecules?  If so, how did you derive their parameters?  Have you demonstrated 
that these parameters are accurate?  Which structure is falling apart, and how 
are you making that assessment?


-Justin


; Pressure coupling is on
Pcoupl  = berendsen
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 = 300.0
gen_seed = 173529

I hope it will help you to guide me futher.
Thanks

--
Sonali Dhindwal


--- On *Wed, 19/5/10, Justin A. Lemkul //* wrote:


From: Justin A. Lemkul 
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" 
Date: Wednesday, 19 May, 2010, 5:17 PM



sonali dhindwal wrote:
 > Hello All
 > This question may sound trivial to many, but as i am new to this
field, please help.
 > I want to ask a question regarding my previous query of
distortion of protein strucutre after molecular dynamcs simulation.

Can you provide a link to your previous post, for reference?

 > I have noticed that after enegry minimisation using steepest
decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 .
 > So is it necessary to do enegry minimisation step before MD,
because this is my modeled protein, and i have  already done energy
minimisation using different program and after that I have done
refinement also.

Have you added solvent or anything else to the protein model?  If
so, then the answer is yes.  Solvation with a regularly-ordered
lattice of solvent molecules can (and often does) lead to bad
clashes with your protein structure, thus necessitating further
minimization.

There are plenty of reasons why a protein structure might be
unstable, most of them related to .mdp file settings, but you
haven't posted those so there's no way to know if you're doing
things correctly.

-Justin

 > Thanks and regards
 > ^
 >
 > --
 > Sonali Dhindwal
 >
 >

-- 

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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--


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

Re: [gmx-users] enegry minimisation

[sonali dhindwal]

Sorry, but I couldnt get your question,
I have used this .mdp file for energy minimisation after addition of water and 
using GROMOS96 43a1 force field :
title    = drg_trp
cpp  = /lib/cpp ; location of cpp on SGI
define   = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4]
constraints  = none
integrator   = steep
dt   = 0.002    ; ps !
nsteps   = 2000
nstlist  = 10
ns_type  = grid
rlist    = 0.9
coulombtype  = PME ; Use particle-mesh ewald
rcoulomb = 0.9
rvdw = 1.0
fourierspacing   = 0.12
fourier_nx =  0
fourier_ny =  0
fourier_nz =  0
pme_order  =  4
ewald_rtol =  1e-5
optimize_fft  = yes
;
;   Energy minimizing stuff
;
emtol   = 1000.0
emstep  = 0.01

I hope it will help you to guide me further
Thanks
--
Sonali Dhindwal

--- On Wed, 19/5/10, Erik Marklund  wrote:

From: Erik Marklund 
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" 
Date: Wednesday, 19 May, 2010, 5:31 PM

sonali dhindwal skrev:
> Hello All
> This question may sound trivial to many, but as i am new to this field, 
> please help.
> I want to ask a question regarding my previous query of distortion of protein 
> strucutre after molecular dynamcs simulation.
> I have noticed that after enegry minimisation using steepest decent 
> algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large amount of distortion 
> occurs.
> So is it necessary to do enegry minimisation step before MD, because this is 
> my modeled protein, and i have  already done energy minimisation using 
> different program and after that I have done refinement also.
> Thanks and regards
> ^
> 
> 
> --
> Sonali Dhindwal
> 
> 
So how has your system setup changed since your previous EM? Addition of water? 
Cutoffs? PME?

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

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Re: [gmx-users] enegry minimisation

[Gaurav Goel]

After adding water you can do energy minimization (EM) in two steps:

1. Constrain the protein backbone and do EM.
2. Now do EM on the full system.
3. Run a short MD simulation by constraining the protein backbone.
The above three steps will help hydrate the protein molecule with minimal
distortion of protein structure.

4. Now run a MD on full system.

for details looks here:
http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ

-Gaurav

On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal <
sonali11dhind...@yahoo.co.in> wrote:

> Sorry, but I couldnt get your question,
> I have used this .mdp file for energy minimisation after addition of water
> and using
>
> GROMOS96 43a1 force field :
>
>
> title= drg_trp
> cpp  = /lib/cpp ; location of cpp on SGI
> define   = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4]
> constraints  = none
> integrator   = steep
> dt   = 0.002; ps !
> nsteps   = 2000
> nstlist  = 10
> ns_type  = grid
> rlist= 0.9
> coulombtype  = PME ; Use particle-mesh ewald
> rcoulomb = 0.9
> rvdw = 1.0
> fourierspacing   = 0.12
> fourier_nx =  0
> fourier_ny =  0
> fourier_nz =  0
> pme_order  =  4
> ewald_rtol =  1e-5
> optimize_fft  = yes
> ;
> ;   Energy minimizing stuff
> ;
> emtol   = 1000.0
> emstep  = 0.01
>
> I hope it will help you to guide me further
> Thanks
> --
> Sonali Dhindwal
>
>
> --- On *Wed, 19/5/10, Erik Marklund * wrote:
>
>
> From: Erik Marklund 
> Subject: Re: [gmx-users] enegry minimisation
> To: "Discussion list for GROMACS users" 
> Date: Wednesday, 19 May, 2010, 5:31 PM
>
>
> sonali dhindwal skrev:
> > Hello All
> > This question may sound trivial to many, but as i am new to this field,
> please help.
> > I want to ask a question regarding my previous query of distortion of
> protein strucutre after molecular dynamcs simulation.
> > I have noticed that after enegry minimisation using steepest decent
> algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large amount of distortion
> occurs.
> > So is it necessary to do enegry minimisation step before MD, because this
> is my modeled protein, and i have  already done energy minimisation using
> different program and after that I have done refinement also.
> > Thanks and regards
> > ^
> >
> >
> > --
> > Sonali Dhindwal
> >
> >
> So how has your system setup changed since your previous EM? Addition of
> water? Cutoffs? PME?
>
> -- ---
> 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.se 
> http://folding.bmc.uu.se/
>
> -- gmx-users mailing list
> gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to 
> gmx-users-requ...@gromacs.org
> .
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] enegry minimisation

[Justin A. Lemkul]

Gaurav Goel wrote:

After adding water you can do energy minimization (EM) in two steps:

1. Constrain the protein backbone and do EM.
2. Now do EM on the full system.
3. Run a short MD simulation by constraining the protein backbone.
The above three steps will help hydrate the protein molecule with 
minimal distortion of protein structure.




Such finesse may certainly be beneficial.  Just for clarity, though, what you 
are referring to is the application of (position) restraints, not constraints.


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

-Justin


4. Now run a MD on full system.

for details looks here:
http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ 



-Gaurav

On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal 
mailto:sonali11dhind...@yahoo.co.in>> wrote:


Sorry, but I couldnt get your question,
I have used this .mdp file for energy minimisation after addition of
water and using

GROMOS96 43a1 force field :


title= drg_trp
cpp  = /lib/cpp ; location of cpp on SGI
define   = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4]
constraints  = none
integrator   = steep
dt   = 0.002; ps !
nsteps   = 2000
nstlist  = 10
ns_type  = grid
rlist= 0.9
coulombtype  = PME ; Use particle-mesh ewald
rcoulomb = 0.9
rvdw = 1.0
fourierspacing   = 0.12
fourier_nx =  0
fourier_ny =  0
fourier_nz =  0
pme_order  =  4
ewald_rtol =  1e-5
optimize_fft  = yes
;
;   Energy minimizing stuff
;
emtol   = 1000.0
emstep  = 0.01

I hope it will help you to guide me further
Thanks
--
Sonali Dhindwal


--- On *Wed, 19/5/10, Erik Marklund /mailto:er...@xray.bmc.uu.se>>/* wrote:


From: Erik Marklund mailto:er...@xray.bmc.uu.se>>
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" mailto:gmx-users@gromacs.org>>
Date: Wednesday, 19 May, 2010, 5:31 PM


sonali dhindwal skrev:
 > Hello All
 > This question may sound trivial to many, but as i am new to
this field, please help.
 > I want to ask a question regarding my previous query of
distortion of protein strucutre after molecular dynamcs simulation.
 > I have noticed that after enegry minimisation using steepest
decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large
amount of distortion occurs.
 > So is it necessary to do enegry minimisation step before MD,
because this is my modeled protein, and i have  already done
energy minimisation using different program and after that I
have done refinement also.
 > Thanks and regards
 > ^
 >
 >
 > --
 > Sonali Dhindwal
 >
 >
So how has your system setup changed since your previous EM?
Addition of water? Cutoffs? PME?

-- ---
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.se
   
http://folding.bmc.uu.se/


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--
===

[gmx-users] g_cluster, RMSD distribution

[Michał Koliński]

Dear All

I’m trying to obtain RMSD distribution of  a ligand in the binding site of the 
receptor protein during 40 ns MD simulation.
Could you please explain:

- what is exactly the yaxis unit  of the plot obtained using g_cluster with 
–dist option
-  how is this distribution calculated?

Thank you in advance,

All best,
Michal
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Re: [gmx-users] enegry minimisation

[Gaurav Goel]

On Wed, May 19, 2010 at 9:18 AM, Justin A. Lemkul  wrote:
>
>
> Gaurav Goel wrote:
>>
>> After adding water you can do energy minimization (EM) in two steps:
>>
>> 1. Constrain the protein backbone and do EM.
>> 2. Now do EM on the full system.
>> 3. Run a short MD simulation by constraining the protein backbone.
>> The above three steps will help hydrate the protein molecule with minimal
>> distortion of protein structure.
>>
>
> Such finesse may certainly be beneficial.  Just for clarity, though, what
> you are referring to is the application of (position) restraints, not
> constraints.
>
> http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
>
Justin, thanks for clarifying. I was referring to position restraints.
-Gaurav
> -Justin
>
>> 4. Now run a MD on full system.
>>
>> for details looks here:
>>
>> http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ
>> 
>>
>> -Gaurav
>>
>> On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal
>> mailto:sonali11dhind...@yahoo.co.in>> wrote:
>>
>>    Sorry, but I couldnt get your question,
>>    I have used this .mdp file for energy minimisation after addition of
>>    water and using
>>
>>    GROMOS96 43a1 force field :
>>
>>
>>    title            = drg_trp
>>    cpp              = /lib/cpp ; location of cpp on SGI
>>    define           = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4]
>>    constraints      = none
>>    integrator       = steep
>>    dt               = 0.002    ; ps !
>>    nsteps           = 2000
>>    nstlist          = 10
>>    ns_type          = grid
>>    rlist            = 0.9
>>    coulombtype      = PME ; Use particle-mesh ewald
>>    rcoulomb         = 0.9
>>    rvdw             = 1.0
>>    fourierspacing   = 0.12
>>    fourier_nx     =  0
>>    fourier_ny     =  0
>>    fourier_nz     =  0
>>    pme_order      =  4
>>    ewald_rtol     =  1e-5
>>    optimize_fft      = yes
>>    ;
>>    ;       Energy minimizing stuff
>>    ;
>>    emtol               = 1000.0
>>    emstep              = 0.01
>>
>>    I hope it will help you to guide me further
>>    Thanks
>>    --
>>    Sonali Dhindwal
>>
>>
>>    --- On *Wed, 19/5/10, Erik Marklund />    >/* wrote:
>>
>>
>>        From: Erik Marklund >        >
>>        Subject: Re: [gmx-users] enegry minimisation
>>        To: "Discussion list for GROMACS users" >        >
>>        Date: Wednesday, 19 May, 2010, 5:31 PM
>>
>>
>>        sonali dhindwal skrev:
>>         > Hello All
>>         > This question may sound trivial to many, but as i am new to
>>        this field, please help.
>>         > I want to ask a question regarding my previous query of
>>        distortion of protein strucutre after molecular dynamcs simulation.
>>         > I have noticed that after enegry minimisation using steepest
>>        decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large
>>        amount of distortion occurs.
>>         > So is it necessary to do enegry minimisation step before MD,
>>        because this is my modeled protein, and i have  already done
>>        energy minimisation using different program and after that I
>>        have done refinement also.
>>         > Thanks and regards
>>         > ^
>>         >
>>         >
>>         > --
>>         > Sonali Dhindwal
>>         >
>>         >
>>        So how has your system setup changed since your previous EM?
>>        Addition of water? Cutoffs? PME?
>>
>>        -- ---
>>        Erik Marklund, PhD student
>>        Dept. of Cell and Molecular Biology, Uppsala University.
>>        Husargatan 3, Box 596,    75124 Uppsala, Sweden
>>        phone:    +46 18 471 4537        fax: +46 18 511 755
>>        er...@xray.bmc.uu.se
>>        
>> http://folding.bmc.uu.se/
>>
>>        -- gmx-users mailing list    gmx-us...@gromacs.org
>>        
>>        http://lists.gromacs.org/mailman/listinfo/gmx-users
>>        Please search the archive at http://www.gromacs.org/search
>>        before posting!
>>        Please don't post (un)subscribe requests to the list. Use the
>>        www interface or send it to gmx-users-requ...@gromacs.org
>>        .
>>        Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>    --
>>    gmx-users mailing list    gmx-us...@gromacs.org
>>    
>>    

[gmx-users] Re: Re: crystallographic water to tip4p model

[Павел Кудрявцев]

>> Hi,
>> I wanna keep crystallographic water with tip4p model for md simulation
but when I use pdb2gmx even if I set "-water tip4p" it protonates oxygens to
spc water model instead.
>> Is there any way to replace spc water molecules with tip4p water
molecules in the same orientation?
>
>What's your GROMACS version and command line?
>
>> Btw what happen if I'll keep 2 types of water models in one simulation?
>
>Your reviewers will giggle.
>
>Mark

Hi
I’m using following lines to prepare structure

pdb2gmx -f 1KEH.pdb -o 1keh.gro -p 1keh.top -ff oplsaa -water tip4p
editconf -f 1keh.gro -d 1 -c -bt cubic -o 1keh.box.gro
genbox -cp 1keh.box.gro -cs tip4p.gro -o 1keh.sol.gro -p 1keh.top

after this in 1keh.sol.gro there are 2 types of water like
 1078HO4HW112050   5.331   6.748   7.575
 1078HO4HW212051   5.413   6.666   7.459
 1078HO4HW312052   5.413   6.748   7.517
 1079HO4 OW12053   7.630   6.590   7.095
 1079HO4HW112054   7.630   6.671   7.037
 1079HO4HW212055   7.630   6.508   7.037
 1079HO4HW312056   7.630   6.590   7.095
 1080HO4 OW12057   3.861   4.563   2.433

and like
 1083SOL OW12069   1.736   0.839   0.257
 1083SOLHW112070   1.777   0.781   0.322
 1083SOLHW212071   1.643   0.831   0.274
 1083SOL MW12072   1.730   0.831   0.267
 1084SOL OW12073   1.602   0.771   1.252
 1084SOLHW112074   1.557   0.838   1.303
 1084SOLHW212075   1.690   0.807   1.238
 1084SOL MW12076   1.608   0.784   1.256
as I can understand pdb2gmx converted crystallographic O into H2O with
additional H in the same place as O instead of additional M near O
how can it be fixed?
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Re: [gmx-users] enegry minimisation

[sonali dhindwal]

Thanks Justin for your help
I checked the mdout.mpd, all the parameters were interpereted correctly, though 
from next time i will take care of putting space.
regarding you asked if those are small molecules, yes those are the ligands and 
i have taken .itp and .gro file from Dundee Prodrg server. I think those are 
acceptable !!
Thermostat setup:
I will now do this thing seperately as protein and non protein only as given in 
manual.

And also I will do that thing suggested by Gaurav, hopefully it will help in 
not distorting the protein structure.
Thanks a lot.

--
Sonali Dhindwal

--- On Wed, 19/5/10, Justin A. Lemkul  wrote:

From: Justin A. Lemkul 
Subject: Re: [gmx-users] enegry minimisation
To: "Gromacs Users' List" 
Date: Wednesday, 19 May, 2010, 5:45 PM



sonali dhindwal wrote:
> Thanks Justin for your reply.
> Yes I have included solvent in the protein using genbox.

Then you should do energy minimization after constructing the system.

> I am pasting .mdp file which I used for MD simulation :
> 
> title               = trp_drg MD
> cpp                 = /lib/cpp ; location of cpp on SGI
> constraints         = all-bonds
> integrator          = md
> dt                  = 0.002 ; ps !
> nsteps              = 50 ; total 1 ns.
> nstcomm             =1

I don't know if this matters or not, but I think your parameters and values
 should be separated from the '=' by whitespace.  I also don't know if that 
will have any effect on your unstable system (see below), but do check to make 
sure that all of your settings have been interpreted correctly.  Confirm your 
input settings with the mdout.mdp file produced by grompp.

> nstxout             = 500 ; output coordinates every 1.0 ps
> nstvout             =0
> nstfout             =0
> nstlist             = 5
> ns_type             = grid
> rlist               = 0.9
> coulombtype         = PME
> rcoulomb            = 0.9
> rvdw           
     = 1.4
> fourierspacing      = 0.12
> fourier_nx        =0
> fourier_ny        =0
> fourier_nz        =0
> pme_order         =6
> ewald_rtol        = 1e-5
> optimize_fft      = yes
> ; Berendsen temperature coupling is on in four groups
> Tcoupl                = berendsen
> tau_t               = 0.1        0.1   0.1   0.1   0.1   0.1
> tc_grps             = Protein    SOL    MG   PEP   E4P   NA+
> ref_t               =
 300        300   300   300   300   300

This thermostat setup is certainly incorrect.  You should not couple all the 
components of your system to separate thermostats.  See here:

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

You have a fairly complicated system.  Are some of these species small 
molecules?  If so, how did you derive their parameters?  Have you demonstrated 
that these parameters are accurate?  Which structure is falling apart, and how 
are you making that assessment?

-Justin

> ; Pressure coupling is on
> Pcoupl              = berendsen
> 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 = 300.0
> gen_seed = 173529
> 
> I hope it will help you to guide me futher.
> Thanks
> 
> --
> Sonali Dhindwal
> 
> 
> --- On *Wed, 19/5/10, Justin A. Lemkul //* wrote:
> 
> 
>     From: Justin A. Lemkul 
>     Subject: Re: [gmx-users] enegry minimisation
>     To: "Discussion list for GROMACS users" 
>     Date: Wednesday, 19 May, 2010, 5:17 PM
> 
> 
> 
>     sonali dhindwal wrote:
>      > Hello All
>      > This question may sound trivial to many, but as i am new to this
>     field, please help.
>      > I want to ask a question regarding my previous query of
>     distortion of protein strucutre after molecular dynamcs simulation.
> 
>     Can you provide a link to your previous post, for reference?
> 
>      > I have noticed that after enegry minimisation using steepest
>     decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 .
>   
   > So is it necessary to do enegry minimisation step before MD,
>     because this is my modeled protein, and i have  already done energy
>     minimisation using different program and after that I have done
>     refinement also.
> 
>     Have you added solvent or anything else to the protein model?  If
>     so, then the answer is yes.  Solvation with a regularly-ordered
>     lattice of solvent molecules can (and often does) lead to bad
>     clashes with your protein structure, thus necessitating further
>     minimization.
> 
>     There are plenty of reasons why a protein structure might be
>     unstable, most of them related to .mdp file settings, but
 you
>     haven't posted those so there's no way to know if you're doing
>     things correctly.
> 
>     -Justin
> 
>      > Thanks and regards
>      > ^
>      >
>      > --
>      > Sonali Dhindwal
>      >
>      >
> 
>     -- 
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctora

Re: [gmx-users] enegry minimisation

[Justin A. Lemkul]

sonali dhindwal wrote:

Thanks Justin for your help
I checked the mdout.mpd, all the parameters were interpereted correctly, 
though from next time i will take care of putting space.
regarding you asked if those are small molecules, yes those are the 
ligands and i have taken .itp and .gro file from Dundee Prodrg server. I 
think those are acceptable !!


I seem to say this several times per week: in my experience (and in the 
experience of many others who have posted here) the charges and charge groups 
output by PRODRG are often unsatisfactory, requiring manual modification and 
validation that they are correct.  This should be absolutely requisite for any 
study involving non-standard small molecules.  Increasingly, I see poor 
parameters used in the literature and it always makes me wonder how the 
simulations can be regarded as valid.  There should be no shortcuts - 
parameterization of small molecules is an advanced topic, requiring great care 
and understanding of the underlying force field.


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

I don't mean to undermine PRODRG entirely - it is a very useful tool for 
generating a framework topology.  But I have yet to see a topology it produced 
that is at all consistent with the parameters in the Gromos96 force field.  Try 
it yourself - run a known species (like an amino acid) through PRODRG.  The 
results it gives are usually wildly inconsistent with the force field parameter 
library.


-Justin


Thermostat setup:
I will now do this thing seperately as protein and non protein only as 
given in manual.


And also I will do that thing suggested by Gaurav, hopefully it will 
help in not distorting the protein structure.

Thanks a lot.

--
Sonali Dhindwal


--- On *Wed, 19/5/10, Justin A. Lemkul //* wrote:


From: Justin A. Lemkul 
Subject: Re: [gmx-users] enegry minimisation
To: "Gromacs Users' List" 
Date: Wednesday, 19 May, 2010, 5:45 PM



sonali dhindwal wrote:
 > Thanks Justin for your reply.
 > Yes I have included solvent in the protein using genbox.

Then you should do energy minimization after constructing the system.

 > I am pasting .mdp file which I used for MD simulation :
 >
 > title   = trp_drg MD
 > cpp = /lib/cpp ; location of cpp on SGI
 > constraints = all-bonds
 > integrator  = md
 > dt  = 0.002 ; ps !
 > nsteps  = 50 ; total 1 ns.
 > nstcomm =1

I don't know if this matters or not, but I think your parameters and
values should be separated from the '=' by whitespace.  I also don't
know if that will have any effect on your unstable system (see
below), but do check to make sure that all of your settings have
been interpreted correctly.  Confirm your input settings with the
mdout.mdp file produced by grompp.

 > nstxout = 500 ; output coordinates every 1.0 ps
 > nstvout =0
 > nstfout =0
 > nstlist = 5
 > ns_type = grid
 > rlist   = 0.9
 > coulombtype = PME
 > rcoulomb= 0.9
 > rvdw= 1.4
 > fourierspacing  = 0.12
 > fourier_nx=0
 > fourier_ny=0
 > fourier_nz=0
 > pme_order =6
 > ewald_rtol= 1e-5
 > optimize_fft  = yes
 > ; Berendsen temperature coupling is on in four groups
 > Tcoupl= berendsen
 > tau_t   = 0.10.1   0.1   0.1   0.1   0.1
 > tc_grps = ProteinSOLMG   PEP   E4P   NA+
 > ref_t   = 300300   300   300   300   300

This thermostat setup is certainly incorrect.  You should not couple
all the components of your system to separate thermostats.  See here:

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

You have a fairly complicated system.  Are some of these species
small molecules?  If so, how did you derive their parameters?  Have
you demonstrated that these parameters are accurate?  Which
structure is falling apart, and how are you making that assessment?

-Justin

 > ; Pressure coupling is on
 > Pcoupl  = berendsen
 > 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 = 300.0
 > gen_seed = 173529
 >
 > I hope it will help you to guide me futher.
 > Thanks
 >
 > --
 > Sonali Dhindwal
 >
 >
 > --- On *Wed, 19/5/10, Justin A. Lemkul //* wrote:
 >
 >
 > From: Justin A. Lemkul 
 > Subject: Re: [gmx-users] enegry minimisation
 > To: "Discussion list for GROMACS users" 
 > Date: Wednesday, 19 May, 2010, 5:17 P

[gmx-users] Phosphorylation of protein

[rituraj purohit]

Cell and Molecular Biology, Uppsala University.
> >>        Husargatan 3, Box 596,    75124 Uppsala, Sweden
> >>        phone:    +46 18 471 4537        fax: +46 18 511 755
> >>        er...@xray.bmc.uu.se
> >>        <http://mc/compose?to=er...@xray.bmc.uu.se>
> >> http://folding.bmc.uu.se/
> >>
> >>        -- gmx-users mailing list    gmx-us...@gromacs.org
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> >>        http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >>        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
> >>        <http://mc/compose?to=gmx-users-requ...@gromacs.org>.
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> >>
> >>
> >>
> >>    --
> >>    gmx-users mailing list    gmx-us...@gromacs.org
> >>    <mailto:gmx-users@gromacs.org>
> >>    http://lists.gromacs.org/mailman/listinfo/gmx-users
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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
> >
> > 
> > --
> > gmx-users mailing list    gmx-us...@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the www interface
> > or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
> --
>
> Message: 4
> Date: Wed, 19 May 2010 17:35:46 +0400
> From: ? ? 
> Subject: [gmx-users] Re: Re: crystallographic water to tip4p model
> To: gmx-users@gromacs.org
> Message-ID:
>        
> Content-Type: text/plain; charset="windows-1252"
>
> >> Hi,
> >> I wanna keep crystallographic water with tip4p model for md simulation
> but when I use pdb2gmx even if I set "-water tip4p" it protonates oxygens to
> spc water model instead.
> >> Is there any way to replace spc water molecules with tip4p water
> molecules in the same orientation?
> >
> >What's your GROMACS version and command line?
> >
> >> Btw what happen if I'll keep 2 types of water models in one simulation?
> >
> >Your reviewers will giggle.
> >
> >Mark
>
> Hi
> I’m using following lines to prepare structure
>
> pdb2gmx -f 1KEH.pdb -o 1keh.gro -p 1keh.top -ff oplsaa -water tip4p
> editconf -f 1keh.gro -d 1 -c -bt cubic -o 1keh.box.gro
> genbox -cp 1keh.box.gro -cs tip4p.gro -o 1keh.sol.gro -p 1keh.top
>
> after this in 1keh.sol.gro there are 2 types of water like
>  1078HO4    HW112050   5.331   6.748   7.575
>  1078HO4    HW212051   5.413   6.666   7.459
>  1078HO4    HW312052   5.413   6.748   7.517
>  1079HO4     OW12053   7.630   6.590   7.095
>  1079HO4    HW112054   7.630   6.671   7.037
>  1079HO4    HW212055   7.630   6.508   7.037
>  1079HO4    HW312056   7.630   6.590   7.095
>  1080HO4     OW12057   3.861   4.563   2.433
>
> and like
>  1083SOL     OW12069   1.736   0.839   0.257
>  1083SOL    HW112070   1.777   0.781   0.322
>  1083SOL    HW212071   1.643   0.831   0.274
>  1083SOL     MW12072   1.730   0.831   0.267
>  1084SOL     OW12073   1.602   0.771   1.252
>  1084SOL    HW112074   1.557   0.838   1.303
>  1084SOL    HW212075   1.690   0.807   1.238
>  1084SOL     MW12076   1.608   0.784   1.256
> as I can understand pdb2gmx converted crystallographic O into H2O with
> additional H in the same place as O instead of additional M near O
> how can it be fixed?
> -- next part --
> An HTML attachment was scrubbed...
> URL: 
> htt

Re: [gmx-users] g_cluster, RMSD distribution

[Ran Friedman]

Hi,

The distribution is calculated as follows:
101 bins are formed between zero and maximum rmsd in equal separation
(by calculating the largest value by 100 to create the separation). Each
rmsd value is put into the right bin and the counter for that bin is
increased by 1. The total number of counts is the size of half a matrix.

Example:
If the maximal rmsd is 10.0 and a certain comparison yield rmsd=0.13 the
value of the second bin in increased by 1.

Ran.

Michał Koliński wrote:
> Dear All
>
> I’m trying to obtain RMSD distribution of  a ligand in the binding site of 
> the receptor protein during 40 ns MD simulation.
> Could you please explain:
>
> - what is exactly the yaxis unit  of the plot obtained using g_cluster with 
> –dist option
> -  how is this distribution calculated?
>
> Thank you in advance,
>
> All best,
> Michal
>   

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[gmx-users] Re: OPLS-AA/L force field

[you zou]

Hi again,  Sorry I confused you with my question. My question is How can I make 
.gro file and .top file from drug.pdb (that removed from drug-enzyme.pdb)? If I 
can use x2top command I will make .top file just, is it true? I think .gro file 
is dependent on forcefiled too so If I use editconf command I will miss 
something, is it true?Thank you again
you zou wrote:
> Hi Justin,
> 
> Thank you for your help, But when I run x2top command there is one error 
> that is:
> "
> Can not find forcefield for atom C1-1 with 2 bonds
> Can not find forcefield for atom C4-4 with 2 bonds
> ...
> Program x2top, VERSION 4.0.5
> Source code file: x2top.c, line: 207
> 
> Fatal error:
> Could only find a forcefield type for 6 out of 24 atoms"
> 

Not all of your atom types are described by ffoplsaa.n2t so you will have to 
add 
them. There are only a limited number of types that are covered by default.

http://www.gromacs.org/Documentation/File_Formats/.n2t_File

> I don't know how can I adjust this error.
> I have one more question again, this command give me a top file, if I 
> want gro file of this pdb (drug that has removed from drug-enzyme 
> complex) how can I do that?
> 

Do you just need a .gro file, and not a .top? My understanding from your first 
message was that you needed a topology. If you just need a .gro, then simply 
pass your .pdb file to editconf.

-Justin

> you zou wrote:
>> Dear Users,
>> 
>> I have one question about Drug-Enzyme Complex,Similar to tutorial If I 
>>
> want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug 
>> but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg 
>> Beta version" server too, or not?
> 
> No. You can't use two different force fields in one simulation system.
> 
>> If I can't use this server, how can I make .gro file and .itp file for 
>> drug that remove from initial .pdb file?
>> 
> 
> There are several programs in the User Contributions from the website, x2top 
> (which is distributed with Gromacs), or you can build the topology by hand. 
> No 
> matter what you choose, you need a thorough understanding of the mechanics of 
> your chosen force field, methods of validation, and of course Chapter 5 in 
> the 
> 
> Gromacs manual.
> 

  
_
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[gmx-users] energy decreasing in NVE simulation

[Yun-an Yan]

Dear all,

When I try to simulation with NVE ensemble, the
total energy keeps decreasing. Geometry optimization
and solvent equilibration are done before the NVE simulation.

I follow the requirements provided in
http://www.gromacs.org/Documentation/Terminology/NVE

Would any one help me to figure out what was wrong with
my settings?

Millions of thanks and best wishes,
Yun-an


BTW: Please check the following for the .mdp file

;Run control: A leap-frog algorithm for integrating Newton's equations.
integrator   = md
;time step in femtoseconds
dt   = 0.001
;number of steps
nsteps   = 1000
;No constraints
constraints  = none
constraint_algorithm = shake
shake_tol= 1e-08

; group(s) for center of mass motion removal
comm-grps= AA CCl4
; frequency for center of mass motion removal
nstcomm  =  1000
;frequency to write coordinates to output trajectory file
nstxout  = 1000
;frequency to write velocities to output trajectory file
nstvout  = 1000
;frequency to write energies to log file
nstlog   = 1000
;frequency to write energies to energy file
nstenergy= 1000
;group(s) to write to energy file
energygrps   = System

;Frequency to update the neighbor list (and the long-range forces,
;when using twin-range cut-off's).
nstlist  = 10
ns_type  = grid
rlist= 1.5

; Use periodic boundary conditions in all directions.
pbc = xyz

;cut-off distance for the short-range neighbor list
;treatment of electrostatic interactions
coulombtype  = PME-switch
fourierspacing   = 0.12
pme_order= 4
ewald_rtol   = 1e-5
rcoulomb_switch  = 1.0
rcoulomb = 1.2

;treatment of van der waals interactions
vdwtype  = Switch
rvdw-switch  = 1.0
rvdw = 1.2
dispcorr = EnerPres

;Temperature coupling
tcoupl  = no

;Pressure coupling
pcoupl   = no

;Velocity generation
gen_vel  = no


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[gmx-users] acetonitrile from amber to gromacs

[vedat durmaz]

hi all together,

this week i'm trying to do some simulations with acetonitrile (AN) as a
solvent and using ffamber99 as force field. on this website

http://www.pharmacy.manchester.ac.uk/bryce/amber#box

i found a gorgeous little box containing a pretty number of 6-site
modeled AN molecules, represented by 3 files:

ch3cn_210.pdb
frcmod.ch3cn
prep.ch3cn

does anyone have an idea, how to generate .gro/.itp files out of these
amber files, preferably by pushing a single button of some proper tool??

i'ld be the happiest guy in world if someone told me the trick!

regards,

vedat


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Re: [gmx-users] acetonitrile from amber to gromacs

[J. Rui Rodrigues]

Hi,

You could use acpype, although you will need to push more than one button :-)
http://code.google.com/p/acpype/

Cheers,
Rui Rodrigues


On Wed, 19 May 2010 18:15:29 +0200, vedat durmaz wrote
> hi all together,
> 
> this week i'm trying to do some simulations with acetonitrile (AN) as a
> solvent and using ffamber99 as force field. on this website
> 
> http://www.pharmacy.manchester.ac.uk/bryce/amber#box
> 
> i found a gorgeous little box containing a pretty number of 6-site
> modeled AN molecules, represented by 3 files:
> 
> ch3cn_210.pdb
> frcmod.ch3cn
> prep.ch3cn
> 
> does anyone have an idea, how to generate .gro/.itp files out of these
> amber files, preferably by pushing a single button of some proper tool??
> 
> i'ld be the happiest guy in world if someone told me the trick!
> 
> regards,
> 
> vedat
> 
> -- 
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Re: [gmx-users] Re: OPLS-AA/L force field

[Justin A. Lemkul]

you zou wrote:

Hi again,

Sorry I confused you with my question. My question is How can I make .gro
file and .top file from drug.pdb (that removed from drug-enzyme.pdb)?

If I can use x2top command I will make .top file just, is it true? I think
.gro file is dependent on forcefiled too so If I use editconf command I will
miss something, is it true?


If you want to use x2top, the assumption is that the structure is already 
appropriate as is, that is it is properly protonated.  The only tool that is 
smart enough to add force field-specific hydrogens is pdb2gmx.  If you're using 
OPLS-AA, then you should have all hydrogens present, anyway.  If that's true, 
then you can use editconf to create a .gro file (which is not absolutely 
necessary; Gromacs can handle .pdb files just fine).  If you don't have all the 
appropriate atoms present in your molecule's structure, then you need to build a 
proper structure.


-Justin



Thank you again


you zou wrote:

Hi Justin,

Thank you for your help, But when I run x2top command there is one error 
that is: " Can not find forcefield for atom C1-1 with 2 bonds Can not find

forcefield for atom C4-4 with 2 bonds ...

&g t; Program x2top, VERSION 4.0.5

Source code file: x2top.c, line: 207

Fatal error: Could only find a forcefield type for 6 out of 24 atoms"



Not all of your atom types are described by ffoplsaa.n2t so you will have to
add them. There are only a limited number of types that are covered by
default.

http://www.gromacs.org/Documentation/File_Formats/.n2t_File


I don't know how can I adjust this error. I have one more question again,
this command give me a top file, if I want gro file of this pdb (drug that
has removed from drug-enzyme complex) how can I do that?



Do you just need a .gro file, and not a .top? My understanding from your
first message was that you needed a topo logy. If you just need a .gro, then
simply pass your .pdb file to editconf.

-Justin


you zou wrote:

Dear Users,

I have one question about Drug-Enzyme Complex,Similar to tutorial If I


want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg 
Beta version" server too, or not?


No. You can't use two different force fields in one simulation system.

If I can't use this server, how can I make .gro file and .itp file for 
drug that remove from initial .pdb file?




There are several programs in the User Contributions from the website,
x2top (which is distributed with Gromacs), or you can build the topology by
hand. No matter what you choose, you ne

ed a thorough understanding of the mechanics of

your chosen force field, methods of validation, and of course Chapter 5 in
the

Gromacs manual.




 
Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up

now. 



--


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: acetonitrile from amber to gromacs

[Vitaly Chaban]

>
> hi all together,
>
> this week i'm trying to do some simulations with acetonitrile (AN) as a
> solvent and using ffamber99 as force field. on this website
>
> http://www.pharmacy.manchester.ac.uk/bryce/amber#box
>
> i found a gorgeous little box containing a pretty number of 6-site
> modeled AN molecules, represented by 3 files:
>
> ch3cn_210.pdb
> frcmod.ch3cn
> prep.ch3cn
>
> does anyone have an idea, how to generate .gro/.itp files out of these
> amber files, preferably by pushing a single button of some proper tool??
>
> i'ld be the happiest guy in world if someone told me the trick!
>
>
To traslate PDB into GRO, use editconf (gromacs utility).
To get ITP, use X2TOP (gromacs utility).

Also see the topology archive on the gromacs website. A few years ago I
uploaded some working examples with ACN.


-- 
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[gmx-users] Constraint distance question

[Warren Gallin]

Hi,

I am trying to look at the free energy differences as a function of 
end-to-end distance of peptides in water.  I am running a set of simulations 
with the two atoms of interest joined by a type 2 constraint, with the length 
varying from 0.5 to 3 nm.  However, these simulations all explode, even though 
I am starting with conformations from an unconstrained simulation that are 
taken through another round of energy minimization and relaxtion before running 
the constrained simulations.

There is an mdrun option, -rcon, that I have not been setting.  I read 
this as the distance over which atoms interacting through the constraint will 
be communicated between processors for the P-LINC algorithm.  since some of the 
end-to-end distances can be relatively large, I was wondering if, in principle, 
I should be setting -rcon to the constarint distance +1 nm to ensure that the 
constraint is not randomly disappearing from consideration when the two ends of 
the peptide are in different domains.

Thanks for any insights.

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Re: [gmx-users] acetonitrile from amber to gromacs

[Anthony Cruz Balberdi]

I did it for other solvent. If you have AMBER is very easy to do. Do
you have AMBER?

On Wed, May 19, 2010 at 12:15 PM, vedat durmaz  wrote:
>
> hi all together,
>
> this week i'm trying to do some simulations with acetonitrile (AN) as a
> solvent and using ffamber99 as force field. on this website
>
> http://www.pharmacy.manchester.ac.uk/bryce/amber#box
>
> i found a gorgeous little box containing a pretty number of 6-site
> modeled AN molecules, represented by 3 files:
>
> ch3cn_210.pdb
> frcmod.ch3cn
> prep.ch3cn
>
> does anyone have an idea, how to generate .gro/.itp files out of these
> amber files, preferably by pushing a single button of some proper tool??
>
> i'ld be the happiest guy in world if someone told me the trick!
>
> regards,
>
> vedat
>
>
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Re: [gmx-users] acetonitrile from amber to gromacs

[durmaz]

thanks to all so far

@anthony
i have amberTools, but not the amber MD package. is that enough for my
purpose?

@rui
acpypi -i ch3cn_210.pdb
says: "cannot find template for residue C3N in our library". and indeed,
there's no residue C3N in my ffamber99sb.rtp file

(and i don't know, how to use it in order to generate my topology or even
an rtp file?!)

but (@vitaly) editconf does create the gro file which is fine.

however, when i use
x2top -f ch3cn_210.pdb -ff select -r x2top.rtp
and choose ffamber99sb as force field, i get the error message
"Library file ffamber99sb.n2t not found in current dir nor in your GMXLIB
path". there are n2t files, but not for the amber ff.

what have i done wrong?



> I did it for other solvent. If you have AMBER is very easy to do. Do
> you have AMBER?
>
> On Wed, May 19, 2010 at 12:15 PM, vedat durmaz  wrote:
>>
>> hi all together,
>>
>> this week i'm trying to do some simulations with acetonitrile (AN) as a
>> solvent and using ffamber99 as force field. on this website
>>
>> http://www.pharmacy.manchester.ac.uk/bryce/amber#box
>>
>> i found a gorgeous little box containing a pretty number of 6-site
>> modeled AN molecules, represented by 3 files:
>>
>> ch3cn_210.pdb
>> frcmod.ch3cn
>> prep.ch3cn
>>
>> does anyone have an idea, how to generate .gro/.itp files out of these
>> amber files, preferably by pushing a single button of some proper tool??
>>
>> i'ld be the happiest guy in world if someone told me the trick!
>>
>> regards,
>>
>> vedat
>>
>>
>> --
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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> posting!
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>>
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[gmx-users] weird problem about editconf and genbox

[Lin Xu]

Hi,
I have two questions concerning generating a solvent box for my protein using 
gromacs 3.3.1. 

1) I used to use editconf to generate a dodecahedron box, then use genbox. It 
used to work fine:
$editconf -f protein.gro -o protein_box.gro -d 0.9 -bt dodecahedron -c
$genbox -cp protein_box.gro -cs spc216.gro -p example.top -o 
protein_box_water.gro

  But recently I found that using exactly the same command and input files, and 
the same program installed, the protein is not centered in the box (I download 
the structure and view it in pymol and vmd). I tried other box types, for 
triclinic and cubic, it seems -c flag can be recognized, but not for octahedron 
(nor dodecahedron). I wonder what things could be wrong. 

2) I have crystal structure for wild type protein, when I generated solvent box 
for it, genbox didn't put waters in active site. Then I made two single-point 
active site residue mutations using pymol: for a mutant Thr->Ala, no water is 
put in active site neither, but for mutant Thr->Ser, a water molecule is found 
in the active site. The presence of waters drastically changed my simulation 
results. This is again different from what I got in the past. I used to work 
with those three proteins and no waters were added in their active sites. I 
assumed mutant Thr->Ser shouldn't have water, since genbox delete extra waters 
according to VanderWaals radii, and the three proteins (one real structure and 
two models built up by pymol) are so highly similar. I wonder why the program 
decide to treat them differently, this time? 

  I also tried using different box types and box dimensions for mutant 
Thr->Ser, and found sometimes a water added, but sometime not. Is this 
inconsistency normal? 

Sorry for the long email. Those problems seem really weird to me. Any guidance 
or hint would be highly appreciated.
Thank you very much,

Lin Xu

Ph.D. Candidate
Boxer lab, Chemistry Department
Stanford University
Stanford CA 94305
(650)6448383
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Re: [gmx-users] weird problem about editconf and genbox

[Justin A. Lemkul]

Lin Xu wrote:

Hi, I have two questions concerning generating a solvent box for my protein
using gromacs 3.3.1.



Any particular reason you're using software that is over four years old? 
Gromacs 4.0.7 will give you a major speed upgrade, and lots of new features.



1) I used to use editconf to generate a dodecahedron box, then use genbox. It
used to work fine: $editconf -f protein.gro -o protein_box.gro -d 0.9 -bt
dodecahedron -c $genbox -cp protein_box.gro -cs spc216.gro -p example.top -o
protein_box_water.gro

But recently I found that using exactly the same command and input files, and
the same program installed, the protein is not centered in the box (I
download the structure and view it in pymol and vmd). I tried other box
types, for triclinic and cubic, it seems -c flag can be recognized, but not
for octahedron (nor dodecahedron). I wonder what things could be wrong.



Nothing is wrong.  Most visualization software defaults to a triclinic 
representation.  If you want the dodecahedral unit cell properly displayed you 
need to use trjconv -ur compact.



2) I have crystal structure for wild type protein, when I generated solvent
box for it, genbox didn't put waters in active site. Then I made two
single-point active site residue mutations using pymol: for a mutant
Thr->Ala, no water is put in active site neither, but for mutant Thr->Ser, a
water molecule is found in the active site. The presence of waters
drastically changed my simulation results. This is again different from what
I got in the past. I used to work with those three proteins and no waters
were added in their active sites. I assumed mutant Thr->Ser shouldn't have
water, since genbox delete extra waters according to VanderWaals radii, and
the three proteins (one real structure and two models built up by pymol) are
so highly similar. I wonder why the program decide to treat them differently,
this time?



I don't know exactly what's going on, but the behavior of genbox can be 
influenced by the values of -seed and -vdwd.  Otherwise, if water should or 
should not be in the active site, sufficiently long restrained equilibration may 
help.



I also tried using different box types and box dimensions for mutant
Thr->Ser, and found sometimes a water added, but sometime not. Is this
inconsistency normal?



Different box types and dimensions will influence the way genbox places cubes of 
water in the active site.  It's not an inconsistency if you're manipulating 
other factors.


-Justin


Sorry for the long email. Those problems seem really weird to me. Any
guidance or hint would be highly appreciated. Thank you very much,

Lin Xu

Ph.D. Candidate Boxer lab, Chemistry Department Stanford University Stanford
CA 94305 (650)6448383


--


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] confusion about segmentation fault during mdrun

[Lan Hua]

Hi All,

  I understand that the error of segmentation fault may come from many
reasons, but I just couldn't figure out the reason of this error in my
simulations.  I want to run md simulations with explicit water for 20
structures of one domain (residue 77-148) of calmodulin (PDB 1CFC).  These
20 starting structures are from one REMD simulation in implicit water.  The
following is what I did to run simulations for these 20 structures.  I used
gromacs version 3.1.4 with ffamber ports.  The force field is amber03 and
water model is TIP3P.

   1.  get rid of the steric clash in the starting structure
   2.  after doing pdb2gmx, then minimze the protein
   3,   use "-bt dodecahedron -d 0.9 -c"  in the command line of editconf
   4,  after doing genbox, first minimize the water with protein rigid and
then minimize the whole system
   5,  run md simulation with position restraint for protein heavy atoms
with nose-hoover thermostat for 20ps
   6,  run NPT simulations with nose-hoover thermostat and Parrinello-Rahman
thermostat for 500ps
   7,  run NVT simulation for another 100ps
   8, then energy minimze the whole system again.

Every time, there are always "segmentation fault" in step 6 for some
starting structures which could be different in every try.  I checked the
energy, volume, pressure, temperature, etc for the trajectories which are
crashed because of segmentation fault,  but nothing was wrong.  I roughly
checked the trajectory which looks fine.  I also couldn't find any useful
information from the log file, which looks like the following:

   Step   Time Lambda  Annealing
 18  360.30.01.0

   Rel. Constraint Deviation:  Maxbetween atoms RMS
   Before LINCS 0.045887 47 48   0.004584
After LINCS 0.20752755   0.03

   Energies (kJ/mol)
  AngleProper Dih. Ryckaert-Bell.  LJ-14 Coulomb-14
2.08335e+031.59908e+022.95659e+031.17109e+031.27711e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coulomb (LR)  Potential
4.10779e+04   -1.37728e+03   -2.89916e+05   -5.82443e+04   -2.89318e+05
Kinetic En.   Total EnergyTemperature Pressure (bar)
5.25584e+04   -2.36759e+052.96920e+02   -1.07683e+02

   Step   Time Lambda  Annealing
 185000  370.30.01.0

   Rel. Constraint Deviation:  Maxbetween atoms RMS
   Before LINCS 0.052014 70 71   0.005149
After LINCS 0.11214215   0.02

   Energies (kJ/mol)
  AngleProper Dih. Ryckaert-Bell.  LJ-14 Coulomb-14
2.33684e+031.42695e+022.91169e+031.18452e+031.28507e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coulomb (LR)  Potential
4.06987e+04   -1.37332e+03   -2.9e+05   -5.83180e+04   -2.88455e+05
Kinetic En.   Total EnergyTemperature

The *.mdp files are also attached.   Any help will be highly appreciated.
Thank you.


Best,
Lan


em_steep_1.mdp
Description: Binary data


em_steep_2.mdp
Description: Binary data


pr.mdp
Description: Binary data


nvt.mdp
Description: Binary data


npt.mdp
Description: Binary data
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Re: [gmx-users] energy decreasing in NVE simulation

[Erik Marklund]

For more exotic NVE-systems I had to do some or several of the following 
things to get stable Etot:
* have an even shorter timestep than one would expect from the applied 
constraints and such.

* use double precision.
* apply the constraints with lower tolerance/more iterations etc.

Then there's a few things I notice in your setup:
* I see that you do not use constrints at all. I would give it a shot.
* Why do you have two separate comm-grps?

Erik Marklund

Yun-an Yan skrev:


Dear all, 

When I try to simulation with NVE ensemble, the 
total energy keeps decreasing. Geometry optimization 
and solvent equilibration are done before the NVE simulation. 

I follow the requirements provided in 
http://www.gromacs.org/Documentation/Terminology/NVE


Would any one help me to figure out what was wrong with
my settings?

Millions of thanks and best wishes,
Yun-an


BTW: Please check the following for the .mdp file

;Run control: A leap-frog algorithm for integrating Newton's equations.
integrator   = md
;time step in femtoseconds
dt   = 0.001
;number of steps
nsteps   = 1000
;No constraints
constraints  = none
constraint_algorithm = shake
shake_tol= 1e-08

; group(s) for center of mass motion removal
comm-grps= AA CCl4
; frequency for center of mass motion removal
nstcomm  =  1000
;frequency to write coordinates to output trajectory file
nstxout  = 1000
;frequency to write velocities to output trajectory file
nstvout  = 1000
;frequency to write energies to log file
nstlog   = 1000
;frequency to write energies to energy file
nstenergy= 1000
;group(s) to write to energy file
energygrps   = System

;Frequency to update the neighbor list (and the long-range forces,
;when using twin-range cut-off's).
nstlist  = 10
ns_type  = grid
rlist= 1.5

; Use periodic boundary conditions in all directions.
pbc = xyz

;cut-off distance for the short-range neighbor list
;treatment of electrostatic interactions
coulombtype  = PME-switch
fourierspacing   = 0.12
pme_order= 4
ewald_rtol   = 1e-5
rcoulomb_switch  = 1.0
rcoulomb = 1.2

;treatment of van der waals interactions
vdwtype  = Switch
rvdw-switch  = 1.0
rvdw = 1.2
dispcorr = EnerPres

;Temperature coupling
tcoupl  = no

;Pressure coupling
pcoupl   = no

;Velocity generation
gen_vel  = no





--
---
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] confusion about segmentation fault during mdrun

[Justin A. Lemkul]

Lan Hua wrote:

Hi All,

  I understand that the error of segmentation fault may come from 
many reasons, but I just couldn't figure out the reason of this error in 
my simulations.  I want to run md simulations with explicit water for 20 
structures of one domain (residue 77-148) of calmodulin (PDB 1CFC).  
These 20 starting structures are from one REMD simulation in implicit 
water.  The following is what I did to run simulations for these 20 
structures.  I used gromacs version 3.1.4 with ffamber ports.  The force 
field is amber03 and water model is TIP3P.




Do you have any particular reason for using software that is eight years old? 
You will get a massive performance upgrade with 4.0.7, as well as the ability to 
use multiple processors per replica.  In versions prior to 4.0, you can only use 
one processor per REMD replica.



   1.  get rid of the steric clash in the starting structure


What do you mean?  Energy minimization?  How did you did do this prior to step 2 
(generating a topology)?



   2.  after doing pdb2gmx, then minimze the protein
   3,   use "-bt dodecahedron -d 0.9 -c"  in the command line of editconf
   4,  after doing genbox, first minimize the water with protein rigid 
and then minimize the whole system


A lot of these steps are redundant and probably unnecessary.  Some tips:

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

   5,  run md simulation with position restraint for protein heavy atoms 
with nose-hoover thermostat for 20ps
   6,  run NPT simulations with nose-hoover thermostat and 
Parrinello-Rahman thermostat for 500ps

   7,  run NVT simulation for another 100ps
   8, then energy minimze the whole system again.

Every time, there are always "segmentation fault" in step 6 for some 
starting structures which could be different in every try.  I checked 
the energy, volume, pressure, temperature, etc for the trajectories 
which are crashed because of segmentation fault,  but nothing was 
wrong.  I roughly checked the trajectory which looks fine.  I also 
couldn't find any useful information from the log file, which looks like 
the following:




Using weak coupling (i.e. Berendsen) coupling is generally recommended for 
initial equilibration.  If a system is far from equilibrium (as it likely will 
be after adding patterned blocks of water with genbox), the N-H thermostat can 
allow for wild changes in the temperature of the system, leading to a collapse.


Your temperature coupling groups are also inappropriate:

Tcoupl   = nose-hoover
tc_grps  = Protein  SOL  Na
tau_t= 0.1  0.1 0.1

Never couple solvent and ions separately; it can lead to instability:

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

-Justin


   Step   Time Lambda  Annealing
 18  360.30.01.0

   Rel. Constraint Deviation:  Maxbetween atoms RMS
   Before LINCS 0.045887 47 48   0.004584
After LINCS 0.20752755   0.03

   Energies (kJ/mol)
  AngleProper Dih. Ryckaert-Bell.  LJ-14 Coulomb-14
2.08335e+031.59908e+022.95659e+031.17109e+031.27711e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coulomb (LR)  Potential
4.10779e+04   -1.37728e+03   -2.89916e+05   -5.82443e+04   -2.89318e+05
Kinetic En.   Total EnergyTemperature Pressure (bar)
5.25584e+04   -2.36759e+052.96920e+02   -1.07683e+02

   Step   Time Lambda  Annealing
 185000  370.30.01.0

   Rel. Constraint Deviation:  Maxbetween atoms RMS
   Before LINCS 0.052014 70 71   0.005149
After LINCS 0.11214215   0.02

   Energies (kJ/mol)
  AngleProper Dih. Ryckaert-Bell.  LJ-14 Coulomb-14
2.33684e+031.42695e+022.91169e+031.18452e+031.28507e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coulomb (LR)  Potential
4.06987e+04   -1.37332e+03   -2.9e+05   -5.83180e+04   -2.88455e+05
Kinetic En.   Total EnergyTemperature

The *.mdp files are also attached.   Any help will be highly 
appreciated.  Thank you.



Best,
Lan



--


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: acetonitrile from amber to gromacs

[Alan]

Dear Vedat,

On Wed, May 19, 2010 at 20:36,  wrote:

> @rui
> acpypi -i ch3cn_210.pdb
> says: "cannot find template for residue C3N in our library". and indeed,
> there's no residue C3N in my ffamber99sb.rtp file
>
> (and i don't know, how to use it in order to generate my topology or even
> an rtp file?!)
>

Have a bit of patience and try to read a bit more about ACPYPE.

1) Read the info there, I am sure you'll find it useful;
2) You'll learn that you need to have just one molecule in a pdb and not the
whole box if you want the topologi of C3N.
3) It took me 2s to get the topology with acpype but months to write the
code, so if you'd take some few minutes to read and use an updated version
(it's not acpypi anymore BTW)...

BTW, how did you get this message "cannot find template for residue C3N in
our library"?

acpype.googlecode.com

Regards,
Alan

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

[Moeed]

Hello,

I am trying to get only interaction energies (vdw  and electrostatics)
between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in
the system. I have added *exclusions section* at the end of top file to
exclude all nonbonded interactions between atom 1 and all other 20 atoms.
Unfortunately, I still have problem monitoring the breakdown of energies.

grompp -f em -c Hexane-Stack125.gro -p Hexane-Stack125-excl.top -o
Hexane-Stack125_em >& output.grompp_em

mdrun -s Hexane-Stack125_em -o Hexane-Stack125_em -c Hexane-Stack125_b4pr -v
>& output.mdrun_em

grompp -f md19 -c Hexane-Stack125_b4pr -p Hexane-Stack125-excl.top -o
Hexane-Stack125_md >& output.grompp_md

*mdrun -rerun -*s Hexane-Stack125_md.tpr -o Hexane-Stack125_md.tpr -c
Hexane-Stack125_after_md -v >& output.mdrun_md

---
Program g_energy, VERSION 4.0.7
Source code file: enxio.c, line: 283

Fatal error:
Energy file ener.edr not recognized, maybe different CPU?


***em output:

Steepest Descents converged to Fmax < 1000 in 1 steps
Potential Energy  = -1.06286703814635e+03
Maximum force =  2.02809790403662e+02 on atom 1183
Norm of force =  1.41349547097082e+02


md output

Program mdrun, VERSION 4.0.7
Source code file: gmxfio.c, line: 737

Can not open file:
rerun.xtc



md.mdp


title   = Hexane
cpp = /lib/cpp

;Run control
integrator  =  md
dt  =  0.002; ps !
nsteps  =  5000; total 1.0 ps.
nstcomm =  1; frequency for center of mass motion
removal

;Output control
nstenergy   =  10; frequency to write energies to energy
file. i.e., energies and other statistical data are stored every 10 steps
nstxout =  10; frequency to write
coordinates/velocity/force to output trajectory file
nstvout =  0
nstfout =  10
nstlog  =  10; frequency to write energies to log file
energygrps  =  Hexane Hexane

;Neighbor searching
nstlist =  10; neighborlist will be updated at least
every 10 steps
;ns_type =  grid

;Electrostatics/VdW
coulombtype =  PME
vdw-type=  cut-off
;Cut-offs
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0

;Temperature couplingBerendsen temperature coupling is on in two
groups
Tcoupl  =  berendsen
tc-grps =  HEX  ;sol
tau_t   =  0.1  ;0.1
ref_t   =  300  ;300

;Pressure coupling: Pressure coupling is not on
Pcoupl  =  no
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0

;Velocity generationGenerate velocites is on at 300 K. Manual
p155
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529

;Bonds
constraints =  all-bonds
constraint-algorithm=  lincs

*;Energy group exclusions
eneegygrp_excl  =  HEX *


pbc=xyz




/*topology file:

;
;File 'Hexane-PRODRG.top' was generated
;By user: moeed (500)
;On host: moeed-desktop
;At date: Tue May 11 09:31:28 2010
;
;This is your topology file
;"Everything He Lacks, He Makes Up In Denial" (Offspring)
;
; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Namenrexcl
Hexane  3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
 1   opls_157  1HEX C1  1  -0.18 12.011   ; qtot
-0.18
 2   opls_140  1HEXH11  1   0.06  1.008   ; qtot
-0.12
 3   opls_140  1HEXH12  1   0.06  1.008   ; qtot
-0.06
 4   opls_140  1HEXH13  1   0.06  1.008   ; qtot
0
 5   opls_158  1HEX C2  2  -0.12 12.011   ; qtot
-0.12
 6   opls_140  1HEXH21  2   0.06  1.008   ; qtot
-0.06
 7   opls_140  1HEXH22  2   0.06  1.008   ; qtot
0
 8   opls_158  1HEX C3  3  -0.12 12.011   ; qtot
-0.12
 9   opls_140  1HEXH31  3   0.06  1.008   ; qtot
-0.06
10   opls_140  1HEXH32  3   0.06  1.008   ; qtot
0
11   opls_158  1HEX C4  4  -0.12 12.011   ; qtot
-0.12
12   opls_140  1HEXH41  4   0.06  1.008   ; qtot
-0.06
13   opls_140  1HEXH42  4   0.06  1.008   ; qtot
0
14   opls_158  1HEX C5  5  -0.12 12.011   ; qtot
-0.12
15   opls_140  1HEXH51  5   0.06  1.008   ; qtot
-0.06
16   opls_140  1HEXH52  5   0.06  1.008   ; qtot
0
17   opls_157  1HEX C6  6  -0.18 12.0

Re: [gmx-users] confusion about segmentation fault during mdrun

[Lan Hua]

Hi Justin,

   Thank you so much for your quick reply and good suggestions. The
following is my answer.

On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul  wrote:

>
>
> Lan Hua wrote:
>
>> Hi All,
>>
>>  I understand that the error of segmentation fault may come from many
>> reasons, but I just couldn't figure out the reason of this error in my
>> simulations.  I want to run md simulations with explicit water for 20
>> structures of one domain (residue 77-148) of calmodulin (PDB 1CFC).  These
>> 20 starting structures are from one REMD simulation in implicit water.  The
>> following is what I did to run simulations for these 20 structures.  I used
>> gromacs version 3.1.4 with ffamber ports.  The force field is amber03 and
>> water model is TIP3P.
>>
>>
> Do you have any particular reason for using software that is eight years
> old? You will get a massive performance upgrade with 4.0.7, as well as the
> ability to use multiple processors per replica.  In versions prior to 4.0,
> you can only use one processor per REMD replica.
>
> The reason that I am using gromacs 3.1.4 is to prepare some input files for
simulations at fold...@home in which version 3.1.4 is recommended.


>
>1.  get rid of the steric clash in the starting structure
>>
>
> What do you mean?  Energy minimization?  How did you did do this prior to
> step 2 (generating a topology)?
>
> I used the "protein preparation wizard" which is implemented in maestro
package to do this.   Actually in this wizard, energy minimization is
performed on protein.


>
>2.  after doing pdb2gmx, then minimze the protein
>>   3,   use "-bt dodecahedron -d 0.9 -c"  in the command line of editconf
>>   4,  after doing genbox, first minimize the water with protein rigid and
>> then minimize the whole system
>>
>
> A lot of these steps are redundant and probably unnecessary.  Some tips:
>
> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>
>
Thanks for the tips. I went to the link, but I am still a little bit
confused about which steps are unnecessary.  You mean step 7 and step 8?  I
did this in case simulations at f...@h would be crashed.


>
>5,  run md simulation with position restraint for protein heavy atoms
>> with nose-hoover thermostat for 20ps
>>   6,  run NPT simulations with nose-hoover thermostat and
>> Parrinello-Rahman thermostat for 500ps
>>   7,  run NVT simulation for another 100ps
>>   8, then energy minimze the whole system again.
>>
>> Every time, there are always "segmentation fault" in step 6 for some
>> starting structures which could be different in every try.  I checked the
>> energy, volume, pressure, temperature, etc for the trajectories which are
>> crashed because of segmentation fault,  but nothing was wrong.  I roughly
>> checked the trajectory which looks fine.  I also couldn't find any useful
>> information from the log file, which looks like the following:
>>
>>
> Using weak coupling (i.e. Berendsen) coupling is generally recommended for
> initial equilibration.  If a system is far from equilibrium (as it likely
> will be after adding patterned blocks of water with genbox), the N-H
> thermostat can allow for wild changes in the temperature of the system,
> leading to a collapse.
>
> Your temperature coupling groups are also inappropriate:
>
> Tcoupl   = nose-hoover
> tc_grps  = Protein  SOL  Na
> tau_t= 0.1  0.1 0.1
>
> Never couple solvent and ions separately; it can lead to instability:
>
> http://www.gromacs.org/Documentation/Terminology/Thermostats
>

These are good suggestions.  Thanks.  So use Berendsen coupling for both
temperature and pressure coupling for initial equilibration, for example
position restrained NVT followed by NPT, right? I have another question.  If
I choose constraints = hbonds instead of constraints = all-bonds in NPT
simulation, what will happen?


Best,

Lan


>
> -Justin
>
>
>Step   Time Lambda  Annealing
>> 18  360.30.01.0
>>
>>   Rel. Constraint Deviation:  Maxbetween atoms RMS
>>   Before LINCS 0.045887 47 48   0.004584
>>After LINCS 0.20752755   0.03
>>
>>   Energies (kJ/mol)
>>  AngleProper Dih. Ryckaert-Bell.  LJ-14 Coulomb-14
>>2.08335e+031.59908e+022.95659e+031.17109e+031.27711e+04
>>LJ (SR)  Disper. corr.   Coulomb (SR)   Coulomb (LR)  Potential
>>4.10779e+04   -1.37728e+03   -2.89916e+05   -5.82443e+04   -2.89318e+05
>>Kinetic En.   Total EnergyTemperature Pressure (bar)
>>5.25584e+04   -2.36759e+052.96920e+02   -1.07683e+02
>>
>>   Step   Time Lambda  Annealing
>> 185000  370.30.01.0
>>
>>   Rel. Constraint Deviation:  Maxbetween atoms RMS
>>   Before LINCS 0.052014 70 71   0.005149
>>  

Re: [gmx-users] energy break down

[Justin A. Lemkul]

Moeed wrote:

Hello,

I am trying to get only interaction energies (vdw  and electrostatics) 
between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules 
in the system. I have added _exclusions section_ at the end of top file 
to exclude all nonbonded interactions between atom 1 and all other 20 
atoms. Unfortunately, I still have problem monitoring the breakdown of 
energies.




Why are exclusions necessary?  What do you hope to prove by excluding 
interactions between one particular atom and the rest of the molecule?  I'm 
sorry, but that sounds like complete nonsense to me.


grompp -f em -c Hexane-Stack125.gro -p Hexane-Stack125-excl.top -o 
Hexane-Stack125_em >& output.grompp_em


mdrun -s Hexane-Stack125_em -o Hexane-Stack125_em -c 
Hexane-Stack125_b4pr -v >& output.mdrun_em


grompp -f md19 -c Hexane-Stack125_b4pr -p Hexane-Stack125-excl.top -o 
Hexane-Stack125_md >& output.grompp_md


*mdrun -rerun -*s Hexane-Stack125_md.tpr -o Hexane-Stack125_md.tpr -c 
Hexane-Stack125_after_md -v >& output.mdrun_md


---
Program g_energy, VERSION 4.0.7
Source code file: enxio.c, line: 283

Fatal error:
Energy file ener.edr not recognized, maybe different CPU?



What does gmxcheck tell you about the .edr file?  What was your g_energy command 
line?  Are your Gromacs versions consistent between the machine running the 
calculation and the one you're using to analyze the .edr file?




***em output:

Steepest Descents converged to Fmax < 1000 in 1 steps
Potential Energy  = -1.06286703814635e+03
Maximum force =  2.02809790403662e+02 on atom 1183
Norm of force =  1.41349547097082e+02


md output

Program mdrun, VERSION 4.0.7
Source code file: gmxfio.c, line: 737

Can not open file:
rerun.xtc




You have to produce a real trajectory (with reasonable physics!) before trying 
to rerun it.  The mdrun -rerun flag expects an .xtc file.  See mdrun -h and read 
about the purpose of this flag in the manual.





*;Energy group exclusions
eneegygrp_excl  =  HEX *



Well, you're not going to get any exclusions using this keyword.  You want 
"energygrp_excl," not "eneegygrp_excl."  If this is what's in your .mdp file, 
grompp should have raised an error.  I still don't know what exactly you're 
trying to do.





[ molecules ]
; Compound#mols
Hexane  125

*[ exclusions ]

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20*




Does this even work?  The [exclusions] directive should be part of the hexane 
[moleculetype] definition.  Putting it after the definition of the system means 
it doesn't apply to hexane at all.  Surely grompp would have raised an error 
(something like "invalid order for directive exclusions")?


-Justin

--


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


--
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Re: [gmx-users] confusion about segmentation fault during mdrun

[Justin A. Lemkul]

Lan Hua wrote:

Hi Justin,

   Thank you so much for your quick reply and good suggestions. The 
following is my answer.


On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul > wrote:




Lan Hua wrote:

Hi All,

 I understand that the error of segmentation fault may come
from many reasons, but I just couldn't figure out the reason of
this error in my simulations.  I want to run md simulations with
explicit water for 20 structures of one domain (residue 77-148)
of calmodulin (PDB 1CFC).  These 20 starting structures are from
one REMD simulation in implicit water.  The following is what I
did to run simulations for these 20 structures.  I used gromacs
version 3.1.4 with ffamber ports.  The force field is amber03
and water model is TIP3P.


Do you have any particular reason for using software that is eight
years old? You will get a massive performance upgrade with 4.0.7, as
well as the ability to use multiple processors per replica.  In
versions prior to 4.0, you can only use one processor per REMD replica.

The reason that I am using gromacs 3.1.4 is to prepare some input files 
for simulations at fold...@home in which version 3.1.4 is recommended.
 


OK, as long as you've got a reason...




  1.  get rid of the steric clash in the starting structure


What do you mean?  Energy minimization?  How did you did do this
prior to step 2 (generating a topology)?

I used the "protein preparation wizard" which is implemented in maestro 
package to do this.   Actually in this wizard, energy minimization is 
performed on protein.
 



  2.  after doing pdb2gmx, then minimze the protein
  3,   use "-bt dodecahedron -d 0.9 -c"  in the command line of
editconf
  4,  after doing genbox, first minimize the water with protein
rigid and then minimize the whole system


A lot of these steps are redundant and probably unnecessary.  Some tips:

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


Thanks for the tips. I went to the link, but I am still a little bit 
confused about which steps are unnecessary.  You mean step 7 and step 
8?  I did this in case simulations at f...@h would be crashed.
 


I just mean the repeated, separate energy minimizations.  I guess there's no 
harm in it, but generally I find that minimizing the protein in vacuo, then with 
and without restraints in solvent, etc. is unnecessary.  I'd suggest just 
building the system (solvent and all), and minimizing the whole thing (without 
restraints).  I don't think you stand to gain anything with your procedure.





  5,  run md simulation with position restraint for protein
heavy atoms with nose-hoover thermostat for 20ps
  6,  run NPT simulations with nose-hoover thermostat and
Parrinello-Rahman thermostat for 500ps
  7,  run NVT simulation for another 100ps
  8, then energy minimze the whole system again.

Every time, there are always "segmentation fault" in step 6 for
some starting structures which could be different in every try.
 I checked the energy, volume, pressure, temperature, etc for
the trajectories which are crashed because of segmentation
fault,  but nothing was wrong.  I roughly checked the trajectory
which looks fine.  I also couldn't find any useful information
from the log file, which looks like the following:


Using weak coupling (i.e. Berendsen) coupling is generally
recommended for initial equilibration.  If a system is far from
equilibrium (as it likely will be after adding patterned blocks of
water with genbox), the N-H thermostat can allow for wild changes in
the temperature of the system, leading to a collapse.

Your temperature coupling groups are also inappropriate:

Tcoupl   = nose-hoover
tc_grps  = Protein  SOL  Na
tau_t= 0.1  0.1 0.1

Never couple solvent and ions separately; it can lead to instability:

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


These are good suggestions.  Thanks.  So use Berendsen coupling for both 
temperature and pressure coupling for initial equilibration, for example 
position restrained NVT followed by NPT, right? I have another 


At least for the thermostat, but yes, probably it can't hurt to use weak 
coupling for both temperature and pressure.


question.  If I choose constraints = hbonds instead of constraints = 
all-bonds in NPT simulation, what will happen?




You constrain heavy atom-H bonds instead of all bonds.  Using fewer constraints 
may or may not affect the magnitude of the time step you can use, but generally 
X-H bonds are the highest frequency and thus are the least stable with long time 
steps.


-Justin



Best,

Lan
 



-Justin


  

RE: [gmx-users] enegry minimisation

[Dallas B. Warren]

> I seem to say this several times per week: in my experience (and in
the
> experience of many others who have posted here) the charges and charge
> groups output by PRODRG are often unsatisfactory, requiring manual

Might be an idea then to put the comments on the PRODRG page on the
GROMACS website / wiki and direct people there?

Catch ya,

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

[Justin A. Lemkul]

Dallas B. Warren wrote:

I seem to say this several times per week: in my experience (and in

the

experience of many others who have posted here) the charges and charge
groups output by PRODRG are often unsatisfactory, requiring manual


Might be an idea then to put the comments on the PRODRG page on the
GROMACS website / wiki and direct people there?


Excellent idea.  Done and done.

http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/PRODRG#Tips

-Justin



Catch ya,

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


--


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 search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] confusion about segmentation fault during mdrun

[Lan Hua]

Hi Justin,

   I appreciated your quick answers.  So if I understand correctly, using
constraints = hbonds with the time step of 2fs, it should be fine, right?

Thanks,
Lan

On Wed, May 19, 2010 at 3:52 PM, Justin A. Lemkul  wrote:

>
>
> Lan Hua wrote:
>
>> Hi Justin,
>>
>>   Thank you so much for your quick reply and good suggestions. The
>> following is my answer.
>>
>> On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Lan Hua wrote:
>>
>>Hi All,
>>
>> I understand that the error of segmentation fault may come
>>from many reasons, but I just couldn't figure out the reason of
>>this error in my simulations.  I want to run md simulations with
>>explicit water for 20 structures of one domain (residue 77-148)
>>of calmodulin (PDB 1CFC).  These 20 starting structures are from
>>one REMD simulation in implicit water.  The following is what I
>>did to run simulations for these 20 structures.  I used gromacs
>>version 3.1.4 with ffamber ports.  The force field is amber03
>>and water model is TIP3P.
>>
>>
>>Do you have any particular reason for using software that is eight
>>years old? You will get a massive performance upgrade with 4.0.7, as
>>well as the ability to use multiple processors per replica.  In
>>versions prior to 4.0, you can only use one processor per REMD replica.
>>
>> The reason that I am using gromacs 3.1.4 is to prepare some input files
>> for simulations at fold...@home in which version 3.1.4 is recommended.
>>
>>
>
> OK, as long as you've got a reason...
>
>
>
>>
>>  1.  get rid of the steric clash in the starting structure
>>
>>
>>What do you mean?  Energy minimization?  How did you did do this
>>prior to step 2 (generating a topology)?
>>
>> I used the "protein preparation wizard" which is implemented in maestro
>> package to do this.   Actually in this wizard, energy minimization is
>> performed on protein.
>>
>>
>>  2.  after doing pdb2gmx, then minimze the protein
>>  3,   use "-bt dodecahedron -d 0.9 -c"  in the command line of
>>editconf
>>  4,  after doing genbox, first minimize the water with protein
>>rigid and then minimize the whole system
>>
>>
>>A lot of these steps are redundant and probably unnecessary.  Some
>> tips:
>>
>>
>> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>>
>>
>> Thanks for the tips. I went to the link, but I am still a little bit
>> confused about which steps are unnecessary.  You mean step 7 and step 8?  I
>> did this in case simulations at f...@h would be crashed.
>>
>>
>
> I just mean the repeated, separate energy minimizations.  I guess there's
> no harm in it, but generally I find that minimizing the protein in vacuo,
> then with and without restraints in solvent, etc. is unnecessary.  I'd
> suggest just building the system (solvent and all), and minimizing the whole
> thing (without restraints).  I don't think you stand to gain anything with
> your procedure.
>
>
>
>>
>>  5,  run md simulation with position restraint for protein
>>heavy atoms with nose-hoover thermostat for 20ps
>>  6,  run NPT simulations with nose-hoover thermostat and
>>Parrinello-Rahman thermostat for 500ps
>>  7,  run NVT simulation for another 100ps
>>  8, then energy minimze the whole system again.
>>
>>Every time, there are always "segmentation fault" in step 6 for
>>some starting structures which could be different in every try.
>> I checked the energy, volume, pressure, temperature, etc for
>>the trajectories which are crashed because of segmentation
>>fault,  but nothing was wrong.  I roughly checked the trajectory
>>which looks fine.  I also couldn't find any useful information
>>from the log file, which looks like the following:
>>
>>
>>Using weak coupling (i.e. Berendsen) coupling is generally
>>recommended for initial equilibration.  If a system is far from
>>equilibrium (as it likely will be after adding patterned blocks of
>>water with genbox), the N-H thermostat can allow for wild changes in
>>the temperature of the system, leading to a collapse.
>>
>>Your temperature coupling groups are also inappropriate:
>>
>>Tcoupl   = nose-hoover
>>tc_grps  = Protein  SOL  Na
>>tau_t= 0.1  0.1 0.1
>>
>>Never couple solvent and ions separately; it can lead to instability:
>>
>>http://www.gromacs.org/Documentation/Terminology/Thermostats
>>
>>
>> These are good suggestions.  Thanks.  So use Berendsen coupling for both
>> temperature and pressure coupling for initial equilibration, for example
>> position restrained NVT followed by NPT, right? I have another
>>
>
> At least for the thermostat, but yes, probably it can't hurt to use weak
> coupling f

Re: [gmx-users] confusion about segmentation fault during mdrun

[Justin A. Lemkul]

Lan Hua wrote:

Hi Justin,

   I appreciated your quick answers.  So if I understand correctly, 
using constraints = hbonds with the time step of 2fs, it should be fine, 
right?




Maybe.  If your goal is REMD (I'm not clear from your original post) then 
stability may be an issue at higher temperatures, in which case you may need to 
constrain all bonds or decrease your time step, maybe both.  At ambient 
temperatures, what you propose is likely stable.  Look into the relevant 
literature for similar force fields and applications to be sure.


-Justin


Thanks,
Lan

On Wed, May 19, 2010 at 3:52 PM, Justin A. Lemkul > wrote:




Lan Hua wrote:

Hi Justin,

  Thank you so much for your quick reply and good suggestions.
The following is my answer.

On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Lan Hua wrote:

   Hi All,

I understand that the error of segmentation fault
may come
   from many reasons, but I just couldn't figure out the
reason of
   this error in my simulations.  I want to run md
simulations with
   explicit water for 20 structures of one domain (residue
77-148)
   of calmodulin (PDB 1CFC).  These 20 starting structures
are from
   one REMD simulation in implicit water.  The following is
what I
   did to run simulations for these 20 structures.  I used
gromacs
   version 3.1.4 with ffamber ports.  The force field is amber03
   and water model is TIP3P.


   Do you have any particular reason for using software that is
eight
   years old? You will get a massive performance upgrade with
4.0.7, as
   well as the ability to use multiple processors per replica.  In
   versions prior to 4.0, you can only use one processor per
REMD replica.

The reason that I am using gromacs 3.1.4 is to prepare some
input files for simulations at fold...@home in which version
3.1.4 is recommended.
 



OK, as long as you've got a reason...




 1.  get rid of the steric clash in the starting structure


   What do you mean?  Energy minimization?  How did you did do this
   prior to step 2 (generating a topology)?

I used the "protein preparation wizard" which is implemented in
maestro package to do this.   Actually in this wizard, energy
minimization is performed on protein.
 


 2.  after doing pdb2gmx, then minimze the protein
 3,   use "-bt dodecahedron -d 0.9 -c"  in the command
line of
   editconf
 4,  after doing genbox, first minimize the water with
protein
   rigid and then minimize the whole system


   A lot of these steps are redundant and probably unnecessary.
 Some tips:

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



Thanks for the tips. I went to the link, but I am still a little
bit confused about which steps are unnecessary.  You mean step 7
and step 8?  I did this in case simulations at f...@h would be crashed.
 



I just mean the repeated, separate energy minimizations.  I guess
there's no harm in it, but generally I find that minimizing the
protein in vacuo, then with and without restraints in solvent, etc.
is unnecessary.  I'd suggest just building the system (solvent and
all), and minimizing the whole thing (without restraints).  I don't
think you stand to gain anything with your procedure.




 5,  run md simulation with position restraint for protein
   heavy atoms with nose-hoover thermostat for 20ps
 6,  run NPT simulations with nose-hoover thermostat and
   Parrinello-Rahman thermostat for 500ps
 7,  run NVT simulation for another 100ps
 8, then energy minimze the whole system again.

   Every time, there are always "segmentation fault" in step
6 for
   some starting structures which could be different in
every try.
I checked the energy, volume, pressure, temperature, etc for
   the trajectories which are crashed because of segmentation
   fault,  but nothing was wrong.  I roughly checked the
trajectory
   which looks fine.  I also couldn't find any useful
information
   from the log file, which looks like the following:


   Using weak coupling (i.e. Berendsen) coupling is generally
   recommended for initial equilibration.  If a system is far from
   

Re: [gmx-users] confusion about segmentation fault during mdrun

[Lan Hua]

Thanks.  The simulations are regular MD in explicit water at room
temperature.


Lan

On Wed, May 19, 2010 at 6:03 PM, Justin A. Lemkul  wrote:

>
>
> Lan Hua wrote:
>
>> Hi Justin,
>>
>>   I appreciated your quick answers.  So if I understand correctly, using
>> constraints = hbonds with the time step of 2fs, it should be fine, right?
>>
>>
> Maybe.  If your goal is REMD (I'm not clear from your original post) then
> stability may be an issue at higher temperatures, in which case you may need
> to constrain all bonds or decrease your time step, maybe both.  At ambient
> temperatures, what you propose is likely stable.  Look into the relevant
> literature for similar force fields and applications to be sure.
>
> -Justin
>
>  Thanks,
>> Lan
>>
>>
>> On Wed, May 19, 2010 at 3:52 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Lan Hua wrote:
>>
>>Hi Justin,
>>
>>  Thank you so much for your quick reply and good suggestions.
>>The following is my answer.
>>
>>On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   Lan Hua wrote:
>>
>>   Hi All,
>>
>>I understand that the error of segmentation fault
>>may come
>>   from many reasons, but I just couldn't figure out the
>>reason of
>>   this error in my simulations.  I want to run md
>>simulations with
>>   explicit water for 20 structures of one domain (residue
>>77-148)
>>   of calmodulin (PDB 1CFC).  These 20 starting structures
>>are from
>>   one REMD simulation in implicit water.  The following is
>>what I
>>   did to run simulations for these 20 structures.  I used
>>gromacs
>>   version 3.1.4 with ffamber ports.  The force field is
>> amber03
>>   and water model is TIP3P.
>>
>>
>>   Do you have any particular reason for using software that is
>>eight
>>   years old? You will get a massive performance upgrade with
>>4.0.7, as
>>   well as the ability to use multiple processors per replica.  In
>>   versions prior to 4.0, you can only use one processor per
>>REMD replica.
>>
>>The reason that I am using gromacs 3.1.4 is to prepare some
>>input files for simulations at fold...@home in which version
>>3.1.4 is recommended.
>>
>>
>>OK, as long as you've got a reason...
>>
>>
>>
>>
>> 1.  get rid of the steric clash in the starting structure
>>
>>
>>   What do you mean?  Energy minimization?  How did you did do this
>>   prior to step 2 (generating a topology)?
>>
>>I used the "protein preparation wizard" which is implemented in
>>maestro package to do this.   Actually in this wizard, energy
>>minimization is performed on protein.
>>
>> 2.  after doing pdb2gmx, then minimze the protein
>> 3,   use "-bt dodecahedron -d 0.9 -c"  in the command
>>line of
>>   editconf
>> 4,  after doing genbox, first minimize the water with
>>protein
>>   rigid and then minimize the whole system
>>
>>
>>   A lot of these steps are redundant and probably unnecessary.
>> Some tips:
>>
>>
>> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>>
>>
>>Thanks for the tips. I went to the link, but I am still a little
>>bit confused about which steps are unnecessary.  You mean step 7
>>and step 8?  I did this in case simulations at f...@h would be
>> crashed.
>>
>>
>>I just mean the repeated, separate energy minimizations.  I guess
>>there's no harm in it, but generally I find that minimizing the
>>protein in vacuo, then with and without restraints in solvent, etc.
>>is unnecessary.  I'd suggest just building the system (solvent and
>>all), and minimizing the whole thing (without restraints).  I don't
>>think you stand to gain anything with your procedure.
>>
>>
>>
>>
>> 5,  run md simulation with position restraint for protein
>>   heavy atoms with nose-hoover thermostat for 20ps
>> 6,  run NPT simulations with nose-hoover thermostat and
>>   Parrinello-Rahman thermostat for 500ps
>> 7,  run NVT simulation for another 100ps
>> 8, then energy minimze the whole system again.
>>
>>   Every time, there are always "segmentation fault" in step
>>6 for
>>   some starting structures which could be different in
>>every try.
>>I checked the energy, volume, pressure, temperature, etc
>> for
>>   the trajectories which are crashed because of segmentation
>>   fault,  but nothing w

[gmx-users] Re: [gmx-user]Error by pdb2gmx (Mark Abraham)

[佘安奇]

Dear Mark:
I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. And 
the rtp of my molecule is in the attached file DRG.txt.
 
Thank you very much!
 
Angel


  [ DRG2  ]
  [ atoms ]
  CCN   CH3 0.0 1
  CCM   CH1 0.08300 2
  CCO   CH3 0.03300 2
  CCK   CH2 0.05000 2
  CCI   CH2 0.08300 2
  CCJ C 0.23500 2
  OCLOA-0.10600 2
  OCT O-0.37800 2
  NCHNR 0.07300 3
  HCH H-0.01100 3
  CCB C 0.22100 3
  OCD O-0.40200 3
  CCA   CH2 0.07600 3
  CCC   CH2 0.04300 3
  CCE   CH1 0.07500 4
  CCG   CH3 0.02500 4
  CCF   CH3 0.02700 4
  NBZNR 0.07200 4
  HBZ H-0.01100 4
  CBT C 0.21900 4
  OBV O-0.40700 4
  CBS   CH2 0.12900 5
  CBU   CH2 0.09200 5
  CBW C 0.33900 5
  OBYOM-0.28000 5
  OBXOM-0.28000 5
  NBRNR 0.06800 6
  HBR H-0.01200 6
  CBM C 0.20900 6
  OBO O-0.42600 6
  CBL   CH2 0.07000 6
  CBN   CH1 0.07000 6
  CBQ   CH3 0.02100 6
  CBP   CH3 0.01800 7
  NBKNR 0.06600 7
  HBK H-0.01200 7
  CBE C 0.20200 7
  OBG O-0.44100 7
  CBD   CH2 0.06600 7
  CBF   CH2 0.03500 7
  CBH   CH1 0.06600 7
  CBJ   CH3 0.0 8
  CBI   CH3 0.01800 9
  NBCNR 0.06600 9
  HBC H-0.01200 9
C C 0.20200 9
O O-0.44100 9
   CA   CH2 0.06600 9
   CB   CH2 0.03500 9
   CG   CH1 0.06600 9
  CD2   CH3 0.0220010
  CD1   CH3 0.0220010
NNR 0.0690010
H H-0.0120010
  CAX C 0.2110010
  OAY O-0.4220010
  CAW   CH2 0.0710010
  CAV   CH2 0.0390010
  CAU   CH2 0.1090011
  CAT C 0.3850011
  OBAOM-0.2470011
  OAZOM-0.2470011
  NBBNR 0.0630012
  HBB H-0.0130012
  CAA C 0.1960012
  OAG O-0.4550012
  CAB   CH2 0.0320012
  CAC   CH1 0.1140012
  CAD   CH2 0.0310012
  CAE   CH2 0.0320012
  CAF   CH2 0.013
  CAH   CH2 0.013
  CAI   CH2 0.013
  CAJ   CH2 0.013
  CAK   CH2 0.013
  CCP   CH2 0.013
  CCQ   CH2-0.0030014
  CCR   CH2-0.0020014
  CCS   CH1 0.0310014
  CCV   CH3-0.0260014
  CCU   CH3 0.015
  [ bonds ]
 CCM   CCN 0.1530   715.0
 CCM   CCO 0.1530   715.0
 CCM   CCK 0.1530   715.0
 CCI   CCK 0.1530   715.0
 CCI   CCJ 0.1390   866.0
 CCI   NCH 0.1480   764.0
 CCJ   OCL 0.1360  1020.0
 CCJ   OCT 0.1230  1660.0
 CAC   OCL 0.1440   610.0
 NCH   HCH 0.1000  1870.0
 CCB   NCH 0.1400   854.0
 CCB   OCD 0.1230  1660.0
 CCA   CCB 0.1390   866.0
 CCA   CCC 0.1530   715.0
 CCA   NBZ 0.1480   764.0
 CCE   CCC 0.1530   715.0
 CCE   CCG 0.1530   715.0
 CCE   CCF 0.1530   715.0
 NBZ   HBZ 0.1000  1870.0
 CBT   NBZ 0.1400   854.0
 CBT   OBV 0.1230  1660.0
 CBS   CBT 0.1390   866.0
 CBS   CBU 0.1530   715.0
 CBS   NBR 0.1480   764.0
 CBW   CBU 0.1530   715.0
 CBW   OBY 0.1250  1340.0
 CBW   OBX 0.1250  1340.0
 NBR   HBR 0.1000  1870.0
 CBM   NBR 0.1400   854.0
 CBM   OBO 0.1230  1660.0
 CBL   CBM 0.1390   866.0
 CBL   CBN 0.1530   715.0
 CBL   NBK 0.1480   764.0
 CBN   CBQ 0.1530   715.0
 CBN   CBP 0.1530   715.0
 NBK   HBK 0.1000  1870.0
 CBE   NBK 0.1400   854.0
 CBE   OBG 0.1230  1660.0
 CBD   CBE 0.1390   866.0
 CBD   CBF 0.1530   715.0
 CBD   NBC 0.1480   764.0
 CBH   CBF 0.1530   715.0
 CBH   CBJ 0.1530   715.0
 CBH   CBI 0.1530   715.0
 NBC   HBC 0.1000  1870.0
   C   NBC 0.1400   854.0
   C O 0.1230  1660.0
  CA C 0.1390   866.0
  CACB 0.1530   715.0
  CA N 0.1480   764.0
  CGCB 0.1530   715.0
  CG   CD2 0.1530   715.0
  CG   CD1 0.1530   715.0
   N H 0.1000  1870.0
 CAX N 0.1400   854.0
 CAX   OAY 0.1230  1660.0
 CAW   CAX 0.1390   866.0
 CAW   CAV 0.1530   715.0
 CAW   NBB 0.1480   764.0
 CAV   CAU 0.1530   715.0
 CAT   CAU 0.1530   715.0
 CAT   OBA 0.1250  1340.0
 CAT   OAZ 0.1250  1340.0
 NBB   HBB 0.1000  1870.0
 CAA   NBB 0.1400   854.0
 CAA   OAG 0.1230  1660.0
 CAA   CAB 0.1390   866.0
 CAC   CAB 0.1520   543.0
 CAC   CAD 0.1530   715.0
 CA

[gmx-users] breaking down total energy

[Moeed]

Hello Justin,

Thanks for your comments. Actually, since I am interested in only
interaction energies *between* molecules I thought by excluding energies
between atoms on a single chain what I get from nonbonded interactions would
not include 1-4 interactions.

*
This is from previous posts:

Question: Can I not take for
instance LJ energy values which are coming from a specific NO. of molecuels
in simulation box and calculate interaction energies for pairs or "mol"
number of molecules?

Your answer:

Not easily.  You will still have intramolecular terms that are not covered
by
the 1-4 interactions.  *For example, if the two ends of your molecule
interact
with one another, this interaction will contribute to your nonbonded
energies.*
*
That is why I thought I have to exclude interaction in a single chain
between atoms, so that for instance atoms 1 and 20 do not see each other.

I manual I found only about how extra exlusion within a molecue cab added in
[exclusions].. I dont think this helps me.

How can I define all possible intramolecular exclusions in order to save
only intermolecular energy contributions?


top file:

Include forcefield parameters

#include "ffoplsaa.itp"

[ moleculetype ]
; Namenrexcl
Hexane  3

[ exclusions ]
??

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
 1   opls_157  1HEX C1  1  -0.18 12.011
; qtot -0.18
 2   opls_140  1HEXH11  1   0.06  1.008
; qtot -0.12
 3   opls_140  1HEXH12  1   0.06  1.008
; qtot -0.06
 4   opls_140  1HEXH13  1   0.06  1.008   ; qtot 0
 5   opls_158  1HEX C2  2  -0.12 12.011
; qtot -0.12
 6   opls_140  1HEXH21  2   0.06  1.008
; qtot -0.06
 7   opls_140  1HEXH22  2   0.06  1.008   ; qtot 0
 8   opls_158  1HEX C3  3  -0.12 12.011
; qtot -0.12
 9   opls_140  1HEXH31  3   0.06  1.008
; qtot -0.06
10   opls_140  1HEXH32  3   0.06  1.008   ; qtot 0
11   opls_158  1HEX C4  4  -0.12 12.011
; qtot -0.12
12   opls_140  1HEXH41  4   0.06  1.008
; qtot -0.06
13   opls_140  1HEXH42  4   0.06  1.008   ; qtot 0
14   opls_158  1HEX C5  5  -0.12 12.011
; qtot -0.12
15   opls_140  1HEXH51  5   0.06  1.008
; qtot -0.06
16   opls_140  1HEXH52  5   0.06  1.008   ; qtot 0
17   opls_157  1HEX C6  6  -0.18 12.011
; qtot -0.18
18   opls_140  1HEXH61  6   0.06  1.008
; qtot -0.12
19   opls_140  1HEXH62  6   0.06  1.008
; qtot -0.06
20   opls_140  1HEXH63  6   0.06  1.008   ; qtot 0

[ bonds ]
;  aiaj functc0c1c2c3
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
5 7 1
5 8 1
8 9 1
810 1
811 1
   1112 1
   1113 1
   1114 1
   1415 1
   1416 1
   1417 1
   1718 1
   1719 1
   1720 1

[ pairs ]
;  aiaj functc0c1c2c3
1 9 1
110 1
111 1
2 6 1
2 7 1
2 8 1
3 6 1
3 7 1
3 8 1
4 6 1
4 7 1
4 8 1
512 1
513 1
514 1
6 9 1
610 1
611 1
7 9 1
710 1
711 1
815 1
816 1
817 1
912 1
913 1
914 1
   1012 1
   1013 1
   1014 1
   1118 1
   1119 1
   1120 1
   1215 1
   1216 1
   1217 1
   1315 1
   1316 1
   1317 1
   1518 1
   1519 1
   1520 1
   1618 1
   1619 1
   1620 1

[ angles ]
;  aiajak functc0c1c2c3
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
1 5 6 1
1 5 7 1
1 5 8 1
6 5 7 1
6 5 8 1
7 5 8 1
5 8 9 1
5 810 1
5 811 1
9 810 1
9 811 1
   10 811 1
81112 1

[gmx-users] g_clustsize output

[toma0052]

Hello,
I have a system of dimers which spontaneously assemble into clusters. 
I would like to get a plot of the number of clusters of size s vs s. In 
looking at g_clustsize I am able to obtain the average number of clusters 
vs time, the average cluster size vs time and a histogram of the average 
number of molecules in a cluster of size s. Am I missing something? Is 
there a way for me to get the number of clusters of a particular size vs 
cluster size?


Thanks,
Mike Tomasini
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Re: [gmx-users] g_clustsize output

[David van der Spoel]

On 2010-05-20 04.55, toma0...@umn.edu wrote:

Hello,
I have a system of dimers which spontaneously assemble into clusters. I
would like to get a plot of the number of clusters of size s vs s. In
looking at g_clustsize I am able to obtain the average number of
clusters vs time, the average cluster size vs time and a histogram of
the average number of molecules in a cluster of size s. Am I missing
something? Is there a way for me to get the number of clusters of a
particular size vs cluster size?

Thanks,
Mike Tomasini
g_clustsize will make an xpm plot for this as well, IIRC it is called 
csize.xpm. You can turn it into eps using xpm2ps.



--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] Charge assignment

[Michael McGovern]

Hi everyone.
  I'm working on getting parameters for a protein system that has some linker 
residues in it.  These linkers are nothing too strange, they just have some 
amine groups.  I can get bonded parameters from the prodrg server.  I know the 
charge groups are unreliable.  I'm using the 53A6 parameter set, and I read how 
the charges there were derived.  They specifically did the iteration 
of parameters manually to give the same charges for the same functional groups. 
 Does this mean I can take charges from the same functional groups in the rtp 
files for amino acids and use those charges in my linkers?  If it is necessary 
to validate, should that be done on the linkers as molecules in their acidic, 
unlinked form?  Thanks everyone.


  -- 
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