Re: [gmx-users] Regarding conversion of C6/C12 parameters to sigma/epsilon

[Mark Abraham]

naga raju wrote:

Dear gmx users,
  I have one doubt regarding conversion of
C6/C12 parameters to sigma /epsilon. 
I added atomtypes, pairtypes and dihedraltypes from

lipid.itp to ffoplsaanb.itp---after changing C6/C12
paramters to sigma/epsilon as given in mailing list
(http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html
). 
 
My questions are

(1) Is it also required to do conversion of C6/C12
parameters of “nonbond_params“to sigma/epsilon and
adding these parameters from lipid.itp to
ffoplsaanb.itp.
 
(2) If it is not required to convert” nonbond_params”

parameters, is it required to call these parameters
without conversion.
 
   Any suggestion is appreciated, thank

you in advance.


Please stop posting the same question. If anybody knows enough to help 
you, they've already read your post. Anybody else is just getting 
annoyed by the repeats.


It is likely the contents of chapter five and a detailed comparative 
reading of all the relevant .itp files will lead you to answer your 
question yourself. If nobody has this knowledge already, you'll need to 
do it yourself.


Mark
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Re: [gmx-users] Fatal error:Atom S in residue TYR 2 not found in rtp entry with 18 atoms

[Tsjerk Wassenaar]

Hi Winter,


I'm a beginner to GMX,
when I use the following command:
"pdb2gmx -f 1G1S.pdb -p gr.top -o gr.gro -missing"


Don't use '-missing'. Since you're a beginner you're not allowed to
(unless you get a permit for it from one of the developers).


"WARNING: atom CD not found in residue 72 while adding improper


This is the result of using '-missing'.


Fatal error:
Atom S in residue TYR 2 not found in rtp entry with 18 atoms
 while sorting atoms"

How to solve this fatal error?


Well, as I recall, but I may need to check my biochemistry books here,
there's no S in tyrosine. Is this a modified residue, or is there just
something _else_ wrong with your starting structure? Note that I say
something else, since you clearly also have missing atoms, which you
need to fix. Go work on the starting structure!

Best,

Tsjerk

--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Very large fluctuations in dg/dl

[Tsjerk Wassenaar]

Hi Berk,

Just a question relating to your reply (should be a new thread
maybe...). The Gromos force fields were parameterized (for use) with
cutoff/RF. PME is of course better for energy conservation, but the
inclusion of the interactions beyond the cut-off may give rise to
deviant behaviour from the force field. Could you enlighten me on this
issue?

Thanks,

Tsjerk

On 5/7/07, Berk Hess <[EMAIL PROTECTED]> wrote:




>From: Patrick Fuchs <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users 
>To: gmx-users@gromacs.org
>Subject: [gmx-users] Very large fluctuations in dg/dl
>Date: Mon, 07 May 2007 16:41:26 +0200
>
>Hi Gromacs users,
>I have a few questions related to solvation free energy calculation via
>thermodynamic integration.
>I'm trying to reproduce some literature data (on e.g. methane,
>methanol...) using the GROMOS G53a6 force field. I followed the tutorial
>of David Mobley (thanks to him BTW), but I used the standard non bonded
>options of the G53a6 force field (instead of OPLS). For each lambda
>value I do a minimization, a 10 ps NVT followed by a 20 ps NPT
>equilibration, and a 1 ns NVT production using the sd integrator. I used
>21 lambda values (0.00, 0.05...1.00).
>Here's my topology file:
>begining of methane.top
>; topology for a methane molecule
>
>; include GROMOS53a6 force field
>#include "ffG53a6.itp"
>
>;;; begin methane definition ;;;
>[ moleculetype ]
>; Name   nrexcl
>METH 3
>
>[ atoms ]
>;nr type resnr residue atom cgnr charge masstypeB chargeB massB
>  1  CH4  1 METHC1   00. 16.0430 DUM   0.  16.04300
>;; end methane definition 
>
>; include water topology
>#ifdef FLEX_SPC
>#include "flexspc.itp"
>#else
>#include "spc.itp"
>#endif
>
>[ system ]
>; name
>1 methane molecule in water
>
>[ molecules ]
>; name  number
>METH1
>SOL 893
>-end of methane.top
>
>And here is my mdp file for lambda=0:
>---begining of prod.mdp-
>title   = production NVT methane/water
>cpp = /lib/cpp
>; OPTIONS FOR BOND CONSTRAINTS
>constraints = all-bonds
>; RUN CONTROL PARAMETERS
>integrator  = sd
>tinit   = 0
>dt  = 0.002
>nsteps  = 50 ; 1000 ps
>; NUMBER OF STEPS FOR CENTER OF MASS MOTION REMOVAL
>nstcomm = 100
>; OUTPUT CONTROL OPTIONS
>nstxout  = 500
>nstvout  = 500
>nstfout  = 0
>nstlog   = 500
>nstenergy= 100
>nstxtcout= 5000
>xtc-precision= 1000
>; NON BONDED STUFF
>ns_type =  grid
>nstlist= 5
>rlist  = 0.8
>coulombtype= generalized-reaction-field
>rcoulomb   = 1.4
>rvdw   = 1.4
>epsilon_rf = 54.0
>;OPTIONS FOR TEMPERATURE COUPLING
>tc_grps  = system
>tau_t= 0.1 ; inverse langevin friction cst
>ref_t= 300
>;OPTIONS FOR PRESSURE COUPLING
>Pcoupl   = no
>tau_p= 0.5
>compressibility  = 4.5e-5
>ref_p= 1.0
>; FREE ENERGY CONTROL STUFF
>free_energy  = yes
>init_lambda  = 0.00
>delta_lambda = 0
>sc_alpha = 0.5
>sc-power = 1.0
>sc-sigma = 0.3
>; VELOCITY GENERATION
>gen_vel  = yes
>gen_temp = 300
>gen_seed = -1
>-end of prod.mdp
>I find a reasonable DeltaGsol value of 8.6 kJ/mol for methane (compared
>to 8.7 in Geerke & van Gunsteren, ChemPhysChem 2006, 7, 671 – 678) but
>I get really huge fluctuations in the values of dg/dl:
>lambda=0.00: 5.0 +/- 10.8 (mean +/- standard deviation)
>lambda=0.05: 4.3 +/- 11.2
>...
>lambda=1.00: -0.3 +/- 4.0
>Furthermore, each of these mean value is very slow at converging (1 ns
>seems a minimum for certain lambda values...).
>I can't get reasonable fluctuations even if I sample more. In addition,
>there are very frequent warnings in the log file such as:
>
>Large VCM(group rest):  0.01363,  0.00818,  0.01147, ekin-cm:
>3.09490e+00
>
>Here are my questions:
>1) Has someone an idea of what could be the cause of these [very] large
>fluctuations? Does it come from my setup, or is this a normal behavior?
>2) Are these 'Large VCM(group rest)' warnings related to the use of sd
>integrator (when I switch to md integrator, I no longer get these warnings)
>?
>Thanks for your answer,
>
>Patrick

Large fluctuations are very common, depending on your system
and how your choose your intermediate states.

But sampling would improve a lot if you use a larger tau_t, for instance
1 ps, this will also solve your large vcm warnings.
Note that with reaction-field your will have bad energy conservati

[gmx-users] Regarding conversion of C6/C12 parameters to sigma/epsilon

[naga raju]

Dear gmx users,
  I have one doubt regarding conversion of
C6/C12 parameters to sigma /epsilon. 
I added atomtypes, pairtypes and dihedraltypes from
lipid.itp to ffoplsaanb.itp---after changing C6/C12
paramters to sigma/epsilon as given in mailing list
(http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html
). 
 
My questions are
(1) Is it also required to do conversion of C6/C12
parameters of “nonbond_params“to sigma/epsilon and
adding these parameters from lipid.itp to
ffoplsaanb.itp.
 
(2) If it is not required to convert” nonbond_params”
parameters, is it required to call these parameters
without conversion.
 
   Any suggestion is appreciated, thank
you in advance.
  

   With best regards,
   Mulpuri.

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RE: [gmx-users] Visualization Problem

[Dallas B. Warren]

Probably means that atoms are moving across the pbc boundary from one
side of the box to another.  The visualiser you are using is trying to
maintain the bond between the atoms after the move, so draws it all the
way across the box itself.  Two ways to fix, don't visualise the bonds,
using either points or ball representations for the atoms, or when
generating the trajectory do so that atoms don't go jump across the box
boundary.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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Re: [gmx-users] Visualization Problem

[George Abadir]

Thanks Itamar for your reply, but the tube actually does not jump, but 
the lines showing the bonds start to show bonding between 
non-neighbouring atoms, i.e., the hexagonal shape characteristic of 
nanotubes is destroyed, and it starts from the third frame regardless of 
the start time. I tried the 'pbc whole' option anyway but it didn't work.

Thank you very much,
Regards,
George

Itamar Kass wrote:


Shalom George

Maybe your nanotube 'jump' over the PBC?

Try 'trjconv -pbc whole ...'

Best,
Itamar

George Abadir wrote:


Hi,
I finished a simulation of a carbon nanotube in water. I made a 
movie of the simulation using 'trjconv' to view with Pymol. The 
problem is that starting from the third frame it messes the carbon 
nanotube bonds. I changed the start time and again in the third 
frames it messed things up. I output each frame in a different file 
using the '-sep' option and it could read each one successfuly, so I 
think the problem is in reading them in sequence. Can anyone help 
with that?

   Thank you very much,
Regards,
George
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Re: [gmx-users] Visualization Problem

[Itamar Kass]

Shalom George

Maybe your nanotube 'jump' over the PBC?

Try 'trjconv -pbc whole ...'

Best,
Itamar

George Abadir wrote:

Hi,
I finished a simulation of a carbon nanotube in water. I made a 
movie of the simulation using 'trjconv' to view with Pymol. The problem 
is that starting from the third frame it messes the carbon nanotube 
bonds. I changed the start time and again in the third frames it messed 
things up. I output each frame in a different file using the '-sep' 
option and it could read each one successfuly, so I think the problem is 
in reading them in sequence. Can anyone help with that?

   Thank you very much,
Regards,
George
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--
"Prediction is very difficult, especially about the future" - Niels Bohr

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Molecular Dynamics Group
| School of Molecular and Microbial Sciences (SMMS)
| Chemistry Building (#68)
| The University of Queensland
| St. Lucia Campus, Brisbane, QLD 4067
| Australia
|
| Tel: +61 7 3365 9922
| Fax: +61 7 3365 3872
| E-mail: [EMAIL PROTECTED]
| Web page: http://www.uq.edu.au/~uqikass/
| Personal web page: http://thekassfamily.blogspot.com/


Unless stated otherwise, this e-mail represents only the views of the 
Sender and not the views of The University of Queensland

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[gmx-users] Fatal error:Atom S in residue TYR 2 not found in rtp entry with 18 atoms

[kong.winter]

Hi all,
I'm a beginner to GMX,
when I use the following command:
"pdb2gmx -f 1G1S.pdb -p gr.top -o gr.gro -missing"

"WARNING: atom CD not found in residue 72 while adding improper

Fatal error:
Atom S in residue TYR 2 not found in rtp entry with 18 atoms
 while sorting atoms"

How to solve this fatal error? 
Thank you very much!
Best wishes,
 Yours, Winter
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[gmx-users] Visualization Problem

[George Abadir]

Hi,
I finished a simulation of a carbon nanotube in water. I made a 
movie of the simulation using 'trjconv' to view with Pymol. The problem 
is that starting from the third frame it messes the carbon nanotube 
bonds. I changed the start time and again in the third frames it messed 
things up. I output each frame in a different file using the '-sep' 
option and it could read each one successfuly, so I think the problem is 
in reading them in sequence. Can anyone help with that?

   Thank you very much,
Regards,
George
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Re: [gmx-users] Problems using grompp and amber force field

[TJ Piggot]

Hi,

With regards to the versions you are correct, ffamber_v3.3.1 is for use 
with Gromacs 3.3.1. As for the error i would suggest you do what Mark says 
and make sure all your inclusions are correct.  If you still can't find the 
problem then you need to post some of your .top file so we can have a look 
at it


Tom

--On 08 May 2007 10:53 +1000 Mark Abraham <[EMAIL PROTECTED]> wrote:


root wrote:

Dear GROMACS user:

Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
http://folding.stanford.edu and now I understand your comments.
We tried with cpp = /lib/cpp -traditional in the mdp file. The warning
desapears, but the error messages is similar.
(Fatal error:

Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms

are numbered

consecutively from 1 to 758.)


Have you inspected the #included files as well? The way cpp works, any
file #included is literally dropped into its parent file, so if you had
something wrong in such an #inclusion you'd need to fix that.

Mark
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--
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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Re: [gmx-users] Cys-Cys Bond

[Mark Abraham]

fulya caglar wrote:

Hi everone.
I'm studying on a protein including two chains with *four* disulfide 
bonds.when I

watched the simulation I saw that A and B chains were splitting from
eachother.


Check your topology. This will mean that you didn't define the 
disulfides in the first place. You should also read your pdb2gmx output 
closely, where it should be telling you how many it did find (and create).



Then I gave that command.
   pdb2gmx-f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro  -merge  
-ss  -inter   -ignh.
But the chains split from eachother again.In specbond.dat only one 
CYS-CYS bond appears.Should I  add three more lines to the file like this?

CYS  SG   1 CYSSG1   0.2   CYS2   CYS2
 
What can I do to identify the  -SS bond other than these?


Identify how far apart those sulfur atoms are in the structure you're 
feeding to pdb2gmx. You may need to edit specbond.dat to increase the 
length that it searches for possible disulfide bonds (search the mailing 
list on this topic). Or you can do a quick geometry optimization with 
restraints on the relevant pairs to bring them close enough that pdb2gmx 
will find them.


Mark
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Re: [gmx-users] (no subject)

[Mark Abraham]

vijaya subramanian wrote:

Hi
I ran an md simulation on speptide, the tutorial example.  The reference 
temperature in the mdp file is

300 K but I find the system equilibrates to 305 K.  Why is this?


Is this an average or the final temperature?

Mark
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Re: [gmx-users] Problems using grompp and amber force field

[Mark Abraham]

root wrote:

Dear GROMACS user:

Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
http://folding.stanford.edu and now I understand your comments.  
We tried with cpp = /lib/cpp -traditional in the mdp file. The warning

desapears, but the error messages is similar.
(Fatal error:

Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms

are numbered

consecutively from 1 to 758.)


Have you inspected the #included files as well? The way cpp works, any 
file #included is literally dropped into its parent file, so if you had 
something wrong in such an #inclusion you'd need to fix that.


Mark
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Re: [gmx-users] Problems using grompp and amber force field

[root]

Dear GROMACS user:

Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
http://folding.stanford.edu and now I understand your comments.  
We tried with cpp = /lib/cpp -traditional in the mdp file. The warning
desapears, but the error messages is similar.
(Fatal error:
> >> Atoms in the .top are not numbered consecutively from 1
> >>
> >> ---
> >>
> >> We tested the dick.top file, and we verified that the atoms
> > are numbered
> >> consecutively from 1 to 758.)

We download the ffamber_v3.3.1-doc.tar.gz, that we considered that
correspond to the 3.3.1 version of GROMACS.
Is this correct?

Thanks in advance.

Mario
 
El lun, 07-05-2007 a las 23:17 +0200, Erik Marklund escribió:
> As someone already mentioned, the following can be found among the  
> AMBERport FAQ:
> 
>  >>
> Why do I get a grompp warning "missing white space after `#define  
> proper_*'?"
> Set "cpp = /lib/cpp -traditional" in your .mdp file to remove these  
> warnings, which result from the use of the N* atom type of the AMBER  
> family of force fields and can be ignored.
> <<
> 
> Did you try doing that?
> 
> Good luck!
> 
> /Erik
> 
> 7 maj 2007 kl. 22.29 skrev root:
> 
> Hi,

>I think if you set "cpp = /lib/cpp -traditional" in your .mdp file then
>it 
>should get rid of the warnings about "spaces are absent in target after
>the 
>name of macro". For more info see 
>

>Tom

>--On 07 May 2007 20:42 +0200 David van der Spoel
><[EMAIL PROTECTED]> 
>wrote:
> > David and GROMACS users:
> > Sorry we changed the error message in ...
> >
> > /usr/local/gromacs/share/top/ffamber03bon.itp:541:22:  warning: spaces
> > are absent in target after the name of macro
> >
> > because of the original message was in spanish.
> >
> > We checked these files above. We run GROMACS in fedora 6.0
> > We analyzed the warning messages. They correspond to a format of
> > description of a dihedral angle. For example the 538:22 warning
> >  correspond to le line 538 column 22
> >
> >  #define proper_X_CT_N*_X
> >  and there are a format problem with the * symbol.
> >
> >  we don't know that to do still with this.
> >
> >
> > Thanks in advance
> >
> > root wrote:
> > De:
> > David van der Spoel
> > <[EMAIL PROTECTED]>
> >Responder a:
> > Discussion list for GROMACS users
> > 
> >   Para:
> > Discussion list for GROMACS users
> > 
> > Asunto:
> > Re: [gmx-users] Problems using
> > grompp and amber force field
> >  Fecha:
> > Mon, 07 May 2007 20:42:51 +0200
> > (15:42 ART)
> >
> > The procedure to simulate the DNA dodecamer was:
> >
> > 1) We generate the DNA topology and coordinates in gromacs format  
> > (with
> > the amber03 force field ) using the pdb2gmx program:
> >
> > pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce
> >
> > 2) and we obtain the box with the dodecamer plus water coordinates
> > using editconf and genbox:
> >
> > editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle  
> > 90 90
> > 90
> > genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top
> >
> > 3) with the files dick03.pdb and dick.top we run grompp:
> >
> > grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top
> >
> > The output of the program indicate
> > ...
> > creating statusfile for 1 node...
> >
> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
> > checking input for internal consistency...
> > calling /usr/bin/cpp...
> > In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
> >  de dick.top:11:
> > /usr/local/gromacs/share/top/ffamber03bon.itp:538:22:
> > warning: spaces are absent in target after the name of macro
> > /usr/local/gromacs/share/top/ffamber03bon.itp:541:22:
> > warning: spaces are absent in target after the name of macro
> > /usr/local/gromacs/share/top/ffamber03bon.itp:543:22:
> > warning: spaces are absent in target after the name of macro
> > /usr/local/gromacs/share/top/ffamber03bon.itp:547:21:
> > warning: spaces are absent in target after the name of macro
> > /usr/local/gromacs/share/top/ffamber03bon.itp:559:19:
> > warning: spaces are absent in target after the name of macro
> > processing topology...
> >
> > check the files above. is the error message correct? then fix
> > it.
> >
> > what kind of system are you running this on?
> >
> >> processing topology...
> >> Generated 2701 of the 2701 non-bonded parameter combinations
> >> Generating 1-4 interactions: fudge = 0.5
> >> Generated 2701 of the 2701 1-4 parameter combinations
> >> ---
> >> Program grompp, VERSION 3.3.1
> >> Source code file: toppush.c, line: 758
> >>
> >> Fatal error:
> >> Atoms in the .top are not numbered consecutively from 1
> >>
> >> --

[gmx-users] (no subject)

[vijaya subramanian]

Hi
I ran an md simulation on speptide, the tutorial example.  The reference 
temperature in the mdp file is

300 K but I find the system equilibrates to 305 K.  Why is this?
VS

_
Watch free concerts with Pink, Rod Stewart, Oasis and more.  Visit MSN In 
Concert today. http://music.msn.com/presents?icid=ncmsnpresentstagline


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Re: [gmx-users] Problems using grompp and amber force field

[Erik Marklund]

As someone already mentioned, the following can be found among the  
AMBERport FAQ:


>>
Why do I get a grompp warning "missing white space after `#define  
proper_*'?"
Set "cpp = /lib/cpp -traditional" in your .mdp file to remove these  
warnings, which result from the use of the N* atom type of the AMBER  
family of force fields and can be ignored.

<<

Did you try doing that?

Good luck!

/Erik

7 maj 2007 kl. 22.29 skrev root:


David and GROMACS users:
Sorry we changed the error message in ...

/usr/local/gromacs/share/top/ffamber03bon.itp:541:22:  warning: spaces
are absent in target after the name of macro

because of the original message was in spanish.

We checked these files above. We run GROMACS in fedora 6.0
We analyzed the warning messages. They correspond to a format of
description of a dihedral angle. For example the 538:22 warning
 correspond to le line 538 column 22

 #define proper_X_CT_N*_X
 and there are a format problem with the * symbol.

 we don't know that to do still with this.


Thanks in advance

root wrote:
De:
David van der Spoel
<[EMAIL PROTECTED]>
   Responder a:
Discussion list for GROMACS users

  Para:
Discussion list for GROMACS users

Asunto:
Re: [gmx-users] Problems using
grompp and amber force field
 Fecha:
Mon, 07 May 2007 20:42:51 +0200
(15:42 ART)

The procedure to simulate the DNA dodecamer was:

1) We generate the DNA topology and coordinates in gromacs format  
(with

the amber03 force field ) using the pdb2gmx program:

pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce

2) and we obtain the box with the dodecamer plus water coordinates
using editconf and genbox:

editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle  
90 90

90
genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top

3) with the files dick03.pdb and dick.top we run grompp:

grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top

The output of the program indicate
...
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /usr/bin/cpp...
In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
 de dick.top:11:
/usr/local/gromacs/share/top/ffamber03bon.itp:538:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:541:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:543:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:547:21:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:559:19:
warning: spaces are absent in target after the name of macro
processing topology...

check the files above. is the error message correct? then fix
it.

what kind of system are you running this on?


processing topology...
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 758

Fatal error:
Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms

are numbered

consecutively from 1 to 758.
We analyzed the warning messages. They correspond to a format

of

desciption of a dihedral angle. For example the 538:22 warning
correspond to le line 538 column 22

#define proper_X_CT_N*_X
and there are a format problem with the * simbol.

we don't know that to do still with this.



Thanks in advance

Mario Campo and Griselda Corral
Fac. de Cs. Exactas y Naturales
UNLPam




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--
David.
 
__ 
__

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics
group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED][EMAIL PROTECTED]
http://folding.bmc.uu.se
 

Re: [gmx-users] Problems using grompp and amber force field

[root]

David and GROMACS users:
Sorry we changed the error message in ...

/usr/local/gromacs/share/top/ffamber03bon.itp:541:22:  warning: spaces
are absent in target after the name of macro

because of the original message was in spanish.

We checked these files above. We run GROMACS in fedora 6.0
We analyzed the warning messages. They correspond to a format of
description of a dihedral angle. For example the 538:22 warning
 correspond to le line 538 column 22
 
 #define proper_X_CT_N*_X  
 and there are a format problem with the * symbol.
 
 we don't know that to do still with this.
 

Thanks in advance

root wrote:
De: 
David van der Spoel
<[EMAIL PROTECTED]>
   Responder a: 
Discussion list for GROMACS users

  Para: 
Discussion list for GROMACS users

Asunto: 
Re: [gmx-users] Problems using
grompp and amber force field
 Fecha: 
Mon, 07 May 2007 20:42:51 +0200
(15:42 ART)

The procedure to simulate the DNA dodecamer was:

1) We generate the DNA topology and coordinates in gromacs format (with
the amber03 force field ) using the pdb2gmx program:

pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce

2) and we obtain the box with the dodecamer plus water coordinates
using editconf and genbox:

editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle 90 90
90
genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top

3) with the files dick03.pdb and dick.top we run grompp:

grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top
 
The output of the program indicate
...
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /usr/bin/cpp...
In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
 de dick.top:11:
/usr/local/gromacs/share/top/ffamber03bon.itp:538:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:541:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:543:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:547:21: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:559:19: 
warning: spaces are absent in target after the name of macro
processing topology...

check the files above. is the error message correct? then fix
it.

what kind of system are you running this on?

> processing topology...
> Generated 2701 of the 2701 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2701 of the 2701 1-4 parameter combinations
> ---
> Program grompp, VERSION 3.3.1
> Source code file: toppush.c, line: 758
> 
> Fatal error:
> Atoms in the .top are not numbered consecutively from 1
> 
> ---
> 
> We tested the dick.top file, and we verified that the atoms
are numbered
> consecutively from 1 to 758. 
> We analyzed the warning messages. They correspond to a format
of
> desciption of a dihedral angle. For example the 538:22 warning
> correspond to le line 538 column 22
> 
> #define proper_X_CT_N*_X  
> and there are a format problem with the * simbol.
> 
> we don't know that to do still with this.
> 
> 
> 
> Thanks in advance
>  
> Mario Campo and Griselda Corral
> Fac. de Cs. Exactas y Naturales
> UNLPam 
> 
> 
> 
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.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 [EMAIL PROTECTED]
> Can't post? Read
http://www.gromacs.org/mailing_lists/users.php


-- 
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics
group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED][EMAIL PROTECTED]
http://folding.bmc.uu.se
+

[gmx-users] Very large fluctuations in dg/dl

[John D. Chodera]

Hi Patrick,

I find a reasonable DeltaGsol value of 8.6 kJ/mol for methane  
(compared

to 8.7 in Geerke & van Gunsteren, ChemPhysChem 2006, 7, 671 – 678) but
I get really huge fluctuations in the values of dg/dl:
lambda=0.00: 5.0 +/- 10.8 (mean +/- standard deviation)
lambda=0.05: 4.3 +/- 11.2


Is the standard deviation you quote here the standard deviation of  
the dg/dl samples, or the standard deviation of the mean?


If the former, then this behavior is totally expected: While the  
standard deviation of a random variable (your dg/dl samples) may be  
large, with enough sampling, we can get a very precise estimate of  
the mean.  More sampling will not change the standard deviation of  
the dg/dl samples, but it will reduce the standard error in the mean,  
which is what we need for precise estimates of free energy differences.


The uncertainty in the estimate of  is given simply by

d = sigma / sqrt(N / g)

where here, sigma is the standard deviation of your dg/dl samples, N  
is the number of data points you have collected, and g is something  
called the "statistical inefficiency", which can be estimated from  
the correlation time of your dg/dl samples.  More information on this  
sort of analysis can be found in reference [1] below.


Once you have the uncertainty in each estimate of , you still  
have to combine these to get the uncertainty estimate for the  
integrated free energy difference using standard propagation of  
error.  This depends on your choice of quadrature for TI.  David  
Mobley has done a lot of this, and I'm sure would be willing to help  
if you had trouble figuring it out.


Good luck!

- John

[1] W. Janke. Statistical analysis of simulations: Data correlations  
and error estimation. In J. Grotendorst, D. Marx, and A. Murmatsu,  
editors, Quantum Simulations of Complex Many-Body Systems: From  
Theory to Algorithms, volume 10, pages 423–445. John von Neumann  
Institute for Computing, 2002.


--
John Chodera <[EMAIL PROTECTED]> | Mobile: 415 867-7384
Postdoctoral researcher, Pande lab| Lab phone : 650.723.1097
Department of Chemistry, Stanford University  | Lab fax   : 650.724.4021
http://www.dillgroup.ucsf.edu/~jchodera
--

Date: Mon, 07 May 2007 16:41:26 +0200
From: Patrick Fuchs <[EMAIL PROTECTED]>
Subject: [gmx-users] Very large fluctuations in dg/dl
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=windows-1252; format=flowed

Hi Gromacs users,
I have a few questions related to solvation free energy calculation via
thermodynamic integration.
I'm trying to reproduce some literature data (on e.g. methane,
methanol...) using the GROMOS G53a6 force field. I followed the tutorial
of David Mobley (thanks to him BTW), but I used the standard non bonded
options of the G53a6 force field (instead of OPLS). For each lambda
value I do a minimization, a 10 ps NVT followed by a 20 ps NPT
equilibration, and a 1 ns NVT production using the sd integrator. I used
21 lambda values (0.00, 0.05...1.00).
Here's my topology file:
begining of methane.top
; topology for a methane molecule

; include GROMOS53a6 force field
#include "ffG53a6.itp"

;;; begin methane definition ;;;
[ moleculetype ]
; Name   nrexcl
METH 3

[ atoms ]
;nr type resnr residue atom cgnr charge masstypeB chargeB massB
  1  CH4  1 METHC1   00. 16.0430 DUM   0.  16.04300
;; end methane definition 

; include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
1 methane molecule in water

[ molecules ]
; name  number
METH1
SOL 893
-end of methane.top

And here is my mdp file for lambda=0:
---begining of prod.mdp-
title   = production NVT methane/water
cpp = /lib/cpp
; OPTIONS FOR BOND CONSTRAINTS
constraints = all-bonds
; RUN CONTROL PARAMETERS
integrator  = sd
tinit   = 0
dt  = 0.002
nsteps  = 50 ; 1000 ps
; NUMBER OF STEPS FOR CENTER OF MASS MOTION REMOVAL
nstcomm = 100
; OUTPUT CONTROL OPTIONS
nstxout  = 500
nstvout  = 500
nstfout  = 0
nstlog   = 500
nstenergy= 100
nstxtcout= 5000
xtc-precision= 1000
; NON BONDED STUFF
ns_type =  grid
nstlist= 5
rlist  = 0.8
coulombtype= generalized-reaction-field
rcoulomb   = 1.4
rvdw   = 1.4
epsilon_rf = 54.0
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps  = system
tau_t= 0.1 ; inverse langevin friction cst
ref_t= 300
;OPTIONS FOR PRESSURE COUPLING
Pcoupl   = no
tau_p= 0.5
compressibility

Re: [gmx-users] Problems using grompp and amber force field

[TJ Piggot]

Hi,

I think if you set "cpp = /lib/cpp -traditional" in your .mdp file then it 
should get rid of the warnings about "spaces are absent in target after the 
name of macro". For more info see 



Tom

--On 07 May 2007 20:42 +0200 David van der Spoel <[EMAIL PROTECTED]> 
wrote:



root wrote:

Dear GROMACS user:
David and Mark, thanks by our comments, suggestions and questions. If
our response is confused, please require us copies of output files (or
fragment).

The procedure to simulate the DNA dodecamer was:

1) We generate the DNA topology and coordinates in gromacs format (with
the amber03 force field ) using the pdb2gmx program:

pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce

2) and we obtain the box with the dodecamer plus water coordinates
using editconf and genbox:

editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle 90 90
90
genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top

3) with the files dick03.pdb and dick.top we run grompp:

grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top

The output of the program indicate
...
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /usr/bin/cpp...
In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
 de dick.top:11:
/usr/local/gromacs/share/top/ffamber03bon.itp:538:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:541:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:543:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:547:21:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:559:19:
warning: spaces are absent in target after the name of macro


check the files above. is the error message correct? then fix it.

what kind of system are you running this on?


processing topology...
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 758

Fatal error:
Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms are numbered
consecutively from 1 to 758.
We analyzed the warning messages. They correspond to a format of
desciption of a dihedral angle. For example the 538:22 warning
correspond to le line 538 column 22

# define proper_X_CT_N*_X
and there are a format problem with the * simbol.

we don't know that to do still with this.


Other coments: Previosly,  we consult the gromacs mailing list,
searching similar DNA simulation and finding suggest about the opls-na
and amber force field. Initially, we attempted to obtain a topology with
the opls-na force fied, but fequent error mesagges about the format of
the input file were generated. In consecuence, we thinked that there was
differences in the input format to the differente versions of the
gromacs package. Of course, it is only a hypothesis.

Thanks in advance

Mario Campo and Griselda Corral
Fac. de Cs. Exactas y Naturales
UNLPam




___
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Please search the archive at http://www.gromacs.org/search before
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www interface or send it to [EMAIL PROTECTED]
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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

___
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--
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
___
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Please search the archive at http://www.gromacs.o

[gmx-users] Cys-Cys Bond

[fulya caglar]

Hi everone.
  I'm studying on a protein including two chains with four disulfide bonds.when 
I
watched the simulation I saw that A and B chains were splitting from
eachother.Then I gave that command.
   pdb2gmx-f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro  -merge  -ss  
-inter   -ignh.
  But the chains split from eachother again.In specbond.dat only one CYS-CYS 
bond appears.Should I  add three more lines to the file like this?
  CYS  SG   1 CYSSG1   0.2   CYS2   CYS2

   
  What can I do to identify the  -SS bond other than these?
   
  Thank you
  Best regards
  Fulya Caglar
  Hacettepe  University

 
-
 Get your own web address.
 Have a HUGE year through Yahoo! Small Business.___
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Re: [gmx-users] Problems using grompp and amber force field

[David van der Spoel]

root wrote:

Dear GROMACS user:
David and Mark, thanks by our comments, suggestions and questions. If
our response is confused, please require us copies of output files (or
fragment). 


The procedure to simulate the DNA dodecamer was:

1) We generate the DNA topology and coordinates in gromacs format (with
the amber03 force field ) using the pdb2gmx program:

pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce

2) and we obtain the box with the dodecamer plus water coordinates
using editconf and genbox:

editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle 90 90
90
genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top

3) with the files dick03.pdb and dick.top we run grompp:

grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top
 
The output of the program indicate

...
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /usr/bin/cpp...
In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
 de dick.top:11:
/usr/local/gromacs/share/top/ffamber03bon.itp:538:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:541:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:543:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:547:21: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:559:19: 
warning: spaces are absent in target after the name of macro


check the files above. is the error message correct? then fix it.

what kind of system are you running this on?


processing topology...
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 758

Fatal error:
Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms are numbered
consecutively from 1 to 758. 
We analyzed the warning messages. They correspond to a format of

desciption of a dihedral angle. For example the 538:22 warning
correspond to le line 538 column 22

#define proper_X_CT_N*_X  
and there are a format problem with the * simbol.


we don't know that to do still with this.


Other coments: Previosly,  we consult the gromacs mailing list,
searching similar DNA simulation and finding suggest about the opls-na
and amber force field. Initially, we attempted to obtain a topology with
the opls-na force fied, but fequent error mesagges about the format of
the input file were generated. In consecuence, we thinked that there was
differences in the input format to the differente versions of the
gromacs package. Of course, it is only a hypothesis.

Thanks in advance
 
Mario Campo and Griselda Corral

Fac. de Cs. Exactas y Naturales
UNLPam 





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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
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[gmx-users] Problems using grompp and amber force field

[root]

Dear GROMACS user:
David and Mark, thanks by our comments, suggestions and questions. If
our response is confused, please require us copies of output files (or
fragment). 

The procedure to simulate the DNA dodecamer was:

1) We generate the DNA topology and coordinates in gromacs format (with
the amber03 force field ) using the pdb2gmx program:

pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce

2) and we obtain the box with the dodecamer plus water coordinates
using editconf and genbox:

editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle 90 90
90
genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top

3) with the files dick03.pdb and dick.top we run grompp:

grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top
 
The output of the program indicate
...
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /usr/bin/cpp...
In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
 de dick.top:11:
/usr/local/gromacs/share/top/ffamber03bon.itp:538:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:541:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:543:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:547:21: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:559:19: 
warning: spaces are absent in target after the name of macro
processing topology...
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 758

Fatal error:
Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms are numbered
consecutively from 1 to 758. 
We analyzed the warning messages. They correspond to a format of
desciption of a dihedral angle. For example the 538:22 warning
correspond to le line 538 column 22

#define proper_X_CT_N*_X  
and there are a format problem with the * simbol.

we don't know that to do still with this.


Other coments: Previosly,  we consult the gromacs mailing list,
searching similar DNA simulation and finding suggest about the opls-na
and amber force field. Initially, we attempted to obtain a topology with
the opls-na force fied, but fequent error mesagges about the format of
the input file were generated. In consecuence, we thinked that there was
differences in the input format to the differente versions of the
gromacs package. Of course, it is only a hypothesis.

Thanks in advance
 
Mario Campo and Griselda Corral
Fac. de Cs. Exactas y Naturales
UNLPam 




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RE: [gmx-users] Very large fluctuations in dg/dl

[Berk Hess]

From: Patrick Fuchs <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: gmx-users@gromacs.org
Subject: [gmx-users] Very large fluctuations in dg/dl
Date: Mon, 07 May 2007 16:41:26 +0200

Hi Gromacs users,
I have a few questions related to solvation free energy calculation via
thermodynamic integration.
I'm trying to reproduce some literature data (on e.g. methane,
methanol...) using the GROMOS G53a6 force field. I followed the tutorial
of David Mobley (thanks to him BTW), but I used the standard non bonded
options of the G53a6 force field (instead of OPLS). For each lambda
value I do a minimization, a 10 ps NVT followed by a 20 ps NPT
equilibration, and a 1 ns NVT production using the sd integrator. I used
21 lambda values (0.00, 0.05...1.00).
Here's my topology file:
begining of methane.top
; topology for a methane molecule

; include GROMOS53a6 force field
#include "ffG53a6.itp"

;;; begin methane definition ;;;
[ moleculetype ]
; Name   nrexcl
METH 3

[ atoms ]
;nr type resnr residue atom cgnr charge masstypeB chargeB massB
 1  CH4  1 METHC1   00. 16.0430 DUM   0.  16.04300
;; end methane definition 

; include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
1 methane molecule in water

[ molecules ]
; name  number
METH1
SOL 893
-end of methane.top

And here is my mdp file for lambda=0:
---begining of prod.mdp-
title   = production NVT methane/water
cpp = /lib/cpp
; OPTIONS FOR BOND CONSTRAINTS
constraints = all-bonds
; RUN CONTROL PARAMETERS
integrator  = sd
tinit   = 0
dt  = 0.002
nsteps  = 50 ; 1000 ps
; NUMBER OF STEPS FOR CENTER OF MASS MOTION REMOVAL
nstcomm = 100
; OUTPUT CONTROL OPTIONS
nstxout  = 500
nstvout  = 500
nstfout  = 0
nstlog   = 500
nstenergy= 100
nstxtcout= 5000
xtc-precision= 1000
; NON BONDED STUFF
ns_type =  grid
nstlist= 5
rlist  = 0.8
coulombtype= generalized-reaction-field
rcoulomb   = 1.4
rvdw   = 1.4
epsilon_rf = 54.0
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps  = system
tau_t= 0.1 ; inverse langevin friction cst
ref_t= 300
;OPTIONS FOR PRESSURE COUPLING
Pcoupl   = no
tau_p= 0.5
compressibility  = 4.5e-5
ref_p= 1.0
; FREE ENERGY CONTROL STUFF
free_energy  = yes
init_lambda  = 0.00
delta_lambda = 0
sc_alpha = 0.5
sc-power = 1.0
sc-sigma = 0.3
; VELOCITY GENERATION
gen_vel  = yes
gen_temp = 300
gen_seed = -1
-end of prod.mdp
I find a reasonable DeltaGsol value of 8.6 kJ/mol for methane (compared
to 8.7 in Geerke & van Gunsteren, ChemPhysChem 2006, 7, 671 – 678) but
I get really huge fluctuations in the values of dg/dl:
lambda=0.00: 5.0 +/- 10.8 (mean +/- standard deviation)
lambda=0.05: 4.3 +/- 11.2
...
lambda=1.00: -0.3 +/- 4.0
Furthermore, each of these mean value is very slow at converging (1 ns
seems a minimum for certain lambda values...).
I can't get reasonable fluctuations even if I sample more. In addition, 
there are very frequent warnings in the log file such as:


Large VCM(group rest):  0.01363,  0.00818,  0.01147, ekin-cm:  
3.09490e+00


Here are my questions:
1) Has someone an idea of what could be the cause of these [very] large
fluctuations? Does it come from my setup, or is this a normal behavior?
2) Are these 'Large VCM(group rest)' warnings related to the use of sd 
integrator (when I switch to md integrator, I no longer get these warnings) 
?

Thanks for your answer,

Patrick


Large fluctuations are very common, depending on your system
and how your choose your intermediate states.

But sampling would improve a lot if you use a larger tau_t, for instance
1 ps, this will also solve your large vcm warnings.
Note that with reaction-field your will have bad energy conservation.
With a tau_t of 1 ps your temperature might go up somewhat.
Using PME is always better.

Berk.

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P

[gmx-users] Very large fluctuations in dg/dl

[Patrick Fuchs]

Hi Gromacs users,
I have a few questions related to solvation free energy calculation via
thermodynamic integration.
I'm trying to reproduce some literature data (on e.g. methane,
methanol...) using the GROMOS G53a6 force field. I followed the tutorial
of David Mobley (thanks to him BTW), but I used the standard non bonded
options of the G53a6 force field (instead of OPLS). For each lambda
value I do a minimization, a 10 ps NVT followed by a 20 ps NPT
equilibration, and a 1 ns NVT production using the sd integrator. I used
21 lambda values (0.00, 0.05...1.00).
Here's my topology file:
begining of methane.top
; topology for a methane molecule

; include GROMOS53a6 force field
#include "ffG53a6.itp"

;;; begin methane definition ;;;
[ moleculetype ]
; Name   nrexcl
METH 3

[ atoms ]
;nr type resnr residue atom cgnr charge masstypeB chargeB massB
 1  CH4  1 METHC1   00. 16.0430 DUM   0.  16.04300
;; end methane definition 

; include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
1 methane molecule in water

[ molecules ]
; name  number
METH1
SOL 893
-end of methane.top

And here is my mdp file for lambda=0:
---begining of prod.mdp-
title   = production NVT methane/water
cpp = /lib/cpp
; OPTIONS FOR BOND CONSTRAINTS
constraints = all-bonds
; RUN CONTROL PARAMETERS
integrator  = sd
tinit   = 0
dt  = 0.002
nsteps  = 50 ; 1000 ps
; NUMBER OF STEPS FOR CENTER OF MASS MOTION REMOVAL
nstcomm = 100
; OUTPUT CONTROL OPTIONS
nstxout  = 500
nstvout  = 500
nstfout  = 0
nstlog   = 500
nstenergy= 100
nstxtcout= 5000
xtc-precision= 1000
; NON BONDED STUFF
ns_type =  grid
nstlist= 5
rlist  = 0.8
coulombtype= generalized-reaction-field
rcoulomb   = 1.4
rvdw   = 1.4
epsilon_rf = 54.0
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps  = system
tau_t= 0.1 ; inverse langevin friction cst
ref_t= 300
;OPTIONS FOR PRESSURE COUPLING
Pcoupl   = no
tau_p= 0.5
compressibility  = 4.5e-5
ref_p= 1.0
; FREE ENERGY CONTROL STUFF
free_energy  = yes
init_lambda  = 0.00
delta_lambda = 0
sc_alpha = 0.5
sc-power = 1.0
sc-sigma = 0.3
; VELOCITY GENERATION
gen_vel  = yes
gen_temp = 300
gen_seed = -1
-end of prod.mdp
I find a reasonable DeltaGsol value of 8.6 kJ/mol for methane (compared
to 8.7 in Geerke & van Gunsteren, ChemPhysChem 2006, 7, 671 – 678) but
I get really huge fluctuations in the values of dg/dl:
lambda=0.00: 5.0 +/- 10.8 (mean +/- standard deviation)
lambda=0.05: 4.3 +/- 11.2
...
lambda=1.00: -0.3 +/- 4.0
Furthermore, each of these mean value is very slow at converging (1 ns
seems a minimum for certain lambda values...).
I can't get reasonable fluctuations even if I sample more. In addition, 
there are very frequent warnings in the log file such as:


Large VCM(group rest):  0.01363,  0.00818,  0.01147, 
ekin-cm:  3.09490e+00


Here are my questions:
1) Has someone an idea of what could be the cause of these [very] large
fluctuations? Does it come from my setup, or is this a normal behavior?
2) Are these 'Large VCM(group rest)' warnings related to the use of sd 
integrator (when I switch to md integrator, I no longer get these 
warnings) ?

Thanks for your answer,

Patrick
--
___
Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
INSERM U726, Universite Paris 7
Case Courrier 7113
2, place Jussieu, 75251 Paris Cedex 05, FRANCE
Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30
E-mail : [EMAIL PROTECTED]
Web Site: http://www.ebgm.jussieu.fr/~fuchs


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Re: [gmx-users] Targeted Molecular dynamics

[Jay Mashl]

I have implemented one approach to targeted MD for version 3.2.1 that uses soft 
restraints to achieve the transformation.  We imagined we would make the code 
available (contribute it to Gromacs)  after we submit the manuscript.


Jay

--
R. Jay Mashl
University of Illinois
[EMAIL PROTECTED]
(Tel)217-244-5818


On Mon, 7 May 2007, Olivier Perin wrote:


Dear gmx users,

OBJECT:
I just contact you to confirm one thing about the ability to run a targeted 
molecular dynamic simulation with gromacs with the help of positional 
restraints.


SITUATION:
If struct1 and struct2 are two near conformations of one same protein could I 
use these two gromacs commands in order to force the first system (struct1) 
to direct to the second system (struct2)?


MY HYPOTHESIS:
pdb2gmx -f struct1.pdb -i posre.itp -posrefc 1000 -p struct1.top

grompp -f MD_050K.mdp -c struct1.pdb -p struct1.top -o struct1_MD.tpr -r 
struct2.pdb


(for me, the option -r of grompp allowed to define with which coordinates the 
positional restraints must be set)


mdrun -s struct1_MD.tpr  -o struct1_MD.trr   -x struct1_MD.xtc  -c 
struct1_DM1.pdb


QUESTIONS:
Do these commands seems to be correct?
What do you think about 1000 for positional restraints? Is it to high?

Thank you all for your answers!


Olivier PERIN - Institut Pasteur
Unite de Bioinformatique Structurale
25-28, rue du Dr Roux 75724 Paris Cedex 15
Tel: +331 40 61 38 84
Fax: +331 45 68 87 19
mail: [EMAIL PROTECTED]



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[gmx-users] Regarding DOPC lipid parameters

[naga raju]

Dear gmx users,
   I have one doubt regarding conversion of 
C6/C12 parameters to sigma /epsilon. As Mr Chris neale said 
(http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html ),  I added 
atomtypes, pairtypes and dihedraltypes from lipid.itp to ffoplsaanb.itp---after 
changing C6/C12 paramters to sigma/epsilon. 
   
  My questions are
  (1) Is it also required to do conversion of C6/C12 parameters of 
“nonbond_params“to sigma/epsilon and adding these parameters from lipid.itp to 
ffoplsaanb.itp.
   
  (2) If it is not required to convert” nonbond_params” parameters, is it 
required to call these parameters without conversion.
   
 Any suggestion is appreciated, thank you in advance.
  
 With best regards,
  Nagaraja Mulpuri.

 
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[gmx-users] Regarding conversion of C6/C12 parameters in .itp file

[naga raju]

Dear gmx users,
   I have one doubt regarding conversion of 
C6/C12 parameters to sigma /epsilon. As Mr Chris neale said 
(http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html ),  I added 
atomtypes, pairtypes and dihedraltypes from lipid.itp to ffoplsaanb.itp---after 
changing C6/C12 paramters to sigma/epsilon. 
   
  My questions are
  (1) Is it also required to do conversion of C6/C12 parameters of 
“nonbond_params“to sigma/epsilon and adding these parameters from lipid.itp to 
ffoplsaanb.itp.
   
  (2) If it is not required to convert” nonbond_params” parameters, is it 
required to call these parameters without conversion.
   
 Any suggestion is appreciated, thank you in advance.
  
 With best regards,
  Nagaraja Mulpuri.
   

   
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RE: [gmx-users] Re: Energy conservation of crystal surface(specification)

[Berk Hess]

From: Janne Hirvi <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: Energy conservation of crystal 
surface(specification)

Date: Mon,  7 May 2007 14:44:34 +0300

>>Hello again!
>>
>>In earlier message I said that double precision (actually same with 
single
>>precision) simulation with 4 processors terminates pretty soon and 
distinct
>>momentary increases in energy at intervals of 0.05ps can be observed 
until

>>that point.
>>
>>Now I have made more tests and noticed that actually the time interval
>>between these "energy steps" is connected to output control parameters - 
at
>>least a value of nstxout has effect on the results. Multiple simulations 
with


>>different values of nstxout (other parameters won't change and 
nstenergy=1)

>>gave different kind of energy curves. Energy values were equal at the
>>beginning but deviated just after the time step, which coordinates were
>>written to trajectory file. Energy always increases sharply at that 
moment

and >>equilibriates to the corresponding value until next sharp increase is
observed >>when coordinates are written to trajectory file next time.
>>
>>This sounds pretty strange and I would like to know if there is some
>>limitations for parallelization when using option pbc=full or if someone 
has
>>good ideas what I might be doing wrong? That hopefully might also solve 
my

>>overall energy conservation problem with this system.
>>
>>Thanks for your time,
>>
>>Janne
>
> This sounds like a bug.
>
> Why do you need pbc=full?
> I assume you did not try without pbc=full?

I supposed that I will need pbc=full option when I have crystal structure 
which
consists of infinite polymer chains. At least when I tried to use pbc=xyz 
for
the constructed topology I got warnings about 1-4 interactions at huge 
distance
which was larger than the 1-4 table size, but afterwards thinking I 
actually
got realistic energies for the starting configuration. So could there still 
be

some problems with the topology which however seems working properly?

> Could you file a bugzilla report, with a setup that produces jump
> within short time?
> Berk.

I will send it tomorrow if you think that there is no explanation - I mean 
if I

haven't screwed up with these pbc options...


You can't screw up with pbc options.
And you can't have screwed up anythins else if you are sure that the jump
move along with nstxout and you have not changed any other parameter.

I assume this problem is not related with double precision and that it would
also occur in single precision.

Berk.

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[gmx-users] Re: Energy conservation of crystal surface (specification)

[Janne Hirvi]

>>Hello again!
>>
>>In earlier message I said that double precision (actually same with single
>>precision) simulation with 4 processors terminates pretty soon and distinct
>>momentary increases in energy at intervals of 0.05ps can be observed until 
>>that point.
>>
>>Now I have made more tests and noticed that actually the time interval 
>>between these "energy steps" is connected to output control parameters - at
>>least a value of nstxout has effect on the results. Multiple simulations with

>>different values of nstxout (other parameters won't change and nstenergy=1)
>>gave different kind of energy curves. Energy values were equal at the
>>beginning but deviated just after the time step, which coordinates were
>>written to trajectory file. Energy always increases sharply at that moment
and >>equilibriates to the corresponding value until next sharp increase is
observed >>when coordinates are written to trajectory file next time.
>>
>>This sounds pretty strange and I would like to know if there is some
>>limitations for parallelization when using option pbc=full or if someone has
>>good ideas what I might be doing wrong? That hopefully might also solve my
>>overall energy conservation problem with this system.
>>
>>Thanks for your time,
>>
>>Janne
> 
> This sounds like a bug.
> 
> Why do you need pbc=full?
> I assume you did not try without pbc=full?

I supposed that I will need pbc=full option when I have crystal structure which
consists of infinite polymer chains. At least when I tried to use pbc=xyz for
the constructed topology I got warnings about 1-4 interactions at huge distance
which was larger than the 1-4 table size, but afterwards thinking I actually 
got realistic energies for the starting configuration. So could there still be
some problems with the topology which however seems working properly?  

> Could you file a bugzilla report, with a setup that produces jump
> within short time?
> Berk.

I will send it tomorrow if you think that there is no explanation - I mean if I
haven't screwed up with these pbc options...

Janne
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Re: [gmx-users] Targeted Molecular dynamics

[Berk Hess]

From: Mark Abraham <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Targeted Molecular dynamics
Date: Mon, 07 May 2007 21:20:23 +1000

Olivier Perin wrote:

Dear gmx users,

OBJECT:
I just contact you to confirm one thing about the ability to run a 
targeted molecular dynamic simulation with gromacs with the help of 
positional restraints.


SITUATION:
If struct1 and struct2 are two near conformations of one same protein 
could I use these two gromacs commands in order to force the first system 
(struct1) to direct to the second system (struct2)?


It will take a finite number of MD steps to get arbitrarily close to 
struct2, but yes this should work.



MY HYPOTHESIS:
pdb2gmx -f struct1.pdb -i posre.itp -posrefc 1000 -p struct1.top

grompp -f MD_050K.mdp -c struct1.pdb -p struct1.top -o struct1_MD.tpr -r 
struct2.pdb


(for me, the option -r of grompp allowed to define with which coordinates 
the positional restraints must be set)


mdrun -s struct1_MD.tpr  -o struct1_MD.trr   -x struct1_MD.xtc  -c 
struct1_DM1.pdb


QUESTIONS:
Do these commands seems to be correct?


Yes


What do you think about 1000 for positional restraints? Is it to high?


I suspect so, but if they are too high, then something in the structure 
will break fairly quickly. If it's a complex structural change, then 1000 
is almost certainly too high. Try it and see :-)


Mark


They might be correct, but this is an extremely rough way to do
targeted MD.
The manual decribes how to do it more properly.

Berk.

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Re: [gmx-users] Targeted Molecular dynamics

[Mark Abraham]

Olivier Perin wrote:

Dear gmx users,

OBJECT:
I just contact you to confirm one thing about the ability to run a 
targeted molecular dynamic simulation with gromacs with the help of 
positional restraints.


SITUATION:
If struct1 and struct2 are two near conformations of one same protein 
could I use these two gromacs commands in order to force the first 
system (struct1) to direct to the second system (struct2)?


It will take a finite number of MD steps to get arbitrarily close to 
struct2, but yes this should work.



MY HYPOTHESIS:
pdb2gmx -f struct1.pdb -i posre.itp -posrefc 1000 -p struct1.top

grompp -f MD_050K.mdp -c struct1.pdb -p struct1.top -o struct1_MD.tpr -r 
struct2.pdb


(for me, the option -r of grompp allowed to define with which 
coordinates the positional restraints must be set)


mdrun -s struct1_MD.tpr  -o struct1_MD.trr   -x struct1_MD.xtc  -c 
struct1_DM1.pdb


QUESTIONS:
Do these commands seems to be correct?


Yes


What do you think about 1000 for positional restraints? Is it to high?


I suspect so, but if they are too high, then something in the structure 
will break fairly quickly. If it's a complex structural change, then 
1000 is almost certainly too high. Try it and see :-)


Mark
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[gmx-users] Targeted Molecular dynamics

[Olivier Perin]

Dear gmx users,

OBJECT:
I just contact you to confirm one thing about the ability to run a 
targeted molecular dynamic simulation with gromacs with the help of 
positional restraints.


SITUATION:
If struct1 and struct2 are two near conformations of one same protein 
could I use these two gromacs commands in order to force the first 
system (struct1) to direct to the second system (struct2)?


MY HYPOTHESIS:
pdb2gmx -f struct1.pdb -i posre.itp -posrefc 1000 -p struct1.top

grompp -f MD_050K.mdp -c struct1.pdb -p struct1.top -o struct1_MD.tpr -r 
struct2.pdb


(for me, the option -r of grompp allowed to define with which 
coordinates the positional restraints must be set)


mdrun -s struct1_MD.tpr  -o struct1_MD.trr   -x struct1_MD.xtc  -c 
struct1_DM1.pdb


QUESTIONS:
Do these commands seems to be correct?
What do you think about 1000 for positional restraints? Is it to high?

Thank you all for your answers!


Olivier PERIN - Institut Pasteur
Unite de Bioinformatique Structurale
25-28, rue du Dr Roux 75724 Paris Cedex 15
Tel: +331 40 61 38 84
Fax: +331 45 68 87 19
mail: [EMAIL PROTECTED]


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RE: [gmx-users] Energy conservation of crystal surface (specification)

[Berk Hess]

From: Janne Hirvi <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: gmx-users@gromacs.org
Subject: [gmx-users] Energy conservation of crystal surface (specification)
Date: Mon,  7 May 2007 12:25:17 +0300

Hello again!

In earlier message I said that double precision (actually same with single
precision) simulation with 4 processors terminates pretty soon and distinct
momentary increases in energy at intervals of 0.05ps can be observed until 
that

point.

Now I have made more tests and noticed that actually the time interval 
between

these "energy steps" is connected to output control parameters - at least a
value of nstxout has effect on the results. Multiple simulations with 
different

values of nstxout (other parameters won't change and nstenergy=1) gave
different kind of energy curves. Energy values were equal at the beginning 
but
deviated just after the time step, which coordinates were written to 
trajectory
file. Energy always increases sharply at that moment and equilibriates to 
the
corresponding value until next sharp increase is observed when coordinates 
are

written to trajectory file next time.

This sounds pretty strange and I would like to know if there is some 
limitations

for parallelization when using option pbc=full or if someone has good ideas
what I might be doing wrong? That hopefully might also solve my overall 
energy

conservation problem with this system.

Thanks for your time,

Janne


This sounds like a bug.

Why do you need pbc=full?
I assume you did not try without pbc=full?

Could you file a bugzilla report, with a setup that produces jump
within short time?

Berk.

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[gmx-users] Energy conservation of crystal surface (specification)

[Janne Hirvi]

Hello again!

In earlier message I said that double precision (actually same with single
precision) simulation with 4 processors terminates pretty soon and distinct
momentary increases in energy at intervals of 0.05ps can be observed until that
point. 

Now I have made more tests and noticed that actually the time interval between
these "energy steps" is connected to output control parameters - at least a
value of nstxout has effect on the results. Multiple simulations with different
values of nstxout (other parameters won't change and nstenergy=1) gave
different kind of energy curves. Energy values were equal at the beginning but
deviated just after the time step, which coordinates were written to trajectory
file. Energy always increases sharply at that moment and equilibriates to the
corresponding value until next sharp increase is observed when coordinates are
written to trajectory file next time.

This sounds pretty strange and I would like to know if there is some limitations
for parallelization when using option pbc=full or if someone has good ideas
what I might be doing wrong? That hopefully might also solve my overall energy
conservation problem with this system.

Thanks for your time,

Janne


>Hello gmx-users!
>
>Sorry that I am bothering you all the time with energy conservation issues but
>this time I have problems with a crystal surface consisting of infinite
polymer
>chains.   
>
>I think that simulation and interaction parameters employed should be
>conserving the total energy: time step of 0.5fs, PME with a slab correction
>for Coulombic interactions (f-spacing=0.1, pme-order=6, ewald-rtol=1E-8), a
>plain cut-off or switch function for LJ interactions (neighborlist updated on
>every time step for test purposes), and double precision. At least there
>hasn't been such problems with these parameters (excluding pure LJ cut-off)
>earlier with other systems. New features in this system for me are positions
>restraints which are used for some atoms (160 of 46080 atoms) to maintain
>"original crystal shape" and option pbc=full due to the infinite chains.  
>
>Could it be that position restraints or full periodic boundary conditions are
>responsible for the energy drift or should I just still try to equilibriate
>system more in NVT ensemble? I guess that this could be the problem, because
>there seems to be also some huge problems depending on number of processors
>used for the simulation. Simulation with 2 processors progresses normally
>although energy drift is observed, but with 4 processors simulation terminates
>pretty soon and huge momentary increases in energy in intervals of 0.05ps can
>be observed earlier.  
>
>Thanks for any help,
>
>Janne

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Re: [gmx-users] Positive and negative ions move in the same direction under a constant electric field?

[Mark Abraham]

林揚善 wrote:
> tc_grps   =SOL NA+CL-
> 
> tau_t   =0.1  0.1  0.1
> 
> ref_t   =300  300 300

I don't know if it's germane to your problem, but this is about the
tenth time this month that someone has reported an .mdp file with groups
of ions coupled independently to thermal baths. This is a Bad Idea, and
means that even if everything else is working correctly, your simulation
isn't as close to accurate as you would want. Search the mailing list
for reasons why.

Mark
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[gmx-users] Positive and negative ions move in the same direction under a constant electric field?

[林揚善]

Dear all：

In order to make sure that my procedure for applying electric field using 
Gromacs is correct, I applied electric fields to sodium chloride solvent 
(SPC216.pdb with NA+ and CL-) in the x direction. After 2 ns running, the 
trajectories of ions and water molecules showed that both types of ions moved 
in the same direction, which is obviously wrong because Na+ and Cl- are not 
discriminated by the electric field. I tried several electric field strengths, 
ranged from 1 to 0.0001, and the observed phenomena are just the same. 

In order to delineate the problem, I changed the charge term of NA+ into 
zero while keeping CL- as -1, in the ions.itp file, and I found that both ions 
will then move in the opposite direction of the NA+=1 CL-= -1 configuration. 

 

In summary, for all the cases I tried, Na+ and Cl- moved in the same direction. 
 



The essential settings for .mdp file are listed below.

 

Comm_mode   =None

Coulombtype   =PME

Optimize_fft=yes

tcoupl =berendsen

tc_grps   =SOL NA+CL-

tau_t   =0.1  0.1  0.1

ref_t   =300  300 300

constraints  =none

E_x=  1   0.1 2.0

 

 

Can anyone give me some clue on this? I’ll appreciate for any hints on this 
question.
;
;   File 'mdout.mdp' was generated
;   By user: Yang_Shan (500)
;   On host: localhost.localdomain
;   At date: Mon Feb  5 10:34:03 2007
;

; VARIOUS PREPROCESSING OPTIONS
title= Yo
; Preprocessor - specify a full path if necessary.
cpp  = /usr/bin/cpp
include  = 
define   = 

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.002
nsteps   = 100
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= none
; number of steps for center of mass motion removal
; nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps= 

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 100
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 20
; Step size (ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep   = 1000
nbfgscorr= 10

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 400
nstvout  = 400
nstfout  = 0
; Checkpointing helps you continue after crashes
nstcheckpoint= 1000

; Output frequency for energies to log file and energy file
nstlog   = 400
nstenergy= 400
; Output frequency and precision for xtc file
; nstxtcout= 50
; xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
; xtc-grps = 
; Selection of energy groups
energygrps   =   SOL   

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off
rlist= 0.9
domain-decomposition = no


; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 0.9
; Relative dielectric constant for the medium and the reaction field
epsilon-r= 1
epsilon_rf   = 1

; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths   
rvdw-switch  = 0
rvdw = 0.9

; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  = 
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = yes

; GENERALIZED BORN ELECTROSTATICS
; Algorit