[gmx-users] Re: Improper dihedrals, which way is correct?

[Vitaly V. Chaban]

Justin,

I think force field specific syntax is important for the utilities
like pdb2gmx or x2top but not for grompp which works with topol.top.
Here, I do not use any "standard" force field but define everything
myself from the very beginning. I believe this format (in topol.top)
should be FF-independent.

Am I not right?

Vitaly


>I mention the syntax because the order of atoms is different between, e.g.,
>Gromos and OPLS (as are the implementations of the forms of the dihedrals).
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Re: [gmx-users] all-bonds

[Mark Abraham]

Enemark Soeren wrote:

Dear GMX-users,

Is it possible to exclude a group of atoms or molecules from having 
their bonds converted to constraints when using the all-bonds mdp-option?


Not automatically, but you can edit the topology manually to specify [ 
constraints ] instead of [ bonds ] for those bonds you wish to be 
constraints. See chapter 5 for detail.


Mark
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Re: [gmx-users] Probelm of g_rms

[Mark Abraham]

nikhil damle wrote:

Hi all,

 I am facing the problem while calculating backbone RMSD over 30 ns. 
upto ~6-7 ns g_rms gives correct RMSDs and later all RMSD values are 
unexpectedly and unusually high (within 20 ps RMSD value shoots up by 
~8A). But when i calculate RMSD using g_confrms programme, it gives me 
expected and usual RMSD. I tried running g_rms separately for that 
particular time range which was giving me high values only to get same 
result once again. Is there problem with g_rms or i am calculating wrongly ?


Well if you read their help pages, one of them is doing a fit 
automatically and one is not.


If you wanted more help than that, you needed to have supplied your 
command lines :-)


Mark
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[gmx-users] Re: Improper dihedrals, which way is correct?

[Vitaly V. Chaban]

Justin,

Thanks. These tidbits are too difficult for my brain to understand.
Let's make the things easier. One has the below compound.

7 -  1 - 2
 /  \
63
  \   /
   5  - 4

I want the atom 7 to be located in the same plane with atoms 1 2 and
6. Then in topol.top:
[ dihedrals ]
atoms   func angle   constant
1 2 6 7   2180  4.602


Will this line do what I want here?

Vitaly

On Wed, Sep 23, 2009 at 1:53 PM, Vitaly V. Chaban  wrote:
> Hi,
>
> I have got confused with setting up improper dihedrals in the gromacs
> topologies. In the manual (ver. 4.0) I see the section named [
> impropers ] (page 104)
> "
> [ impropers ]
> C O1 O2 CA
> "
>
> but in the example system of the peptide
> (share/gromacs/tutor/speptide) one finds defining impropers using the
> second (in the same file) [ dihedrals ] section.
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1
> c2            c3
>    1    23     5     6     1    improper_X_X_C_X
>    1    23     5     7     1    improper_N_A_C1_C
>    2     5     1     3     1    improper_X_X_M3_X
>    2     5     1     4     1    improper_X_X_M3_X
>
> What is the correct way to work with improper dihedrals? I have four
> sites, then angle value and then one force constant. What should my
> topology line look like to accomplish that?
>
> I would also be very grateful if somebody could share some topology
> with improper angles to understand how it works.
>
> Vitaly
>
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[gmx-users] Re: Improper dihedrals, which way is correct?

[Justin A. Lemkul]

Vitaly V. Chaban wrote:

Justin,

Thanks. These tidbits are too difficult for my brain to understand.
Let's make the things easier. One has the below compound.

7 -  1 - 2
 /  \
63
  \   /
   5  - 4

I want the atom 7 to be located in the same plane with atoms 1 2 and
6. Then in topol.top:
[ dihedrals ]
atoms   func angle   constant
1 2 6 7   2180  4.602




If this is the appropriate syntax for whatever force field you are using, yes. 
The reference atom is 1, and is held in a plane defined by 7, 2, and 6.  If atom 
7 is part of a planar group, you need to define a separate improper for it.


I mention the syntax because the order of atoms is different between, e.g., 
Gromos and OPLS (as are the implementations of the forms of the dihedrals).



Will this line do what I want here?



Try it and see :)

-Justin


Vitaly

On Wed, Sep 23, 2009 at 1:53 PM, Vitaly V. Chaban  wrote:

Hi,

I have got confused with setting up improper dihedrals in the gromacs
topologies. In the manual (ver. 4.0) I see the section named [
impropers ] (page 104)
"
[ impropers ]
C O1 O2 CA
"

but in the example system of the peptide
(share/gromacs/tutor/speptide) one finds defining impropers using the
second (in the same file) [ dihedrals ] section.
[ dihedrals ]
;  aiajakal functc0c1
c2c3
   123 5 6 1improper_X_X_C_X
   123 5 7 1improper_N_A_C1_C
   2 5 1 3 1improper_X_X_M3_X
   2 5 1 4 1improper_X_X_M3_X

What is the correct way to work with improper dihedrals? I have four
sites, then angle value and then one force constant. What should my
topology line look like to accomplish that?

I would also be very grateful if somebody could share some topology
with improper angles to understand how it works.

Vitaly





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] About gromacs installation

[Carsten Kutzner]

On Sep 23, 2009, at 2:12 PM, Enamul Haque wrote:


Hi gromacs experts,

I am trying to install gromacs version 4.0 to my laptop running  
under ubuntu. But I can't. It shows some error like --



  ./configure
checking build system type... i686-pc-linux-gnulibc1
checking host system type... i686-pc-linux-gnulibc1
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for cc... cc
checking for C compiler default output file name...
configure: error: C compiler cannot create executables
See `config.log' for more details.

I really don't know what actually I need to do. Could someone pls  
help me how can I properly installed gromacs on my pc.

Well, have you looked at 'config.log' to see why exactly the
C compiler fails in creating an executable?

Carsten




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Re: [gmx-users] Re: help with gmx C source code

[aherz]

You will have to set the right environment variable for CFLAGS to get
debug symbols:


cd gromacs_directory
CFLAGS="-O0 -g3"
./configure

might do the trick.

you can use gdb to check whether there are debug symbols in an executable.

Alex


Inon Sharony schrieb:
>
> reply to:
> http://lists.gromacs.org/pipermail/gmx-users/2009-September/045006.html
>
>
> "...
> My usual advice is to compile GROMACS with -g, get a graphical
> debugger(Totalview, ddd, insight, whatever) and spend a day stepping
> through ashort mdrun to get some understanding about what is really
> happening.
> You will find it simpler if you've set the environment
> variableGMX_NB_GENERIC=1 so that the nonbonded kernels are more
> transparent.
> ..."
>
>
>
>
> Dear Mark and other GMX users,
>
> I've been trying to compile GMX for debugging, as you suggested, and
> itappears that I'm not doing it correctly. I've added the "-g" flag
> onthe "make" command's "CFLAGS" variable, and the installation seemed
> tohave completed successfully, however when I try to preform some
> simpledebugging (suggested
> byhttp://www.gromacs.org/Developer_Zone/Programming_Guide/Programmers%27s_Guide)I
> get error messages.
> I've included the commands I ran for the installation of gromacs
> withdebugging enabled, and the debugging commands I issued and their
> result.
>
>
>
> A. *
> fftw-3.2.2 installation:
> 
>
> ./configure
> make
> make install
>
>
> B. 
>
> gromacs-4.0.5 installation in double-precission
> ---
>
> ./configure --disable-float
> make CFLAGS=-g
> make install
>
>
> C. *
>
> "cat /tmp/gdb_cmds":
> 
>
> break _gmx_error
> break do_force
> run -v
>
>
> D. **
>
> "gdb -x gdb_cmds /usr/bin/mdrun":
> -
>
> GNU gdb 6.8-debian
> Copyright (C) 2008 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later
> 
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
> and "show warranty" for details.
> This GDB was configured as "i486-linux-gnu"...
> (no debugging symbols found)
> Function "_gmx_error" not defined.
> Make breakpoint pending on future shared library load? (y or [n])
> [answered N; input not
> from terminal]
> Function "do_force" not defined.
> Make breakpoint pending on future shared library load? (y or [n])
> [answered N; input not
> from terminal]
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> [Thread debugging using libthread_db enabled]
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
>
> --
> Inon   Sharony
> ינון שרוני
> +972(3)6407634
> atto.TAU.ac.IL/~inonshar
> Please consider your environmental responsibility before printing this
> e-mail.
>
> 
>
> ___
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> www interface or send it to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] viscovity with a help of g_energy

[Vitaly V. Chaban]

Justin,

It looks especially strange for me that all these files contain only
the columns of data
but not the resulting shear viscosity value.

Vitaly

On Tue, Sep 22, 2009 at 8:26 PM, Justin A. Lemkul  wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> Hi,
>>
>> I which file should one look for the value of shear viscosity as using
>> "g_energy -vis" to calculate it?
>
> A variety of output files are generated with this command.  Either visco.xvg
> or evisco.xvg should have what you're looking for, according to the headers
> of the .xvg files printed.
>
> -Justin
>
>>
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[gmx-users] About gromacs installation

[Enamul Haque]

Hi gromacs experts,

I am trying to install gromacs version 4.0 to my laptop running under
ubuntu. But I can't. It shows some error like --


 * ./configure
checking build system type... i686-pc-linux-gnulibc1
checking host system type... i686-pc-linux-gnulibc1
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for cc... cc
checking for C compiler default output file name...
configure: error: C compiler cannot create executables
See `config.log' for more details.
*
I really don't know what actually I need to do. Could someone pls help me
how can I properly installed gromacs on my pc.

Thanks in advance..

/nittopuran
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Re: [gmx-users] Improper dihedrals, which way is correct?

[Justin A. Lemkul]

Vitaly V. Chaban wrote:

Hi,

I have got confused with setting up improper dihedrals in the gromacs
topologies. In the manual (ver. 4.0) I see the section named [
impropers ] (page 104)
"
[ impropers ]
C O1 O2 CA
"



This section exists in a .tdb file, and analogous entries are in the .rtp for 
use by pdb2gmx.  Recognizing an [impropers] directive simply leads to an 
additional, separate, [dihedrals] directive written to the topology.



but in the example system of the peptide
(share/gromacs/tutor/speptide) one finds defining impropers using the
second (in the same file) [ dihedrals ] section.
[ dihedrals ]
;  aiajakal functc0c1
c2c3
123 5 6 1improper_X_X_C_X
123 5 7 1improper_N_A_C1_C
2 5 1 3 1improper_X_X_M3_X
2 5 1 4 1improper_X_X_M3_X

What is the correct way to work with improper dihedrals? I have four
sites, then angle value and then one force constant. What should my
topology line look like to accomplish that?


The parameters you quote come from ffencadvbon.itp, which also contains this 
helpful tidbit:


; Encad out-of-plane potentials are the same functional form as
; Gromacs proper dihedrals (i.e. cosine, but with shifted sign).
; Note that the atom order is different too; In Gromacs, the first atom
; of an improper is the center one, while it is the 3rd in Encad.

Each ff*bon.itp file tends to have some information about the implementation of 
impropers in each force field, this is just one example.




I would also be very grateful if somebody could share some topology
with improper angles to understand how it works.


You could try a couple of model structures (simple peptides/proteins) under the 
force field you want to use and get some examples by mapping the atom numbers 
back to the structure.


-Justin



Vitaly
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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: help with gmx C source code

[Inon Sharony]

reply to: 
http://lists.gromacs.org/pipermail/gmx-users/2009-September/045006.html

"...
My usual advice is to compile GROMACS with -g, get a graphical 
debugger(Totalview, ddd, insight, whatever) and spend a day stepping through 
ashort mdrun to get some understanding about what is really happening.
You will find it simpler if you've set the environment variableGMX_NB_GENERIC=1 
so that the nonbonded kernels are more transparent.
..."

Dear Mark and other GMX users,

I've been trying to compile GMX for debugging, as you suggested, and itappears 
that I'm not doing it correctly. I've added the "-g" flag onthe "make" 
command's "CFLAGS" variable, and the installation seemed tohave completed 
successfully, however when I try to preform some simpledebugging (suggested 
byhttp://www.gromacs.org/Developer_Zone/Programming_Guide/Programmers%27s_Guide)I
 get error messages.
I've included the commands I ran for the installation of gromacs withdebugging 
enabled, and the debugging commands I issued and their result.

A. *
fftw-3.2.2 installation:


./configure
make
make install

B. 

gromacs-4.0.5 installation in double-precission
---

./configure --disable-float
make CFLAGS=-g
make install

C. *

"cat /tmp/gdb_cmds":


break _gmx_error
break do_force
run -v

D. **

"gdb -x gdb_cmds /usr/bin/mdrun":
-

GNU gdb 6.8-debian
Copyright (C) 2008 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later 

This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show 
copying"
and "show warranty" for details.
This GDB was configured as "i486-linux-gnu"...
(no debugging symbols found)
Function "_gmx_error" not defined.
Make breakpoint pending on future shared library load? (y or [n]) 
[answered N; input not
from terminal]
Function "do_force" not defined.
Make breakpoint pending on future shared library load? (y or [n]) 
[answered N; input not
from terminal]
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
[Thread debugging using libthread_db enabled]
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found) 

-- 
Inon   Sharony
ינון שרוני
+972(3)6407634
atto.TAU.ac.IL/~inonshar
Please consider your environmental responsibility before printing this e-mail.___
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[gmx-users] Improper dihedrals, which way is correct?

[Vitaly V. Chaban]

Hi,

I have got confused with setting up improper dihedrals in the gromacs
topologies. In the manual (ver. 4.0) I see the section named [
impropers ] (page 104)
"
[ impropers ]
C O1 O2 CA
"

but in the example system of the peptide
(share/gromacs/tutor/speptide) one finds defining impropers using the
second (in the same file) [ dihedrals ] section.
[ dihedrals ]
;  aiajakal functc0c1
c2c3
123 5 6 1improper_X_X_C_X
123 5 7 1improper_N_A_C1_C
2 5 1 3 1improper_X_X_M3_X
2 5 1 4 1improper_X_X_M3_X

What is the correct way to work with improper dihedrals? I have four
sites, then angle value and then one force constant. What should my
topology line look like to accomplish that?

I would also be very grateful if somebody could share some topology
with improper angles to understand how it works.

Vitaly
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[gmx-users] Regarding g_rms

[nikhil damle]

Hi,

  I am simulating a protein system and willing to compute rmsd over entire 
trajectory wrt a starting crystal structure. i use g_rms programme for this 
purpose starting from 0th frame until last frame of time. But rmsd shows 
abnormal spikes between successive time-frames. Height of spikes is as high as 
15A in some cases. But when i compute lsq fit rmsd using g_confrms programme, 
it gives rmsd comparable to other neighbouring time-frames. As given in the 
manual, both g_confrms and g_rms compute rmsd using lsq fitting of conformers. 
so why there should be such a vast difference ?? 

regards,
Nikhil



  Add whatever you love to the Yahoo! India homepage. Try now! 
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Re: [gmx-users] Re: gmx-users Digest, Vol 65, Issue 122

[Mark Abraham]

xiao shijun wrote:


  Thanks for Mark's fast reply, and It really works.
  Then, I have another qusetion about the manual: It seems that the 
exclusion just excludes the nonbond potential of LJ interaction, but 
Buckingham. If we want to turn off all VDW interaction between some 
atoms, the energy monitor group is a nice choice. I have no idea if I 
got it right.
   And, we can't use LJ and Buckingham in a same system. Unfortunately, 
I met a force-field that most of the nonbond interactions were described 
by Buckingham, but LJ only for Ow-Ow among water. I chose nbfunct=2 in 
[defaults] section,and nbfunct=1 in [nonbond_params] for Ow-Ow. As a 
result, a error message read:  *Trying to add LJ (SR) while the default 
nonbond type is Buck.ham (SR).  *I don't know whether it could be 
settled in gromacs.


AFAIK, you could only do this with tabulated functions. You can supply a 
normal Buckingham table (generated with mdrun -debug?) with vdwtype = 
User, and water-water tables separately with energygrp_table. This will 
be slower than any native implementation, but still decent.


See manual section 6.7 and 7.3.12. I'd strongly suggest starting with 
peptide-in-water test case that was mixing different degrees of LJ 
parameters so that you're confident of your use of the table and 
energygrp_table mechanisms, before trying to mix Buckingham and LJ in 
the way you're describing.


Mark
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[gmx-users] Re: gmx-users Digest, Vol 65, Issue 122

[xiao shijun]

  Thanks for Mark's fast reply, and It really works.
  Then, I have another qusetion about the manual: It seems that the
exclusion just excludes the nonbond potential of LJ interaction, but
Buckingham. If we want to turn off all VDW interaction between some atoms,
the energy monitor group is a nice choice. I have no idea if I got it right.
   And, we can't use LJ and Buckingham in a same system. Unfortunately, I
met a force-field that most of the nonbond interactions were described by
Buckingham, but LJ only for Ow-Ow among water. I chose nbfunct=2 in
[defaults] section,and nbfunct=1 in [nonbond_params] for Ow-Ow. As a result,
a error message read:  *Trying to add LJ (SR) while the default nonbond type
is Buck.ham (SR).  *I don't know whether it could be settled in gromacs.

   Sincerely
 Shijun


> --
>

> Message: 1
> Date: Mon, 21 Sep 2009 06:24:34 + (GMT)
> From: Mark Abraham 
> Subject: Re: [gmx-users] Re: who can help me with the force-field?
> To: Discussion list for GROMACS users 
> Message-ID: 
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 09/21/09, xiao shijun   wrote:
> >
> >Mark wrote:
> >>  xiao shijun wrote:
> >
> > >> Hi everyone,
> > >> Recently, I met a problem on the force-field. I am doing something
> > >> on the calcium carbonate, and want to simulation it with gromacs.
> > >> The shell model for oxygen has been emploied in my system. When I
> > >> considered the non-boned potential associated with interactions
> between
> > >> atoms
> > >> in the same CO3 group, I only need to take O-O buckingham interaction
> > >> into account, but any electric interaction. How could I realize that
> in
> > >> my .top file.
> > >> First, I tried to use [pairs] to eliminate electric interaction,
> but
> > >> I can't add the buckingham interaction of O-O because there is no
> > >> buckingham
> > >> options for LJC14. I want to know if anyone of you have such the
> > >> experience. Thanks!!
> >
> >>Usually you would not define a nonbonded interaction for atoms
> that are
> >>so close together, since their interaction should be able to be
> modelled
> >>adequately with the C-O bond and O-C-O angle (and perhaps with
> CHARMM,
> >>an interaction harmonic the O-O distance as a Urey-Bradley term).
> >
> >Thanks for Mark's suggestion. But I want to reproduce the simulation
> from the other paper,
> >  The paper describe the force-field that O-O nonbonded interaction in the
> same carbonate should be considered.
> >  In addition to that, I can't use buckingham potential in [pairs], even
> choose funct = 2. I am wondering
> >  if I want to describe 1-4 interaction by Buckingham, what could I do?
> This is one application for setting nrexcl for moleculetypes. You don't
> want exclusions for particles 2 bonds apart, so set this to one. See chapter
> 5.
>
> If that doesn't work, then if the "bonded" interactions are merely harmonic
> distance potentials, then GROMACS permits a form of them that doesn't create
> a bond (bond type 6, IIRC, check chapter 5; or constraint type 2). Thus, the
> automated exclusion mechanism won't be involved, and you can have Buckingham
> O-O so long as you have Buckingham for all other LJ interactions. You will
> need manual exclusions for C-O pairs, I guess.  Thus
>
> [ atomtypes ]
> C #nonbonded parameters go here
>
> O #nonbonded parameters go here
>
> [moleculetype]
> carbonate
>
> [atoms]
> C
> O1
> O2
> O3
>
> [bonds]
> C-O1 # type 6
> C-O2 # type 6
> C-O3 # type 6
>
> [exclusions]
> 1 2
> 1 3
> 1 4
>
> Whether this works may depend on whatever else is in your system, though.
>
> Mark
>
>
>
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